Starting phenix.real_space_refine on Sun Mar 17 12:48:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8o_27945/03_2024/8e8o_27945_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8o_27945/03_2024/8e8o_27945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8o_27945/03_2024/8e8o_27945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8o_27945/03_2024/8e8o_27945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8o_27945/03_2024/8e8o_27945_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8o_27945/03_2024/8e8o_27945_updated.pdb" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 92 5.16 5 C 11284 2.51 5 N 3040 2.21 5 O 3276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 430": "OD1" <-> "OD2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 535": "OD1" <-> "OD2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 430": "OD1" <-> "OD2" Residue "B ASP 495": "OD1" <-> "OD2" Residue "B TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 535": "OD1" <-> "OD2" Residue "B PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 430": "OD1" <-> "OD2" Residue "C ASP 495": "OD1" <-> "OD2" Residue "C TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 535": "OD1" <-> "OD2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 430": "OD1" <-> "OD2" Residue "D ASP 495": "OD1" <-> "OD2" Residue "D TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 535": "OD1" <-> "OD2" Residue "D PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 549": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17704 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4378 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 529} Chain: "B" Number of atoms: 4378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4378 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 529} Chain: "C" Number of atoms: 4378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4378 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 529} Chain: "D" Number of atoms: 4378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4378 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 529} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.24, per 1000 atoms: 0.52 Number of scatterers: 17704 At special positions: 0 Unit cell: (132.08, 80.08, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 12 15.00 O 3276 8.00 N 3040 7.00 C 11284 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: 7.48 Conformation dependent library (CDL) restraints added in 3.2 seconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 8 sheets defined 48.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 2 through 5 Processing helix chain 'A' and resid 14 through 16 No H-bonds generated for 'chain 'A' and resid 14 through 16' Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 38 through 49 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 70 through 79 Processing helix chain 'A' and resid 81 through 88 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 92 through 98 Processing helix chain 'A' and resid 100 through 103 No H-bonds generated for 'chain 'A' and resid 100 through 103' Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 150 through 166 removed outlier: 3.567A pdb=" N MET A 154 " --> pdb=" O CYS A 151 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 155 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Proline residue: A 157 - end of helix removed outlier: 3.956A pdb=" N ALA A 166 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 258 through 275 removed outlier: 3.607A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 291 through 306 removed outlier: 3.523A pdb=" N GLY A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.765A pdb=" N LYS A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 No H-bonds generated for 'chain 'A' and resid 336 through 339' Processing helix chain 'A' and resid 351 through 357 removed outlier: 4.146A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 462 through 475 Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.537A pdb=" N GLN A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 510 removed outlier: 5.414A pdb=" N ARG A 494 " --> pdb=" O SER A 491 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 502 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR A 507 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'B' and resid 2 through 5 Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 38 through 49 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 81 through 88 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 92 through 98 Processing helix chain 'B' and resid 100 through 103 No H-bonds generated for 'chain 'B' and resid 100 through 103' Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 150 through 166 removed outlier: 3.567A pdb=" N MET B 154 " --> pdb=" O CYS B 151 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 155 " --> pdb=" O TYR B 152 " (cutoff:3.500A) Proline