Starting phenix.real_space_refine on Fri Feb 16 21:00:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvd_17962/02_2024/8pvd_17962_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvd_17962/02_2024/8pvd_17962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvd_17962/02_2024/8pvd_17962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvd_17962/02_2024/8pvd_17962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvd_17962/02_2024/8pvd_17962_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvd_17962/02_2024/8pvd_17962_updated.pdb" } resolution = 3.4 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= 0.007 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10480 2.51 5 N 2908 2.21 5 O 3056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 17": "OE1" <-> "OE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ASP 128": "OD1" <-> "OD2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 437": "OD1" <-> "OD2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ASP 128": "OD1" <-> "OD2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 437": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16512 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.17, per 1000 atoms: 0.56 Number of scatterers: 16512 At special positions: 0 Unit cell: (108.141, 109.792, 83.3755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 12 15.00 O 3056 8.00 N 2908 7.00 C 10480 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.73 Conformation dependent library (CDL) restraints added in 2.7 seconds 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 4 sheets defined 35.1% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.592A pdb=" N ARG A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 158 through 168 Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'A' and resid 190 through 200 removed outlier: 4.145A pdb=" N HIS A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 200 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 325 through 328 No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 349 through 365 removed outlier: 3.792A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Proline residue: A 359 - end of helix removed outlier: 3.563A pdb=" N HIS A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 441 through 449 Processing helix chain 'A' and resid 453 through 469 removed outlier: 5.346A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 487 through 503 Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.592A pdb=" N ARG B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 158 through 168 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 190 through 200 removed outlier: 4.145A pdb=" N HIS B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 200 " --> pdb=" O SER B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 325 through 328 No H-bonds generated for 'chain 'B' and resid 325 through 328' Processing helix chain 'B' and resid 349 through 365 removed outlier: 3.792A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix removed outlier: 3.563A pdb=" N HIS B 364 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 441 through 449 Processing helix chain 'B' and resid 453 through 469 removed outlier: 5.346A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 487 through 503 Processing helix chain 'C' and resid 11 through 19 Processing helix chain 'C' and resid 55 through 66 removed outlier: 3.592A pdb=" N ARG C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 158 through 168 Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 179 through 188 Processing helix chain 'C' and resid 190 through 200 removed outlier: 4.145A pdb=" N HIS C 194 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 200 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 325 through 328 No H-bonds generated for 'chain 'C' and resid 325 through 328' Processing helix chain 'C' and resid 349 through 365 removed outlier: 3.792A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Proline residue: C 359 - end of helix removed outlier: 3.563A pdb=" N HIS C 364 " --> pdb=" O ASP C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 441 through 449 Processing helix chain 'C' and resid 453 