Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 13 03:13:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7m_29816/10_2023/8g7m_29816_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7m_29816/10_2023/8g7m_29816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7m_29816/10_2023/8g7m_29816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7m_29816/10_2023/8g7m_29816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7m_29816/10_2023/8g7m_29816_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7m_29816/10_2023/8g7m_29816_updated.pdb" } resolution = 3.2 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= 0.002 sd= 0.120 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 7 8.98 5 P 21 5.49 5 Mg 7 5.21 5 S 94 5.16 5 C 16434 2.51 5 N 4491 2.21 5 O 5280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 426": "OD1" <-> "OD2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B ASP 494": "OD1" <-> "OD2" Residue "C ASP 74": "OD1" <-> "OD2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C ASP 393": "OD1" <-> "OD2" Residue "C ASP 426": "OD1" <-> "OD2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D ASP 328": "OD1" <-> "OD2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D ASP 483": "OD1" <-> "OD2" Residue "D ASP 505": "OD1" <-> "OD2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E ASP 153": "OD1" <-> "OD2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E ASP 483": "OD1" <-> "OD2" Residue "E ASP 494": "OD1" <-> "OD2" Residue "F ASP 3": "OD1" <-> "OD2" Residue "F ASP 62": "OD1" <-> "OD2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F ASP 183": "OD1" <-> "OD2" Residue "F TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 393": "OD1" <-> "OD2" Residue "F GLU 460": "OE1" <-> "OE2" Residue "F ASP 483": "OD1" <-> "OD2" Residue "F ASP 494": "OD1" <-> "OD2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 407": "OE1" <-> "OE2" Residue "G GLU 489": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 26334 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "B" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "C" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "D" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "E" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "F" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "G" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2511 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 10, 'TRANS': 332} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.65, per 1000 atoms: 0.52 Number of scatterers: 26334 At special positions: 0 Unit cell: (157.59, 160.371, 95.481, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 7 19.00 S 94 16.00 P 21 15.00 Mg 7 11.99 O 5280 8.00 N 4491 7.00 C 16434 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: 10.93 Conformation dependent library (CDL) restraints added in 4.3 seconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 135 helices and 47 sheets defined 53.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 8 through 28 removed outlier: 3.919A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.648A pdb=" N SER A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 82 Processing helix chain 'A' and resid 87 through 103 Processing helix chain 'A' and resid 111 through 132 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 229 through 241 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 338 through 353 removed outlier: 3.692A pdb=" N ASP A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 372 Processing helix chain 'A' and resid 385 through 407 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.805A pdb=" N CYS A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.809A pdb=" N SER A 427 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 457 removed outlier: 4.472A pdb=" N LYS A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE A 448 " --> pdb=" O ARG A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 487 through 490 No H-bonds generated for 'chain 'A' and resid 487 through 490' Processing helix chain 'A' and resid 496 through 515 removed outlier: 3.796A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.948A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.709A pdb=" N SER B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 87 through 103 Processing helix chain 'B' and resid 111 through 132 Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 229 through 241 Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 254 through 266 Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 338 through 354 removed outlier: 3.671A pdb=" N ASP B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 372 Processing helix chain 'B' and resid 385 through 407 Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.811A pdb=" N CYS B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 4.139A pdb=" N ASP B 426 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 457 removed