residue: B 157 - end of helix removed outlier: 3.956A pdb=" N ALA B 166 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'B' and resid 236 through 246 Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.607A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.523A pdb=" N GLY B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 317 removed outlier: 3.765A pdb=" N LYS B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 339 No H-bonds generated for 'chain 'B' and resid 336 through 339' Processing helix chain 'B' and resid 351 through 357 removed outlier: 4.146A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 384 Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 462 through 475 Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.537A pdb=" N GLN B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 510 removed outlier: 5.414A pdb=" N ARG B 494 " --> pdb=" O SER B 491 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 502 " --> pdb=" O ARG B 499 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR B 507 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'C' and resid 2 through 5 Processing helix chain 'C' and resid 14 through 16 No H-bonds generated for 'chain 'C' and resid 14 through 16' Processing helix chain 'C' and resid 19 through 25 Processing helix chain 'C' and resid 38 through 49 Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 70 through 79 Processing helix chain 'C' and resid 81 through 88 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 100 through 103 No H-bonds generated for 'chain 'C' and resid 100 through 103' Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 150 through 166 removed outlier: 3.567A pdb=" N MET C 154 " --> pdb=" O CYS C 151 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 155 " --> pdb=" O TYR C 152 " (cutoff:3.500A) Proline residue: C 157 - end of helix removed outlier: 3.956A pdb=" N ALA C 166 " --> pdb=" O LEU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 206 through 223 Processing helix chain 'C' and resid 236 through 246 Processing helix chain 'C' and resid 258 through 275 removed outlier: 3.607A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 291 through 306 removed outlier: 3.523A pdb=" N GLY C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 317 removed outlier: 3.765A pdb=" N LYS C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 339 No H-bonds generated for 'chain 'C' and resid 336 through 339' Processing helix chain 'C' and resid 351 through 357 removed outlier: 4.146A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 384 Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 441 through 443 No H-bonds generated for 'chain 'C' and resid 441 through 443' Processing helix chain 'C' and resid 445 through 455 Processing helix chain 'C' and resid 462 through 475 Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.537A pdb=" N GLN C 483 " --> pdb=" O GLN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 510 removed outlier: 5.414A pdb=" N ARG C 494 " --> pdb=" O SER C 491 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE C 502 " --> pdb=" O ARG C 499 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR C 507 " --> pdb=" O VAL C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 Processing helix chain 'D' and resid 2 through 5 Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 19 through 25 Processing helix chain 'D' and resid 38 through 49 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 70 through 79 Processing helix chain 'D' and resid 81 through 88 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'D' and resid 100 through 103 No H-bonds generated for 'chain 'D' and resid 100 through 103' Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 150 through 166 removed outlier: 3.567A pdb=" N MET D 154 " --> pdb=" O CYS D 151 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY D 155 " --> pdb=" O TYR D 152 " (cutoff:3.500A) Proline residue: D 157 - end of helix removed outlier: 3.956A pdb=" N ALA D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 206 through 223 Processing helix chain 'D' and resid 236 through 246 Processing helix chain 'D' and resid 258 through 275 removed outlier: 3.607A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 291 through 306 removed outlier: 3.523A pdb=" N GLY D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 317 removed outlier: 3.765A pdb=" N LYS D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 339 No H-bonds generated for 'chain 'D' and resid 336 through 339' Processing helix chain 'D' and resid 351 through 357 removed outlier: 4.146A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 384 Processing helix chain 'D' and resid 404 through 410 Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 445 through 455 Processing helix chain 'D' and resid 462 through 475 Processing helix chain 'D' and resid 478 through 483 removed outlier: 3.537A pdb=" N