through 469 removed outlier: 5.346A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 487 through 503 Processing helix chain 'D' and resid 11 through 19 Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.592A pdb=" N ARG D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 158 through 168 Proline residue: D 162 - end of helix Processing helix chain 'D' and resid 179 through 188 Processing helix chain 'D' and resid 190 through 200 removed outlier: 4.145A pdb=" N HIS D 194 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 200 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 325 through 328 No H-bonds generated for 'chain 'D' and resid 325 through 328' Processing helix chain 'D' and resid 349 through 365 removed outlier: 3.792A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) Proline residue: D 359 - end of helix removed outlier: 3.563A pdb=" N HIS D 364 " --> pdb=" O ASP D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 374 through 376 No H-bonds generated for 'chain 'D' and resid 374 through 376' Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 441 through 449 Processing helix chain 'D' and resid 453 through 469 removed outlier: 5.346A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 487 through 503 Processing sheet with id= A, first strand: chain 'A' and resid 141 through 148 removed outlier: 7.081A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE A 279 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS A 315 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP A 277 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 141 through 148 removed outlier: 7.081A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE B 279 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS B 315 " --> pdb=" O TRP B 277 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP B 277 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 141 through 148 removed outlier: 7.081A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 141 through 148 removed outlier: 7.081A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE D 279 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS D 315 " --> pdb=" O TRP D 277 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP D 277 " --> pdb=" O LYS D 315 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1416 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: 5.31 Time building geometry restraints manager: 7.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 7116 1.39 - 1.57: 9796 1.57 - 1.76: 20 1.76 - 1.94: 92 1.94 - 2.12: 12 Bond restraints: 17036 Sorted by residual: bond pdb=" O2B NDP D 601 " pdb=" P2B NDP D 601 " ideal model delta sigma weight residual 1.833 1.636 0.197 3.80e-02 6.93e+02 2.68e+01 bond pdb=" O2B NDP A 601 " pdb=" P2B NDP A 601 " ideal model delta sigma weight residual 1.833 1.636 0.197 3.80e-02 6.93e+02 2.68e+01 bond pdb=" O2B NDP C 601 " pdb=" P2B NDP C 601 " ideal model delta sigma weight residual 1.833 1.636 0.197 3.80e-02 6.93e+02 2.68e+01 bond pdb=" O2B NDP B 601 " pdb=" P2B NDP B 601 " ideal model delta sigma weight residual 1.833 1.636 0.197 3.80e-02 6.93e+02 2.68e+01 bond pdb=" O5D NDP B 601 " pdb=" PN NDP B 601 " ideal model delta sigma weight residual 1.757 1.594 0.163 3.50e-02 8.16e+02 2.17e+01 ... (remaining 17031 not shown) Histogram of bond angle deviations from ideal: 87.67 - 105.38: 624 105.38 - 123.10: 19564 123.10 - 140.81: 3044 140.81 - 158.52: 0 158.52 - 176.23: 8 Bond angle restraints: 23240 Sorted by residual: angle pdb=" PA NDP A 601 " pdb=" O3 NDP A 601 " pdb=" PN NDP A 601 " ideal model delta sigma weight residual 107.74 131.91 -24.17 1.95e+00 2.62e-01 1.53e+02 angle pdb=" PA NDP B 601 " pdb=" O3 NDP B 601 " pdb=" PN NDP B 601 " ideal model delta sigma weight residual 107.74 131.91 -24.17 1.95e+00 2.62e-01 1.53e+02 angle pdb=" PA NDP D 601 " pdb=" O3 NDP D 601 " pdb=" PN NDP D 601 " ideal model delta sigma weight residual 107.74 131.91 -24.17 1.95e+00 2.62e-01 1.53e+02 angle pdb=" PA NDP C 601 " pdb=" O3 NDP C 601 " pdb=" PN NDP C 601 " ideal model delta sigma weight residual 107.74 131.91 -24.17 1.95e+00 2.62e-01 1.53e+02 angle pdb=" C5B NDP D 601 " pdb=" O5B NDP D 601 " pdb=" PA NDP D 601 " ideal model delta sigma weight residual 103.84 119.74 -15.90 1.91e+00 2.73e-01 6.90e+01 ... (remaining 23235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.52: 9244 19.52 - 39.05: 532 39.05 - 58.57: 112 58.57 - 78.09: 60 78.09 - 97.61: 16 Dihedral angle restraints: 9964 sinusoidal: 4124 harmonic: 5840 Sorted by residual: dihedral pdb=" CA HIS A 218 " pdb=" C HIS A 218 " pdb=" N THR A 219 " pdb=" CA THR A 219 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA HIS B 218 " pdb=" C HIS B 218 " pdb=" N THR B 219 " pdb=" CA THR B 219 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA HIS D 218 " pdb=" C HIS D 218 " pdb=" N THR D 219 " pdb=" CA THR D 219 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 9961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1276 0.061 - 0.121: 668 0.121 - 0.182: 328 0.182 - 0.243: 72 0.243 - 0.303: 4 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA TYR A 236 " pdb=" N TYR A 236 " pdb=" C TYR A 236 " pdb=" CB TYR A 236 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA TYR C 236 " pdb=" N TYR C 236 " pdb=" C TYR C 236 " pdb=" CB TYR C 236 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA TYR B 236 " pdb=" N TYR B 236 " pdb=" C TYR B 236 " pdb=" CB TYR B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 2345 not shown) Planarity restraints: 3080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP D 601 " -0.100 2.00e-02 2.50e+03 6.06e-02 4.59e+01 pdb=" C3N NDP D 601 " -0.005 2.00e-02 2.50e+03 pdb=" C4N NDP D 601 " -0.018 2.00e-02 2.50e+03 pdb=" C7N NDP D 601 " 0.048 2.00e-02 2.50e+03 pdb=" N1N NDP D 601 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP C 601 " -0.100 2.00e-02 2.50e+03 6.06e-02 4.59e+01 pdb=" C3N NDP C 601 " -0.005 2.00e-02 2.50e+03 pdb=" C4N NDP C 601 " -0.018 2.00e-02 2.50e+03 pdb=" C7N NDP C 601 " 0.048 2.00e-02 2.50e+03 pdb=" N1N NDP C 601 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 601 " 0.100 2.00e-02 2.50e+03 6.06e-02 4.59e+01 pdb=" C3N NDP A 601 " 0.005 2.00e-02 2.50e+03 pdb=" C4N NDP A 601 " 0.018 2.00e-02 2.50e+03 pdb=" C7N NDP A 601 " -0.048 2.00e-02 2.50e+03 pdb=" N1N NDP A 601 " -0.075 2.00e-02 2.50e+03 ... (remaining 3077 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 6996 2.96 - 3.44: 16878 3.44 - 3.93: 31666 3.93 - 4.41: 35701 4.41 - 4.90: 56155 Nonbonded interactions: 147396 Sorted by model distance: nonbonded pdb=" OH TYR B 386 " pdb=" O PRO B 412 " model vdw 2.473 2.440 nonbonded pdb=" OH TYR D 386 " pdb=" O PRO D 412 " model vdw 2.473 2.440 nonbonded pdb=" OH TYR C 386 " pdb=" O PRO C 412 " model vdw 2.473 2.440 nonbonded pdb=" OH TYR A 386 " pdb=" O PRO A 412 " model vdw 2.473 2.440 nonbonded pdb=" O PHE D 164 " pdb=" OG SER D 167 " model vdw 2.484 2.440 ... (remaining 147391 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.330 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 46.230 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.012 0.197 17036 Z= 0.801 Angle : 1.852 24.172 23240 Z= 1.197 Chirality : 0.086 0.303 2348 Planarity : 0.012 0.116 3080 Dihedral : 15.253 97.608 6212 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.80 % Favored : 96.00 % Rotamer: Outliers : 1.39 % Allowed : 4.40 % Favored : 94.21 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 2.70 % 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: -1.14 (0.17), residues: 2000 helix: -0.84 (0.16), residues: 712 sheet: 0.24 (0.30), residues: 276 loop : -0.88 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.007 TRP B 277 HIS 0.018 0.004 HIS D 63 PHE 0.048 0.009 PHE B 334 TYR 0.052 0.009 TYR B 137 ARG 0.038 0.006 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 324 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8342 (ptt) cc_final: 0.8036 (ptt) REVERT: A 240 GLN cc_start: 0.6953 (mp-120) cc_final: 0.6386 (mp10) REVERT: A 259 ASP cc_start: 0.6082 (m-30) cc_final: 0.5667 (m-30) REVERT: A 424 GLN cc_start: 0.7233 (tt0) cc_final: 0.6335 (mp10) REVERT: A 428 GLU cc_start: 0.7148 (mt-10) cc_final: 0.5904 (pm20) REVERT: A 430 ARG cc_start: 0.5540 (ptt90) cc_final: 0.5024 (ptt-90) REVERT: A 454 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6707 (mp0) REVERT: A 457 LYS cc_start: 