outlier: 4.423A pdb=" N LYS B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 487 through 490 No H-bonds generated for 'chain 'B' and resid 487 through 490' Processing helix chain 'B' and resid 496 through 515 removed outlier: 3.844A pdb=" N LEU B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.951A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N THR C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 57 removed outlier: 3.587A pdb=" N SER C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 82 Processing helix chain 'C' and resid 87 through 103 Processing helix chain 'C' and resid 111 through 132 Processing helix chain 'C' and resid 139 through 149 Processing helix chain 'C' and resid 154 through 167 Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 229 through 241 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 254 through 266 Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 338 through 354 removed outlier: 3.536A pdb=" N ASP C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 372 Processing helix chain 'C' and resid 385 through 407 Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.791A pdb=" N CYS C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 4.073A pdb=" N ASP C 426 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER C 427 " --> pdb=" O PRO C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 456 removed outlier: 4.426A pdb=" N LYS C 447 " --> pdb=" O LYS C 443 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE C 448 " --> pdb=" O ARG C 444 " (cutoff:3.500A) Proline residue: C 449 - end of helix Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 487 through 490 No H-bonds generated for 'chain 'C' and resid 487 through 490' Processing helix chain 'C' and resid 496 through 515 removed outlier: 3.861A pdb=" N LEU C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 28 removed outlier: 3.931A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 57 removed outlier: 3.678A pdb=" N SER D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 82 Processing helix chain 'D' and resid 87 through 103 Processing helix chain 'D' and resid 111 through 132 Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'D' and resid 154 through 167 Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 229 through 241 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 254 through 266 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 338 through 353 removed outlier: 3.518A pdb=" N ASP D 353 " --> pdb=" O ILE D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 372 Processing helix chain 'D' and resid 385 through 407 Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.731A pdb=" N CYS D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 4.126A pdb=" N ASP D 426 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER D 427 " --> pdb=" O PRO D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 457 removed outlier: 4.460A pdb=" N LYS D 447 " --> pdb=" O LYS D 443 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE D 448 " --> pdb=" O ARG D 444 " (cutoff:3.500A) Proline residue: D 449 - end of helix Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 487 through 490 No H-bonds generated for 'chain 'D' and resid 487 through 490' Processing helix chain 'D' and resid 496 through 515 removed outlier: 3.911A pdb=" N LEU D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR D 515 " --> pdb=" O SER D 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 28 removed outlier: 3.938A pdb=" N VAL E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N THR E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 57 removed outlier: 3.781A pdb=" N SER E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 83 Processing helix chain 'E' and resid 87 through 103 Processing helix chain 'E' and resid 111 through 132 Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'E' and resid 154 through 167 Processing helix chain 'E' and resid 200 through 202 No H-bonds generated for 'chain 'E' and resid 200 through 202' Processing helix chain 'E' and resid 229 through 240 Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 254 through 266 Processing helix chain 'E' and resid 281 through 294 Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 338 through 353 removed outlier: 3.580A pdb=" N ASP E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 372 Processing helix chain 'E' and resid 385 through 407 Processing helix chain 'E' and resid 416 through 421 removed outlier: 3.778A pdb=" N CYS E 421 " --> pdb=" O ALA E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 removed outlier: 3.751A pdb=" N SER E 427 " --> pdb=" O ALA E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 456 removed outlier: 4.453A pdb=" N LYS E 447 " --> pdb=" O LYS E 443 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE E 448 " --> pdb=" O ARG E 444 " (cutoff:3.500A) Proline residue: E 449 - end of helix Processing helix chain 