GLN D 483 " --> pdb=" O GLN D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 510 removed outlier: 5.414A pdb=" N ARG D 494 " --> pdb=" O SER D 491 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE D 502 " --> pdb=" O ARG D 499 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR D 507 " --> pdb=" O VAL D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 Processing sheet with id= A, first strand: chain 'A' and resid 110 through 113 removed outlier: 6.797A pdb=" N ALA A 134 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A 178 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 136 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU A 180 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR A 138 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 228 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL A 137 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN A 230 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.449A pdb=" N PHE A 284 " --> pdb=" O TRP A 319 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA A 362 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE A 389 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLY A 365 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE A 391 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE A 416 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA A 392 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 418 " --> pdb=" O ALA A 392 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 110 through 113 removed outlier: 6.797A pdb=" N ALA B 134 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL B 178 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 136 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU B 180 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR B 138 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 228 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL B 137 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN B 230 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.449A pdb=" N PHE B 284 " --> pdb=" O TRP B 319 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA B 362 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B 389 " --> pdb=" O ILE B 363 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLY B 365 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE B 391 " --> pdb=" O GLY B 365 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE B 416 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA B 392 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 418 " --> pdb=" O ALA B 392 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 110 through 113 removed outlier: 6.797A pdb=" N ALA C 134 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL C 178 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL C 136 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU C 180 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR C 138 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 228 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL C 137 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN C 230 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.449A pdb=" N PHE C 284 " --> pdb=" O TRP C 319 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA C 362 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE C 389 " --> pdb=" O ILE C 363 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLY C 365 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE C 391 " --> pdb=" O GLY C 365 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE C 416 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA C 392 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA C 418 " --> pdb=" O ALA C 392 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 110 through 113 removed outlier: 6.797A pdb=" N ALA D 134 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL D 178 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL D 136 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU D 180 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR D 138 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU D 228 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL D 137 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN D 230 " --> pdb=" O VAL D 137 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.449A pdb=" N PHE D 284 " --> pdb=" O TRP D 319 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA D 362 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE D 389 " --> pdb=" O ILE D 363 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLY D 365 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE D 391 " --> pdb=" O GLY D 365 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE D 416 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA D 392 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA D 418 " --> pdb=" O ALA D 392 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 568 hydrogen bonds defined for protein. 