0.5836 (tttm) cc_final: 0.5464 (mptt) REVERT: A 461 GLU cc_start: 0.6143 (mt-10) cc_final: 0.5917 (mt-10) REVERT: B 212 MET cc_start: 0.8348 (ptt) cc_final: 0.8044 (ptt) REVERT: B 240 GLN cc_start: 0.6944 (mp-120) cc_final: 0.6381 (mp10) REVERT: B 259 ASP cc_start: 0.6077 (m-30) cc_final: 0.5667 (m-30) REVERT: B 424 GLN cc_start: 0.7232 (tt0) cc_final: 0.6335 (mp10) REVERT: B 428 GLU cc_start: 0.7148 (mt-10) cc_final: 0.5901 (pm20) REVERT: B 430 ARG cc_start: 0.5541 (ptt90) cc_final: 0.5015 (ptt-90) REVERT: B 454 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6707 (mp0) REVERT: B 457 LYS cc_start: 0.5839 (tttm) cc_final: 0.5464 (mptt) REVERT: B 461 GLU cc_start: 0.6142 (mt-10) cc_final: 0.5918 (mt-10) REVERT: C 212 MET cc_start: 0.8346 (ptt) cc_final: 0.8042 (ptt) REVERT: C 240 GLN cc_start: 0.6946 (mp-120) cc_final: 0.6378 (mp10) REVERT: C 259 ASP cc_start: 0.6082 (m-30) cc_final: 0.5861 (m-30) REVERT: C 424 GLN cc_start: 0.7234 (tt0) cc_final: 0.6330 (mp10) REVERT: C 428 GLU cc_start: 0.7145 (mt-10) cc_final: 0.5940 (pm20) REVERT: C 430 ARG cc_start: 0.5539 (ptt90) cc_final: 0.5020 (ptt-90) REVERT: C 454 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6706 (mp0) REVERT: C 457 LYS cc_start: 0.5838 (tttm) cc_final: 0.5462 (mptt) REVERT: C 461 GLU cc_start: 0.6142 (mt-10) cc_final: 0.5915 (mt-10) REVERT: D 212 MET cc_start: 0.8347 (ptt) cc_final: 0.8042 (ptt) REVERT: D 240 GLN cc_start: 0.6946 (mp-120) cc_final: 0.6382 (mp10) REVERT: D 259 ASP cc_start: 0.6080 (m-30) cc_final: 0.5859 (m-30) REVERT: D 424 GLN cc_start: 0.7233 (tt0) cc_final: 0.6328 (mp10) REVERT: D 428 GLU cc_start: 0.7149 (mt-10) cc_final: 0.5942 (pm20) REVERT: D 430 ARG cc_start: 0.5530 (ptt90) cc_final: 0.5018 (ptt-90) REVERT: D 454 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6703 (mp0) REVERT: D 457 LYS cc_start: 0.5841 (tttm) cc_final: 0.5465 (mptt) REVERT: D 461 GLU cc_start: 0.6145 (mt-10) cc_final: 0.5920 (mt-10) outliers start: 24 outliers final: 0 residues processed: 340 average time/residue: 0.3541 time to fit residues: 169.7228 Evaluate side-chains 162 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 181 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 471 GLN B 168 GLN B 471 GLN C 168 GLN C 471 GLN D 168 GLN D 471 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17036 Z= 0.186 Angle : 0.576 5.414 23240 Z= 0.292 Chirality : 0.044 0.150 2348 Planarity : 0.004 0.036 3080 Dihedral : 7.541 81.209 2272 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.50 % Allowed : 8.45 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.41 (0.18), residues: 2000 helix: 0.91 (0.18), residues: 716 sheet: 0.50 (0.27), residues: 332 loop : -0.20 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 183 HIS 0.005 0.001 HIS A 235 PHE 0.010 0.001 PHE C 294 TYR 0.023 0.001 TYR D 236 ARG 0.003 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 1.731 Fit side-chains REVERT: A 60 GLU cc_start: 0.6852 (tt0) cc_final: 0.6539 (tp30) REVERT: A 101 GLU cc_start: 0.6646 (tt0) cc_final: 0.6348 (mt-10) REVERT: A 212 MET cc_start: 0.8230 (ptt) cc_final: 0.7992 (ptt) REVERT: A 240 GLN cc_start: 0.7281 (mp-120) cc_final: 0.6368 (mp-120) REVERT: A 259 ASP cc_start: 0.6037 (m-30) cc_final: 0.5805 (m-30) REVERT: A 293 PRO cc_start: 0.7451 (Cg_exo) cc_final: 0.7231 (Cg_endo) REVERT: A 360 ASP cc_start: 0.8082 (t70) cc_final: 0.7427 (t0) REVERT: A 428 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6022 (mp0) REVERT: A 453 GLU cc_start: 0.4192 (mm-30) cc_final: 0.3782 (mm-30) REVERT: A 457 LYS cc_start: 0.5727 (tttm) cc_final: 0.5390 (mptt) REVERT: A 461 GLU cc_start: 0.5918 (mt-10) cc_final: 0.5692 (mt-10) REVERT: B 60 GLU cc_start: 0.6850 (tt0) cc_final: 0.6539 (tp30) REVERT: B 101 GLU cc_start: 0.6646 (tt0) cc_final: 0.6347 (mt-10) REVERT: B 212 MET cc_start: 0.8233 (ptt) cc_final: 0.7993 (ptt) REVERT: B 240 GLN cc_start: 0.7284 (mp-120) cc_final: 0.6369 (mp-120) REVERT: B 259 ASP cc_start: 0.6034 (m-30) cc_final: 0.5801 (m-30) REVERT: B 293 PRO cc_start: 0.7452 (Cg_exo) cc_final: 0.7232 (Cg_endo) REVERT: B 360 ASP cc_start: 0.8082 (t70) cc_final: 0.7427 (t0) REVERT: B 428 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6022 (mp0) REVERT: B 453 GLU cc_start: 0.4188 (mm-30) cc_final: 0.3780 (mm-30) REVERT: B 457 LYS cc_start: 0.5729 (tttm) cc_final: 0.5389 (mptt) REVERT: B 461 GLU cc_start: 0.5916 (mt-10) cc_final: 0.5689 (mt-10) REVERT: C 60 GLU cc_start: 0.6849 (tt0) cc_final: 0.6536 (tp30) REVERT: C 101 GLU cc_start: 0.6654 (tt0) cc_final: 0.6356 (mt-10) REVERT: C 212 MET cc_start: 0.8232 (ptt) cc_final: 0.7994 (ptt) REVERT: C 240 GLN cc_start: 0.7281 (mp-120) cc_final: 0.6368 (mp-120) REVERT: C 259 ASP cc_start: 0.6253 (m-30) cc_final: 0.5312 (p0) REVERT: C 293 PRO cc_start: 0.7452 (Cg_exo) cc_final: 0.7231 (Cg_endo) REVERT: C 360 ASP cc_start: 0.8072 (t70) cc_final: 0.7421 (t0) REVERT: C 424 GLN cc_start: 0.7039 (tt0) cc_final: 0.6041 (mp10) REVERT: C 428 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6015 (mp0) REVERT: C 453 GLU cc_start: 0.4191 (mm-30) cc_final: 0.3780 (mm-30) REVERT: C 457 LYS cc_start: 0.5723 (tttm) cc_final: 0.5386 (mptt) REVERT: C 461 GLU cc_start: 0.5916 (mt-10) cc_final: 0.5688 (mt-10) REVERT: D 60 GLU cc_start: 0.6843 (tt0) cc_final: 0.6532 (tp30) REVERT: D 101 GLU cc_start: 0.6648 (tt0) cc_final: 0.6349 (mt-10) REVERT: D 212 MET cc_start: 0.8235 (ptt) cc_final: 0.7996 (ptt) REVERT: D 240 GLN cc_start: 0.7285 (mp-120) cc_final: 0.6376 (mp-120) REVERT: D 259 ASP cc_start: 0.6250 (m-30) cc_final: 0.5309 (p0) REVERT: D 293 PRO cc_start: 0.7451 (Cg_exo) cc_final: 0.7231 (Cg_endo) REVERT: D 360 ASP cc_start: 0.8080 (t70) cc_final: 0.7427 (t0) REVERT: D 424 GLN cc_start: 0.7040 (tt0) cc_final: 0.6042 (mp10) REVERT: D 428 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6016 (mp0) REVERT: D 453 GLU cc_start: 0.4187 (mm-30) cc_final: 0.3776 (mm-30) REVERT: D 457 LYS cc_start: 0.5727 (tttm) cc_final: 0.5389 (mptt) REVERT: D 461 GLU cc_start: 0.5922 (mt-10) cc_final: 0.5694 (mt-10) outliers start: 26 outliers final: 18 residues processed: 198 average time/residue: 0.2693 time to fit residues: 83.0714 Evaluate side-chains 184 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 372 HIS C 372 HIS D 372 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17036 Z= 0.410 Angle : 0.661 7.848 23240 Z= 0.330 Chirality : 0.049 0.156 2348 Planarity : 0.006 0.048 3080 Dihedral : 7.504 80.868 2272 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.62 % Allowed : 9.38 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.10 (0.18), residues: 2000 helix: 0.49 (0.18), residues: 688 sheet: 0.73 (0.30), residues: 284 loop : -0.63 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 183 HIS 0.004 0.001 HIS A 235 PHE 0.016 0.002 PHE C 294 TYR 0.024 0.002 TYR C 236 ARG 0.004 0.001 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.989 Fit side-chains REVERT: A 60 GLU cc_start: 0.6830 (tt0) cc_final: 0.6591 (tp30) REVERT: A 98 LYS cc_start: 0.7408 (mttt) cc_final: 0.6932 (mttp) REVERT: A 128 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6511 (t0) REVERT: A 212 MET cc_start: 0.8572 (ptt) cc_final: 0.8310 (ptt) REVERT: A 360 ASP cc_start: 0.8022 (t70) cc_final: 0.7302 (t0) REVERT: A 428 GLU cc_start: 0.6978 (mt-10) cc_final: 0.5971 (mp0) REVERT: B 60 GLU cc_start: 0.6831 (tt0) cc_final: 0.6592 (tp30) REVERT: B 98 LYS cc_start: 0.7403 (mttt) cc_final: 0.6931 (mttp) REVERT: B 128 ASP cc_start: 0.6822 (OUTLIER) cc_final: 0.6513 (t0) REVERT: B 212 MET cc_start: 0.8580 (ptt) cc_final: 0.8316 (ptt) REVERT: B 360 ASP cc_start: 0.8025 (t70) cc_final: 0.7304 (t0) REVERT: B 428 GLU cc_start: 0.6979 (mt-10) cc_final: 0.5971 (mp0) REVERT: C 60 GLU cc_start: 0.6827 (tt0) cc_final: 0.6589 (tp30) REVERT: C 98 LYS cc_start: 0.7408 (mttt) cc_final: 0.6933 (mttp) REVERT: C 128 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6510 (t0) REVERT: C 212 MET cc_start: 0.8575 (ptt) cc_final: 0.8312 (ptt) REVERT: C 360 ASP cc_start: 0.8015 (t70) cc_final: 0.7295 (t0) REVERT: C 424 GLN cc_start: 0.7098 (tt0) cc_final: 0.6804 (tt0) REVERT: C 428 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6032 (mp0) REVERT: D 60 GLU cc_start: 0.6828 (tt0) cc_final: 0.6588 (tp30) REVERT: D 98 LYS cc_start: 0.7412 (mttt) cc_final: 0.6938 (mttp) REVERT: D 128 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6508 (t0) REVERT: D 