'E' and resid 461 through 469 Processing helix chain 'E' and resid 487 through 490 No H-bonds generated for 'chain 'E' and resid 487 through 490' Processing helix chain 'E' and resid 496 through 515 removed outlier: 3.855A pdb=" N LEU E 512 " --> pdb=" O GLY E 508 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 28 removed outlier: 3.938A pdb=" N VAL F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N THR F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 57 removed outlier: 3.708A pdb=" N SER F 57 " --> pdb=" O THR F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 82 Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 111 through 132 Processing helix chain 'F' and resid 139 through 149 Processing helix chain 'F' and resid 154 through 167 Processing helix chain 'F' and resid 200 through 202 No H-bonds generated for 'chain 'F' and resid 200 through 202' Processing helix chain 'F' and resid 229 through 241 Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 254 through 266 Processing helix chain 'F' and resid 281 through 294 Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 338 through 353 removed outlier: 3.569A pdb=" N ASP F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 372 Processing helix chain 'F' and resid 385 through 407 Processing helix chain 'F' and resid 416 through 427 removed outlier: 3.806A pdb=" N CYS F 421 " --> pdb=" O ALA F 417 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE F 422 " --> pdb=" O LEU F 418 " (cutoff:3.500A) Proline residue: F 423 - end of helix removed outlier: 4.155A pdb=" N ASP F 426 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER F 427 " --> pdb=" O PRO F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 457 removed outlier: 4.404A pdb=" N LYS F 447 " --> pdb=" O LYS F 443 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE F 448 " --> pdb=" O ARG F 444 " (cutoff:3.500A) Proline residue: F 449 - end of helix Processing helix chain 'F' and resid 461 through 469 Processing helix chain 'F' and resid 487 through 490 No H-bonds generated for 'chain 'F' and resid 487 through 490' Processing helix chain 'F' and resid 496 through 515 removed outlier: 3.933A pdb=" N LEU F 512 " --> pdb=" O GLY F 508 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 28 removed outlier: 3.920A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N THR G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 57 removed outlier: 3.708A pdb=" N SER G 57 " --> pdb=" O THR G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 82 Processing helix chain 'G' and resid 87 through 103 Processing helix chain 'G' and resid 111 through 132 Processing helix chain 'G' and resid 139 through 149 Processing helix chain 'G' and resid 154 through 167 Processing helix chain 'G' and resid 385 through 407 Processing helix chain 'G' and resid 416 through 427 removed outlier: 3.892A pdb=" N CYS G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE G 422 " --> pdb=" O LEU G 418 " (cutoff:3.500A) Proline residue: G 423 - end of helix removed outlier: 4.140A pdb=" N ASP G 426 " --> pdb=" O ILE G 422 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER G 427 " --> pdb=" O PRO G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 457 removed outlier: 4.442A pdb=" N LYS G 447 " --> pdb=" O LYS G 443 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE G 448 " --> pdb=" O ARG G 444 " (cutoff:3.500A) Proline residue: G 449 - end of helix removed outlier: 3.542A pdb=" N ALA G 457 " --> pdb=" O ILE G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 469 Processing helix chain 'G' and resid 487 through 490 No H-bonds generated for 'chain 'G' and resid 487 through 490' Processing helix chain 'G' and resid 496 through 515 removed outlier: 3.817A pdb=" N LEU G 512 " --> pdb=" O GLY G 508 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR G 515 " --> pdb=" O SER G 511 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 6 Processing sheet with id= B, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 173 through 177 removed outlier: 6.772A pdb=" N ALA A 376 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LYS A 176 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 378 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 184 " --> pdb=" O LYS A 379 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 211 through 214 Processing sheet with id= E, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= F, first strand: chain 'A' and resid 410 through 412 Processing sheet with id= G, first strand: chain 'A' and resid 475 through 478 Processing sheet with id= H, first strand: chain 'B' and resid 2 through 6 Processing sheet with id= I, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= J, first strand: chain 'B' and resid 173 through 177 removed outlier: 6.499A pdb=" N ALA B 376 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LYS B 176 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 378 