1404 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: 5.34 Time building geometry restraints manager: 7.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4972 1.33 - 1.45: 2836 1.45 - 1.57: 10124 1.57 - 1.68: 20 1.68 - 1.80: 148 Bond restraints: 18100 Sorted by residual: bond pdb=" O2B NAP D 601 " pdb=" P2B NAP D 601 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" O2B NAP B 601 " pdb=" P2B NAP B 601 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" O2B NAP C 601 " pdb=" P2B NAP C 601 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" O2B NAP A 601 " pdb=" P2B NAP A 601 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C4A NAP D 601 " pdb=" C5A NAP D 601 " ideal model delta sigma weight residual 1.385 1.465 -0.080 2.00e-02 2.50e+03 1.62e+01 ... (remaining 18095 not shown) Histogram of bond angle deviations from ideal: 97.48 - 105.21: 376 105.21 - 112.94: 9856 112.94 - 120.67: 8300 120.67 - 128.40: 5900 128.40 - 136.13: 128 Bond angle restraints: 24560 Sorted by residual: angle pdb=" N LYS C 324 " pdb=" CA LYS C 324 " pdb=" C LYS C 324 " ideal model delta sigma weight residual 114.75 109.88 4.87 1.26e+00 6.30e-01 1.50e+01 angle pdb=" N LYS B 324 " pdb=" CA LYS B 324 " pdb=" C LYS B 324 " ideal model delta sigma weight residual 114.75 109.88 4.87 1.26e+00 6.30e-01 1.50e+01 angle pdb=" N LYS D 324 " pdb=" CA LYS D 324 " pdb=" C LYS D 324 " ideal model delta sigma weight residual 114.75 109.88 4.87 1.26e+00 6.30e-01 1.50e+01 angle pdb=" N LYS A 324 " pdb=" CA LYS A 324 " pdb=" C LYS A 324 " ideal model delta sigma weight residual 114.75 109.88 4.87 1.26e+00 6.30e-01 1.50e+01 angle pdb=" C2A NAP B 601 " pdb=" N3A NAP B 601 " pdb=" C4A NAP B 601 " ideal model delta sigma weight residual 111.82 120.85 -9.03 3.00e+00 1.11e-01 9.05e+00 ... (remaining 24555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 9708 17.26 - 34.51: 1020 34.51 - 51.77: 236 51.77 - 69.03: 44 69.03 - 86.29: 8 Dihedral angle restraints: 11016 sinusoidal: 4592 harmonic: 6424 Sorted by residual: dihedral pdb=" CA GLY C 330 " pdb=" C GLY C 330 " pdb=" N ARG C 331 " pdb=" CA ARG C 331 " ideal model delta harmonic sigma weight residual 180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLY B 330 " pdb=" C GLY B 330 " pdb=" N ARG B 331 " pdb=" CA ARG B 331 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLY D 330 " pdb=" C GLY D 330 " pdb=" N ARG D 331 " pdb=" CA ARG D 331 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 11013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1656 0.039 - 0.079: 832 0.079 - 0.118: 212 0.118 - 0.158: 36 0.158 - 0.197: 8 Chirality restraints: 2744 Sorted by residual: chirality pdb=" C1B NAP A 601 " pdb=" C2B NAP A 601 " pdb=" N9A NAP A 601 " pdb=" O4B NAP A 601 " both_signs ideal model delta sigma weight residual False 2.31 2.51 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C1B NAP C 601 " pdb=" C2B NAP C 601 " pdb=" N9A NAP C 601 " pdb=" O4B NAP C 601 " both_signs ideal model delta sigma weight residual False 2.31 2.51 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C1B NAP B 601 " pdb=" C2B NAP B 601 " pdb=" N9A NAP B 601 " pdb=" O4B NAP B 601 " both_signs ideal model delta sigma weight residual False 2.31 2.51 -0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 2741 not shown) Planarity restraints: 3152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 345 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO D 346 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 346 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 346 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 345 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO B 346 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 346 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 346 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 345 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO C 346 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 346 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 346 " -0.018 5.00e-02 4.00e+02 ... (remaining 3149 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 512 2.70 - 3.25: 18656 3.25 - 3.80: 30924 3.80 - 4.35: 41896 4.35 - 4.90: 66320 Nonbonded interactions: 158308 Sorted by model distance: nonbonded pdb=" OG SER B 350 " pdb=" OE1 GLU B 353 " model vdw 2.148 2.440 nonbonded pdb=" OG SER A 350 " pdb=" OE1 GLU A 353 " model vdw 2.148 2.440 nonbonded pdb=" OG SER C 350 " pdb=" OE1 GLU C 353 " model vdw 2.148 2.440 nonbonded pdb=" OG SER D 350 " pdb=" OE1 GLU D 353 " model vdw 2.148 2.440 nonbonded pdb=" OG SER A 394 " pdb=" OE2 GLU A 401 " model vdw 2.186 2.440 ... (remaining 158303 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' } 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: 2.500 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: 0.010 Extract