212 MET cc_start: 0.8580 (ptt) cc_final: 0.8316 (ptt) REVERT: D 360 ASP cc_start: 0.8020 (t70) cc_final: 0.7302 (t0) REVERT: D 424 GLN cc_start: 0.7102 (tt0) cc_final: 0.6810 (tt0) REVERT: D 428 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6039 (mp0) outliers start: 28 outliers final: 22 residues processed: 158 average time/residue: 0.2950 time to fit residues: 71.5867 Evaluate side-chains 166 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.7433 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17036 Z= 0.186 Angle : 0.516 6.036 23240 Z= 0.257 Chirality : 0.043 0.151 2348 Planarity : 0.005 0.049 3080 Dihedral : 7.094 75.706 2272 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.20 % Allowed : 10.19 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.24 (0.18), residues: 2000 helix: 0.77 (0.19), residues: 716 sheet: 0.83 (0.31), residues: 288 loop : -0.43 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 183 HIS 0.003 0.001 HIS D 235 PHE 0.011 0.001 PHE A 136 TYR 0.019 0.001 TYR A 236 ARG 0.002 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 1.824 Fit side-chains REVERT: A 60 GLU cc_start: 0.6628 (tt0) cc_final: 0.6407 (tp30) REVERT: A 98 LYS cc_start: 0.7246 (mttt) cc_final: 0.6871 (mttp) REVERT: A 212 MET cc_start: 0.8600 (ptt) cc_final: 0.8387 (ptt) REVERT: A 360 ASP cc_start: 0.7989 (t70) cc_final: 0.7114 (t0) REVERT: A 428 GLU cc_start: 0.6861 (mt-10) cc_final: 0.5867 (mp0) REVERT: B 60 GLU cc_start: 0.6620 (tt0) cc_final: 0.6401 (tp30) REVERT: B 98 LYS cc_start: 0.7242 (mttt) cc_final: 0.6869 (mttp) REVERT: B 212 MET cc_start: 0.8607 (ptt) cc_final: 0.8395 (ptt) REVERT: B 360 ASP cc_start: 0.7989 (t70) cc_final: 0.7113 (t0) REVERT: B 428 GLU cc_start: 0.6859 (mt-10) cc_final: 0.5865 (mp0) REVERT: C 60 GLU cc_start: 0.6622 (tt0) cc_final: 0.6399 (tp30) REVERT: C 98 LYS cc_start: 0.7246 (mttt) cc_final: 0.6872 (mttp) REVERT: C 212 MET cc_start: 0.8599 (ptt) cc_final: 0.8388 (ptt) REVERT: C 360 ASP cc_start: 0.7983 (t70) cc_final: 0.7109 (t0) REVERT: C 424 GLN cc_start: 0.7137 (tt0) cc_final: 0.6843 (tt0) REVERT: C 428 GLU cc_start: 0.6834 (mt-10) cc_final: 0.5947 (mp0) REVERT: D 60 GLU cc_start: 0.6626 (tt0) cc_final: 0.6402 (tp30) REVERT: D 98 LYS cc_start: 0.7249 (mttt) cc_final: 0.6875 (mttp) REVERT: D 212 MET cc_start: 0.8606 (ptt) cc_final: 0.8392 (ptt) REVERT: D 360 ASP cc_start: 0.7986 (t70) cc_final: 0.7113 (t0) REVERT: D 424 GLN cc_start: 0.7137 (tt0) cc_final: 0.6844 (tt0) REVERT: D 428 GLU cc_start: 0.6843 (mt-10) cc_final: 0.5955 (mp0) outliers start: 38 outliers final: 14 residues processed: 182 average time/residue: 0.2824 time to fit residues: 79.1013 Evaluate side-chains 162 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 0.1980 chunk 133 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- 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: 0.7492 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17036 Z= 0.390 Angle : 0.624 6.593 23240 Z= 0.308 Chirality : 0.047 0.145 2348 Planarity : 0.005 0.047 3080 Dihedral : 7.384 78.129 2272 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.97 % Allowed : 11.00 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.10 (0.18), residues: 2000 helix: 0.50 (0.19), residues: 692 sheet: 0.86 (0.31), residues: 284 loop : -0.69 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 183 HIS 0.004 0.001 HIS C 235 PHE 0.015 0.002 PHE B 334 TYR 0.024 0.002 TYR B 236 ARG 0.005 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.958 Fit side-chains REVERT: A 60 GLU cc_start: 0.6587 (tt0) cc_final: 0.6376 (tp30) REVERT: A 98 LYS cc_start: 0.7491 (mttt) cc_final: 0.7098 (mttp) REVERT: A 360 ASP cc_start: 0.7904 (t70) cc_final: 0.7087 (t0) REVERT: A 428 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6012 (mp0) REVERT: B 60 GLU cc_start: 0.6582 (tt0) cc_final: 0.6372 (tp30) REVERT: B 98 LYS cc_start: 0.7489 (mttt) cc_final: 0.7098 (mttp) REVERT: B 360 ASP cc_start: 0.7905 (t70) cc_final: 0.7085 (t0) REVERT: B 428 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6014 (mp0) REVERT: C 60 GLU cc_start: 0.6586 (tt0) cc_final: 0.6370 (tp30) REVERT: C 98 LYS cc_start: 0.7490 (mttt) cc_final: 0.7097 (mttp) REVERT: C 360 ASP cc_start: 0.7894 (t70) cc_final: 0.7076 (t0) REVERT: C 424 GLN cc_start: 0.6994 (tt0) cc_final: 0.6756 (tt0) REVERT: C 428 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6003 (mp0) REVERT: D 60 GLU cc_start: 0.6592 (tt0) cc_final: 0.6374 (tp30) REVERT: D 98 LYS cc_start: 0.7492 (mttt) cc_final: 0.7099 (mttp) REVERT: D 360 ASP cc_start: 0.7902 (t70) cc_final: 0.7084 (t0) REVERT: D 424 GLN cc_start: 0.6995 (tt0) cc_final: 0.6759 (tt0) REVERT: D 428 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6014 (mp0) outliers start: 34 outliers final: 24 residues processed: 164 average time/residue: 0.2782 time to fit residues: 71.7328 Evaluate side-chains 158 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 496 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.7454 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17036 Z= 0.215 Angle : 0.531 6.180 23240 Z= 0.260 Chirality : 0.043 0.150 2348 Planarity : 0.005 0.049 3080 Dihedral : 7.088 74.374 2272 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.50 % Allowed : 11.69 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.04 (0.18), residues: 2000 helix: 0.63 (0.19), residues: 688 sheet: 0.75 (0.31), residues: 288 loop : -0.55 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 183 HIS 0.003 0.001 HIS C 235 PHE 0.010 0.001 PHE D 136 TYR 0.020 0.001 TYR B 236 ARG 0.004 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.910 Fit side-chains REVERT: A 6 ASP cc_start: 0.6124 (p0) cc_final: 0.5916 (p0) REVERT: A 98 LYS cc_start: 0.7458 (mttt) cc_final: 0.7117 (mttp) REVERT: A 122 SER cc_start: 0.8099 (t) cc_final: 0.7825 (m) REVERT: A 360 ASP cc_start: 0.7968 (t70) cc_final: 0.7109 (t0) REVERT: A 428 GLU cc_start: 0.6832 (mt-10) cc_final: 0.5891 (mp0) REVERT: B 6 ASP cc_start: 0.6132 (p0) cc_final: 0.5921 (p0) REVERT: B 98 LYS cc_start: 0.7453 (mttt) cc_final: 0.7115 (mttp) REVERT: B 122 SER cc_start: 0.8098 (t) cc_final: 0.7827 (m) REVERT: B 360 ASP cc_start: 0.7967 (t70) cc_final: 0.7107 (t0) REVERT: B 428 GLU cc_start: 0.6832 (mt-10) cc_final: 0.5891 (mp0) REVERT: C 6 ASP cc_start: 0.6133 (p0) cc_final: 0.5925 (p0) REVERT: C 98 LYS cc_start: 0.7452 (mttt) cc_final: 0.7114 (mttp) REVERT: C 360 ASP cc_start: 0.7960 (t70) cc_final: 0.7101 (t0) REVERT: C 424 GLN cc_start: 0.7084 (tt0) cc_final: 0.6816 (tt0) REVERT: C 428 GLU cc_start: 0.6846 (mt-10) cc_final: 0.5925 (mp0) REVERT: D 6 ASP cc_start: 0.6129 (p0) cc_final: 0.5919 (p0) REVERT: D 98 LYS cc_start: 0.7457 (mttt) cc_final: 0.7117 (mttp) REVERT: D 360 ASP cc_start: 0.7963 (t70) cc_final: 0.7103 (t0) REVERT: D 424 GLN cc_start: 0.7082 (tt0) cc_final: 0.6816 (tt0) REVERT: D 428 GLU cc_start: 0.6852 (mt-10) cc_final: 0.5930 (mp0) outliers start: 26 outliers final: 16 residues processed: 166 average time/residue: 0.2814 time to fit residues: 72.0296 Evaluate side-chains 162 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 141 optimal weight: 0.3980 chunk 109 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 192 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.7437 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17036 Z= 0.194 Angle : 0.520 6.245 23240 Z= 0.253 Chirality : 0.042 0.149 2348 Planarity : 0.005 0.049 3080 Dihedral : 6.923 72.219 2272 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.39 % Allowed : 12.15 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.22 (0.18), residues: 2000 helix: 0.76 (0.19), residues: 688 sheet: 0.78 (0.31), residues: 288 loop : -0.41 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 183 HIS 0.004 0.001 HIS A 235 PHE 0.010 0.001 PHE A 136 TYR 0.019 0.001 TYR A 236 ARG 0.004 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 2.013 Fit side-chains REVERT: A 6 ASP cc_start: 0.6115 (p0) cc_final: 0.5873 (p0) REVERT: A 98 LYS cc_start: 0.7331 (mttt) cc_final: 0.7027 (mttp) REVERT: A 122 SER cc_start: 0.8056 (t) cc_final: 0.7806 (m) REVERT: A 180 ASP cc_start: 0.6217 (m-30) cc_final: 0.5597 (m-30) REVERT: A 212 MET cc_start: 0.8555 (ptt) cc_final: 0.8314 (ptt) REVERT: A 360 ASP cc_start: 0.7870 (t70) cc_final: 0.7033 (t0) REVERT: A 425 TYR cc_start: 0.7713 (m-80) cc_final: 0.7504 (m-80) REVERT: A 428 GLU cc_start: 