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 184 " --> pdb=" O LYS B 379 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 211 through 214 removed outlier: 3.622A pdb=" N ILE B 323 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 317 through 319 Processing sheet with id= M, first strand: chain 'B' and resid 410 through 412 Processing sheet with id= N, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.519A pdb=" N ASP B 483 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 2 through 6 Processing sheet with id= P, first strand: chain 'C' and resid 36 through 38 Processing sheet with id= Q, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= R, first strand: chain 'C' and resid 211 through 214 Processing sheet with id= S, first strand: chain 'C' and resid 317 through 319 removed outlier: 3.860A pdb=" N ALA C 249 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 410 through 412 Processing sheet with id= U, first strand: chain 'C' and resid 475 through 478 Processing sheet with id= V, first strand: chain 'D' and resid 2 through 6 Processing sheet with id= W, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= X, first strand: chain 'D' and resid 173 through 177 removed outlier: 6.398A pdb=" N ALA D 376 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LYS D 176 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU D 378 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 211 through 214 Processing sheet with id= Z, first strand: chain 'D' and resid 317 through 319 removed outlier: 3.645A pdb=" N ALA D 249 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 410 through 412 Processing sheet with id= AB, first strand: chain 'D' and resid 475 through 478 removed outlier: 3.523A pdb=" N ASP D 483 " --> pdb=" O ASP D 478 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 2 through 6 Processing sheet with id= AD, first strand: chain 'E' and resid 36 through 38 Processing sheet with id= AE, first strand: chain 'E' and resid 172 through 177 Processing sheet with id= AF, first strand: chain 'E' and resid 211 through 214 Processing sheet with id= AG, first strand: chain 'E' and resid 317 through 319 removed outlier: 3.547A pdb=" N ALA E 249 " --> pdb=" O VAL E 274 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 410 through 412 Processing sheet with id= AI, first strand: chain 'E' and resid 475 through 478 Processing sheet with id= AJ, first strand: chain 'F' and resid 2 through 6 Processing sheet with id= AK, first strand: chain 'F' and resid 36 through 38 Processing sheet with id= AL, first strand: chain 'F' and resid 172 through 177 removed outlier: 3.514A pdb=" N VAL F 380 " --> pdb=" O LYS F 176 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'F' and resid 211 through 214 Processing sheet with id= AN, first strand: chain 'F' and resid 317 through 319 removed outlier: 3.520A pdb=" N SER F 221 " --> pdb=" O ILE F 248 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 410 through 412 Processing sheet with id= AP, first strand: chain 'F' and resid 475 through 478 removed outlier: 3.504A pdb=" N ASP F 483 " --> pdb=" O ASP F 478 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 2 through 6 Processing sheet with id= AR, first strand: chain 'G' and resid 36 through 38 Processing sheet with id= AS, first strand: chain 'G' and resid 173 through 177 removed outlier: 6.644A pdb=" N ALA G 376 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LYS G 176 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU G 378 " --> pdb=" O LYS G 176 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'G' and resid 410 through 412 Processing sheet with id= AU, first strand: chain 'G' and resid 475 through 478 1474 hydrogen bonds defined for protein. 4272 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: 9.53 Time building geometry restraints manager: 11.66 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: 8528 1.34 - 1.45: 2040 1.45 - 1.57: 15770 1.57 - 1.69: 35 1.69 - 1.81: 168 Bond restraints: 26541 Sorted by residual: bond pdb=" CA ASP D 289 " pdb=" C ASP D 289 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.29e-02 6.01e+03 4.33e+01 bond pdb=" ND1 HIS C 314 " pdb=" CE1 HIS C 314 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.80e+01 bond pdb=" ND1 HIS D 241 " pdb=" CE1 HIS D 241 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.76e+01 bond pdb=" CD GLN C 351 " pdb=" OE1 GLN C 351 " ideal model delta sigma weight residual 1.231 1.325 -0.094 1.90e-02 2.77e+03 2.43e+01 bond pdb=" CG ASN B 239 " pdb=" OD1 ASN B 239 " ideal model delta sigma weight residual 1.231 1.324 -0.093 1.90e-02 2.77e+03 2.40e+01 ... (remaining 26536 not shown) Histogram of bond angle deviations from ideal: 99.70 - 107.72: 663 107.72 - 115.75: 17611 115.75 - 123.77: 17251 123.77 - 131.80: 304 131.80 - 139.83: 28 Bond angle restraints: 35857 Sorted by residual: angle pdb=" CB HIS C 314 " pdb=" CG HIS C 314 " pdb=" CD2 HIS