box with map and model: 2.760 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 47.990 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.110 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: 0.020 Load rotamer database and sin/cos tables:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.007 0.128 18100 Z= 0.490 Angle : 0.745 9.026 24560 Z= 0.382 Chirality : 0.047 0.197 2744 Planarity : 0.004 0.032 3152 Dihedral : 14.956 86.285 6904 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.82 (0.16), residues: 2216 helix: -1.69 (0.14), residues: 1044 sheet: -2.52 (0.34), residues: 216 loop : -1.73 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 319 HIS 0.005 0.001 HIS A 200 PHE 0.017 0.002 PHE D 445 TYR 0.015 0.002 TYR D 74 ARG 0.005 0.001 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 1.5108 time to fit residues: 188.6176 Evaluate side-chains 76 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 52 GLN A 66 GLN A 226 ASN A 282 HIS A 335 ASN A 385 HIS A 395 ASN A 474 GLN A 479 GLN A 554 GLN B 8 ASN B 52 GLN B 66 GLN B 226 ASN B 282 HIS B 335 ASN B 385 HIS B 395 ASN B 474 GLN B 479 GLN B 554 GLN C 8 ASN C 52 GLN C 66 GLN C 226 ASN C 282 HIS C 335 ASN C 385 HIS C 395 ASN C 474 GLN C 479 GLN C 554 GLN D 8 ASN D 52 GLN D 66 GLN D 226 ASN D 282 HIS D 335 ASN D 385 HIS D 395 ASN D 474 GLN D 479 GLN D 554 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18100 Z= 0.175 Angle : 0.548 9.015 24560 Z= 0.267 Chirality : 0.041 0.153 2744 Planarity : 0.004 0.035 3152 Dihedral : 9.804 56.673 2696 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.64 % Allowed : 10.00 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.65 (0.17), residues: 2216 helix: -0.62 (0.16), residues: 1028 sheet: -2.38 (0.40), residues: 132 loop : -1.31 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 319 HIS 0.004 0.001 HIS A 200 PHE 0.012 0.001 PHE B 445 TYR 0.011 0.001 TYR A 517 ARG 0.003 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 1.1382 time to fit residues: 110.8720 Evaluate side-chains 80 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18100 Z= 0.282 Angle : 0.592 9.321 24560 Z= 0.283 Chirality : 0.041 0.144 2744 Planarity : 0.004 0.033 3152 Dihedral : 9.274 57.064 2696 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.91 % Allowed : 10.00 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.02 (0.18), residues: 2216 helix: -0.02 (0.16), residues: 1056 sheet: -1.87 (0.37), residues: 204 loop : -1.01 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 319 HIS 0.002 0.001 HIS C 200 PHE 0.011 0.001 PHE C 445 TYR 0.010 0.001 TYR A 517 ARG 0.002 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 76 time to evaluate : 2.098 Fit side-chains outliers start: 36 outliers final: 4 residues processed: 100 average time/residue: 1.0134 time to fit residues: 118.7993 Evaluate side-chains 76 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18100 Z= 0.258 Angle : 0.575 9.408 24560 Z= 0.276 Chirality : 0.041 0.154 2744 Planarity : 0.004 0.032 3152 Dihedral : 8.832 57.386 2696 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.49 % Allowed : 11.28 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2216 helix: 0.28 (0.17), residues: 1056 sheet: -1.69 (0.38), residues: 204 loop : -0.88 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 319 HIS 0.003 0.001 HIS D 200 PHE 0.012 0.001 PHE C 445 TYR 0.010 0.001 TYR C 74 ARG 0.002 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 76 time to evaluate : 2.069 Fit side-chains outliers start: 28 outliers final: 12 residues processed: 92 average time/residue: 1.1998 time to fit residues: 127.8955 Evaluate side-chains 84 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 395 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18100 Z= 0.262 Angle : 0.582 10.244 24560 Z= 0.276 Chirality : 0.042 0.146 2744 Planarity : 0.004 0.033 3152 Dihedral : 8.595 58.464 2696 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.28 % Allowed : 11.28 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2216 helix: 0.40 (0.17), residues: 1036 sheet: -1.46 (0.39), residues: 204 loop : -0.65 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 319 HIS 0.002 0.001 HIS B 200 PHE 0.011 0.001 PHE A 445 TYR 0.012 0.001 TYR D 208 ARG 0.002 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 2.049 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 92 average time/residue: 1.1434 time to fit residues: 122.1639 Evaluate side-chains 84 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 395 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18100 Z= 0.147 Angle : 0.550 10.533 24560 Z= 0.257 Chirality : 0.040 0.150 2744 Planarity : 0.003 0.034 3152 Dihedral : 8.329 59.112 2696 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.06 % Allowed : 13.62 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2216 helix: 0.56 (0.17), residues: 1028 sheet: -1.18 (0.40), residues: 204 loop : -0.62 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 319 HIS 0.003 0.000 HIS A 200 PHE 0.012 0.001 PHE D 445 TYR 0.013 0.001 TYR D 208 ARG 0.001 0.000 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 2.008 Fit side-chains outliers start: 20 outliers final: 4 residues processed: 104 average time/residue: 1.2308 time to fit residues: 146.2910 Evaluate side-chains 80 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 18100 Z= 0.457 Angle : 0.706 12.703 24560 Z= 0.335 Chirality : 0.043 0.144 2744 Planarity : 0.004 0.033 3152 Dihedral : 8.251 59.663 2696 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.64 % Allowed : 15.32 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2216 helix: 0.65 (0.17), residues: 1024 sheet: -1.82 (0.41), residues: 164 loop : -0.40 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 319 HIS 0.003 0.001 HIS D 115 PHE 0.011 0.002 PHE A 445 TYR 0.011 0.002 TYR A 74 ARG 0.003 0.001 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 2.388 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 84 average time/residue: 1.1286 time to fit residues: 109.2568 Evaluate side-chains 80 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 63 optimal weight: 0.0050 chunk 41 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18100 Z= 0.167 Angle : 0.601 12.900 24560 Z= 0.277 Chirality : 0.041 0.153 2744 Planarity : 0.003 0.033 3152 Dihedral : 8.192 59.363 2696 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.43 % Allowed : 15.74 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 2216 helix: 0.91 (0.17), residues: 984 sheet: -1.60 (0.42), residues: 164 loop : -0.39 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 127 HIS 0.003 0.000 HIS B 200 PHE 0.012 0.001 PHE D 445 TYR 0.013 0.001 TYR B 208 ARG 0.002 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 2.206 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 88 average time/residue: 1.1178 time to fit residues: 113.5473 Evaluate side-chains 80 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 197 optimal weight: 0.0170 chunk 118 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 overall best weight: 2.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18100 Z= 0.205 Angle : 0.627 13.257 24560 Z= 0.286 Chirality : 0.041 0.140 2744 Planarity : 0.003 0.034 3152 Dihedral : 8.097 59.658 2696 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.64 % Allowed : 15.53 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2216 helix: 0.90 (0.17), residues: 992 sheet: -1.50 (0.43), residues: 164 loop : -0.37 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 319 HIS 0.003 0.001 HIS D 200 PHE 0.009 0.001 PHE A 445 TYR 0.012 0.001 TYR D 208 ARG 0.002 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 2.020 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 80 average time/residue: 1.2515 time to fit residues: 115.0195 Evaluate side-chains 84 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 2.9990 chunk 127 optimal weight: 0.0070 chunk 99 optimal weight: 0.1980 chunk 145 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 201 optimal weight: 8.9990 chunk 174 optimal weight: 0.6980 chunk 18 optimal weight: 0.0170 chunk 134 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18100 Z= 0.152 Angle : 0.620 13.103 24560 Z= 0.281 Chirality : 0.041 0.149 2744 Planarity : 0.003 0.036 3152 Dihedral : 7.937 59.437 2696 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.64 % Allowed : 15.53 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2216 helix: 0.87 (0.17), residues: 984 sheet: -1.50 (0.39), residues: 188 loop : -0.38 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 319 HIS 0.002 0.000 HIS B 200 PHE 0.011 0.001 PHE A 445 TYR 0.013 0.001 TYR D 208 ARG 0.002 0.000 ARG D 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.889 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 1.1210 time to fit residues: 114.2308 Evaluate side-chains 80 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 174 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.053284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.040224 restraints weight = 61589.347| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.50 r_work: 0.2566 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18100 Z= 0.166 Angle : 0.608 12.498 24560 Z= 0.275 Chirality : 0.041 0.159 2744 Planarity : 0.003 0.034 3152 Dihedral : 7.805 59.971 2696 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.21 % Allowed : 15.96 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 2216 helix: 0.99 (0.17), residues: 984 sheet: -1.34 (0.40), residues: 188 loop : -0.37 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 319 HIS 0.002 0.000 HIS C 200 PHE 0.009 0.001 PHE A 253 TYR 0.013 0.001 TYR D 208 ARG 0.002 0.000 ARG C 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3553.38 seconds wall clock time: 65 minutes 52.93 seconds (3952.93 seconds total)