C 314 " ideal model delta sigma weight residual 131.20 122.59 8.61 1.30e+00 5.92e-01 4.39e+01 angle pdb=" CB HIS D 241 " pdb=" CG HIS D 241 " pdb=" CD2 HIS D 241 " ideal model delta sigma weight residual 131.20 122.71 8.49 1.30e+00 5.92e-01 4.27e+01 angle pdb=" CA ASP D 289 " pdb=" C ASP D 289 " pdb=" N MET D 290 " ideal model delta sigma weight residual 117.39 110.26 7.13 1.24e+00 6.50e-01 3.30e+01 angle pdb=" CB HIS D 241 " pdb=" CG HIS D 241 " pdb=" ND1 HIS D 241 " ideal model delta sigma weight residual 122.70 131.25 -8.55 1.50e+00 4.44e-01 3.25e+01 angle pdb=" CB HIS C 314 " pdb=" CG HIS C 314 " pdb=" ND1 HIS C 314 " ideal model delta sigma weight residual 122.70 131.25 -8.55 1.50e+00 4.44e-01 3.25e+01 ... (remaining 35852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15300 17.93 - 35.85: 895 35.85 - 53.78: 161 53.78 - 71.70: 60 71.70 - 89.63: 21 Dihedral angle restraints: 16437 sinusoidal: 6506 harmonic: 9931 Sorted by residual: dihedral pdb=" CA GLN D 312 " pdb=" C GLN D 312 " pdb=" N PRO D 313 " pdb=" CA PRO D 313 " ideal model delta harmonic sigma weight residual -180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA VAL G 25 " pdb=" C VAL G 25 " pdb=" N ALA G 26 " pdb=" CA ALA G 26 " ideal model delta harmonic sigma weight residual -180.00 -163.06 -16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PHE F 6 " pdb=" C PHE F 6 " pdb=" N GLY F 7 " pdb=" CA GLY F 7 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 16434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3033 0.035 - 0.071: 953 0.071 - 0.106: 265 0.106 - 0.141: 125 0.141 - 0.177: 5 Chirality restraints: 4381 Sorted by residual: chirality pdb=" CA GLU C 347 " pdb=" N GLU C 347 " pdb=" C GLU C 347 " pdb=" CB GLU C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CA PRO D 313 " pdb=" N PRO D 313 " pdb=" C PRO D 313 " pdb=" CB PRO D 313 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA GLN D 346 " pdb=" N GLN D 346 " pdb=" C GLN D 346 " pdb=" CB GLN D 346 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 4378 not shown) Planarity restraints: 4578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 288 " 0.029 2.00e-02 2.50e+03 5.77e-02 3.33e+01 pdb=" C LYS D 288 " -0.100 2.00e-02 2.50e+03 pdb=" O LYS D 288 " 0.039 2.00e-02 2.50e+03 pdb=" N ASP D 289 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 199 " -0.060 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO C 200 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 276 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 277 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 277 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 277 " -0.026 5.00e-02 4.00e+02 ... (remaining 4575 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.67: 345 2.67 - 3.29: 28336 3.29 - 3.91: 51640 3.91 - 4.52: 65311 4.52 - 5.14: 106757 Nonbonded interactions: 252389 Sorted by model distance: nonbonded pdb=" OD1 ASP D 85 " pdb="MG MG D 602 " model vdw 2.057 2.170 nonbonded pdb=" O2G ATP E 601 " pdb="MG MG E 602 " model vdw 2.079 2.170 nonbonded pdb=" O1A ATP E 601 " pdb="MG MG E 602 " model vdw 2.100 2.170 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 2.118 2.170 nonbonded pdb=" OD1 ASP F 85 " pdb="MG MG F 602 " model vdw 2.139 2.170 ... (remaining 252384 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: 1.840 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: 0.030 Extract box with map and model: 10.440 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 70.830 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.180 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.003 0.098 26541 Z= 0.198 Angle : 0.487 9.054 35857 Z= 0.281 Chirality : 0.041 0.177 4381 Planarity : 0.004 0.091 4578 Dihedral : 12.659 89.629 10041 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 2.22 (0.14), residues: 3489 helix: 2.52 (0.12), residues: 1859 sheet: 1.35 (0.24), residues: 455 loop : -0.20 (0.16), residues: 1175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 3.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.3455 time to fit residues: 125.6833 Evaluate side-chains 182 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.953 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 0.9980 chunk 262 optimal weight: 0.2980 chunk 145 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 314 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN C 78 ASN D 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26541 Z= 0.121 Angle : 0.423 7.053 35857 Z= 0.227 Chirality : 0.041 0.173 4381 Planarity : 0.003 0.063 4578 Dihedral : 4.220 75.626 3669 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.42 % Allowed : 3.36 % Favored : 96.22 % 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: 2.26 (0.14), residues: 3489 helix: 2.54 (0.12), residues: 1901 sheet: 1.48 (0.25), residues: 432 loop : -0.29 (0.16), residues: 1156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 194 time to evaluate : 2.940 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 198 average time/residue: 0.3362 time to fit residues: 112.9062 Evaluate side-chains 184 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 2.892 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2349 time to fit residues: 7.2663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 213 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 314 optimal weight: 0.0270 chunk 340 optimal weight: 0.8980 chunk 280 optimal weight: 7.9990 chunk 312 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 252 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26541 Z= 0.120 Angle : 0.410 8.153 35857 Z= 0.218 Chirality : 0.041 0.170 4381 Planarity : 0.003 0.051 4578 Dihedral : 4.113 75.003 3669 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.42 % Allowed : 4.60 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.14), residues: 3489 helix: 2.59 (0.12), residues: 1901 sheet: 1.51 (0.25), residues: 432 loop : -0.27 (0.16), residues: 1156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 200 average time/residue: 0.3382 time to fit residues: 114.3125 Evaluate side-chains 181 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 2.992 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2379 time to fit residues: 5.9970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 150 optimal weight: 0.3980 chunk 211 optimal weight: 0.0060 chunk 315 optimal weight: 3.9990 chunk 334 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 299 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 26541 Z= 0.109 Angle : 0.409 10.058 35857 Z= 0.216 Chirality : 0.040 0.175 4381 Planarity : 0.003 0.044 4578 Dihedral : 3.978 73.105 3669 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.39 % Allowed : 5.52 % Favored : 94.09 % 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: 2.36 (0.14), residues: 3489 helix: 2.64 (0.12), residues: 1898 sheet: 1.55 (0.25), residues: 438 loop : -0.32 (0.16), residues: 1153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 199 average time/residue: 0.3395 time to fit residues: 114.1821 Evaluate side-chains 183 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 2.728 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2561 time to fit residues: 6.2270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 249 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 chunk 285 optimal weight: 4.9990 chunk 231 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 300 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN B 312 GLN C 351 GLN D 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26541 Z= 0.283 Angle : 0.488 9.309 35857 Z= 0.258 Chirality : 0.043 0.173 4381 Planarity : 0.003 0.044 4578 Dihedral : 4.424 83.152 3669 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.42 % Allowed : 6.69 % Favored : 92.89 % 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: 2.05 (0.14), residues: 3489 helix: 2.39 (0.12), residues: 1877 sheet: 1.40 (0.25), residues: 426 loop : -0.36 (0.16), residues: 1186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 183 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 191 average time/residue: 0.3722 time to fit residues: 119.9434 Evaluate side-chains 178 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 2.940 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2298 time to fit residues: 5.8466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 0.9980 chunk 301 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 196 optimal weight: 0.5980 chunk 82 optimal weight: 0.0030 chunk 334 optimal weight: 0.7980 chunk 277 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 26541 Z= 0.121 Angle : 0.422 10.791 35857 Z= 0.222 Chirality : 0.041 0.240 4381 Planarity : 0.003 0.043 4578 Dihedral : 4.154 78.757 3669 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.50 % Allowed : 7.04 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.14), residues: 3489 helix: 2.57 (0.12), residues: 1888 sheet: 1.39 (0.25), residues: 438 loop : -0.45 (0.16), residues: 1163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 188 time to evaluate : 2.785 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 195 average time/residue: 0.3324 time to fit residues: 109.1785 Evaluate side-chains 184 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 2.697 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2283 time to fit residues: 6.8097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 189 optimal weight: 0.3980 chunk 281 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 chunk 333 optimal weight: 0.9990 chunk 208 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26541 Z= 0.200 Angle : 0.467 15.470 35857 Z= 0.243 Chirality : 0.042 0.159 4381 Planarity : 0.003 0.047 4578 Dihedral : 4.219 81.113 3669 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.21 % Allowed : 7.78 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.14), residues: 3489 helix: 2.48 (0.12), residues: 1889 sheet: 1.29 (0.25), residues: 428 loop : -0.44 (0.16), residues: 1172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 181 time to evaluate : 2.981 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 184 average time/residue: 0.3414 time to fit residues: 105.8569 Evaluate side-chains 178 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 2.716 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2290 time to fit residues: 5.9084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 199 optimal weight: 0.9980 chunk 100 optimal weight: 0.0770 chunk 65 optimal weight: 0.0040 chunk 64 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 227 optimal weight: 30.0000 chunk 164 optimal weight: 7.9990 chunk 31 optimal weight: 0.0370 chunk 262 optimal weight: 0.9990 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26541 Z= 0.115 Angle : 0.441 16.056 35857 Z= 0.226 Chirality : 0.041 0.204 4381 Planarity : 0.003 0.047 4578 Dihedral : 3.992 77.070 3669 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.14 % Allowed : 8.28 % Favored : 91.58 % 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: 2.26 (0.14), residues: 3489 helix: 2.65 (0.12), residues: 1885 sheet: 1.45 (0.25), residues: 433 loop : -0.45 (0.16), residues: 1171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 3.058 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 193 average time/residue: 0.3402 time to fit residues: 111.0675 Evaluate side-chains 183 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 180 time to evaluate : 2.896 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2249 time to fit residues: 5.4381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 0.9980 chunk 319 optimal weight: 0.6980 chunk 291 optimal weight: 9.9990 chunk 310 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 95 optimal weight: 0.0010 chunk 280 optimal weight: 0.0670 chunk 293 optimal weight: 20.0000 chunk 309 optimal weight: 0.9990 overall best weight: 0.5526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN C 78 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26541 Z= 0.120 Angle : 0.444 16.983 35857 Z= 0.227 Chirality : 0.041 0.179 4381 Planarity : 0.003 0.050 4578 Dihedral : 3.835 75.267 3669 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.18 % Allowed : 8.60 % Favored : 91.23 % 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 (0.14), residues: 3489 helix: 2.66 (0.12), residues: 1893 sheet: 1.43 (0.25), residues: 433 loop : -0.44 (0.16), residues: 1163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 3.244 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 185 average time/residue: 0.3360 time to fit residues: 106.2152 Evaluate side-chains 178 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 2.724 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2224 time to fit residues: 5.5884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 204 optimal weight: 0.0870 chunk 328 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 228 optimal weight: 30.0000 chunk 344 optimal weight: 5.9990 chunk 317 optimal weight: 0.0010 chunk 274 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 212 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 overall best weight: 0.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26541 Z= 0.119 Angle : 0.444 17.207 35857 Z= 0.227 Chirality : 0.041 0.157 4381 Planarity : 0.003 0.050 4578 Dihedral : 3.744 73.084 3669 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % 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: 2.31 (0.14), residues: 3489 helix: 2.68 (0.12), residues: 1893 sheet: 1.45 (0.25), residues: 433 loop : -0.42 (0.16), residues: 1163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.968 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3375 time to fit residues: 105.3951 Evaluate side-chains 175 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.834 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 218 optimal weight: 3.9990 chunk 292 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 253 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.161612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.095045 restraints weight = 34959.689| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.10 r_work: 0.3006 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26541 Z= 0.291 Angle : 0.521 17.110 35857 Z= 0.269 Chirality : 0.043 0.189 4381 Planarity : 0.003 0.049 4578 Dihedral : 4.202 82.186 3669 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.25 % Allowed : 9.02 % Favored : 90.73 % 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: 1.98 (0.14), residues: 3489 helix: 2.40 (0.12), residues: 1873 sheet: 1.33 (0.26), residues: 382 loop : -0.40 (0.16), residues: 1234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4766.57 seconds wall clock time: 87 minutes 52.63 seconds (5272.63 seconds total)