0.6861 (mt-10) cc_final: 0.5889 (mp0) REVERT: B 6 ASP cc_start: 0.6119 (p0) cc_final: 0.5877 (p0) REVERT: B 98 LYS cc_start: 0.7325 (mttt) cc_final: 0.7025 (mttp) REVERT: B 122 SER cc_start: 0.8054 (t) cc_final: 0.7808 (m) REVERT: B 180 ASP cc_start: 0.6210 (m-30) cc_final: 0.5592 (m-30) REVERT: B 212 MET cc_start: 0.8561 (ptt) cc_final: 0.8319 (ptt) REVERT: B 360 ASP cc_start: 0.7871 (t70) cc_final: 0.7030 (t0) REVERT: B 425 TYR cc_start: 0.7712 (m-80) cc_final: 0.7504 (m-80) REVERT: B 428 GLU cc_start: 0.6861 (mt-10) cc_final: 0.5890 (mp0) REVERT: C 6 ASP cc_start: 0.6122 (p0) cc_final: 0.5881 (p0) REVERT: C 98 LYS cc_start: 0.7325 (mttt) cc_final: 0.7024 (mttp) REVERT: C 122 SER cc_start: 0.8068 (t) cc_final: 0.7814 (m) REVERT: C 180 ASP cc_start: 0.6210 (m-30) cc_final: 0.5598 (m-30) REVERT: C 212 MET cc_start: 0.8557 (ptt) cc_final: 0.8318 (ptt) REVERT: C 360 ASP cc_start: 0.7863 (t70) cc_final: 0.7026 (t0) REVERT: C 424 GLN cc_start: 0.7044 (tt0) cc_final: 0.6738 (tt0) REVERT: C 425 TYR cc_start: 0.7773 (m-80) cc_final: 0.7542 (m-80) REVERT: C 428 GLU cc_start: 0.6805 (mt-10) cc_final: 0.5885 (mp0) REVERT: D 6 ASP cc_start: 0.6118 (p0) cc_final: 0.5877 (p0) REVERT: D 98 LYS cc_start: 0.7328 (mttt) cc_final: 0.7027 (mttp) REVERT: D 122 SER cc_start: 0.8066 (t) cc_final: 0.7812 (m) REVERT: D 180 ASP cc_start: 0.6210 (m-30) cc_final: 0.5593 (m-30) REVERT: D 212 MET cc_start: 0.8558 (ptt) cc_final: 0.8317 (ptt) REVERT: D 360 ASP cc_start: 0.7866 (t70) cc_final: 0.7029 (t0) REVERT: D 424 GLN cc_start: 0.7041 (tt0) cc_final: 0.6736 (tt0) REVERT: D 425 TYR cc_start: 0.7769 (m-80) cc_final: 0.7538 (m-80) REVERT: D 428 GLU cc_start: 0.6815 (mt-10) cc_final: 0.5893 (mp0) outliers start: 24 outliers final: 16 residues processed: 174 average time/residue: 0.2700 time to fit residues: 74.8408 Evaluate side-chains 178 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 122 optimal weight: 0.0470 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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: 0.7434 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17036 Z= 0.195 Angle : 0.521 6.258 23240 Z= 0.252 Chirality : 0.042 0.149 2348 Planarity : 0.005 0.050 3080 Dihedral : 6.837 70.123 2272 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.93 % Allowed : 13.37 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.25 (0.18), residues: 2000 helix: 0.82 (0.20), residues: 688 sheet: 0.79 (0.31), residues: 288 loop : -0.41 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 183 HIS 0.004 0.001 HIS A 235 PHE 0.010 0.001 PHE A 136 TYR 0.019 0.001 TYR B 236 ARG 0.004 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 1.879 Fit side-chains REVERT: A 6 ASP cc_start: 0.6123 (p0) cc_final: 0.5868 (p0) REVERT: A 98 LYS cc_start: 0.7406 (mttt) cc_final: 0.7104 (mttp) REVERT: A 122 SER cc_start: 0.7973 (t) cc_final: 0.7720 (m) REVERT: A 180 ASP cc_start: 0.6029 (m-30) cc_final: 0.5474 (m-30) REVERT: A 212 MET cc_start: 0.8542 (ptt) cc_final: 0.8287 (ptt) REVERT: A 284 MET cc_start: 0.8114 (ttm) cc_final: 0.7857 (ttm) REVERT: A 360 ASP cc_start: 0.7858 (t70) cc_final: 0.7015 (t0) REVERT: A 425 TYR cc_start: 0.7737 (m-80) cc_final: 0.7444 (m-80) REVERT: A 428 GLU cc_start: 0.6863 (mt-10) cc_final: 0.5888 (mp0) REVERT: B 6 ASP cc_start: 0.6127 (p0) cc_final: 0.5872 (p0) REVERT: B 98 LYS cc_start: 0.7401 (mttt) cc_final: 0.7101 (mttp) REVERT: B 122 SER cc_start: 0.7971 (t) cc_final: 0.7719 (m) REVERT: B 180 ASP cc_start: 0.6025 (m-30) cc_final: 0.5469 (m-30) REVERT: B 212 MET cc_start: 0.8548 (ptt) cc_final: 0.8291 (ptt) REVERT: B 284 MET cc_start: 0.8116 (ttm) cc_final: 0.7861 (ttm) REVERT: B 360 ASP cc_start: 0.7857 (t70) cc_final: 0.7013 (t0) REVERT: B 425 TYR cc_start: 0.7735 (m-80) cc_final: 0.7440 (m-80) REVERT: B 428 GLU cc_start: 0.6864 (mt-10) cc_final: 0.5890 (mp0) REVERT: C 6 ASP cc_start: 0.6127 (p0) cc_final: 0.5872 (p0) REVERT: C 98 LYS cc_start: 0.7399 (mttt) cc_final: 0.7099 (mttp) REVERT: C 122 SER cc_start: 0.7994 (t) cc_final: 0.7730 (m) REVERT: C 180 ASP cc_start: 0.5993 (m-30) cc_final: 0.5445 (m-30) REVERT: C 212 MET cc_start: 0.8544 (ptt) cc_final: 0.8288 (ptt) REVERT: C 284 MET cc_start: 0.8115 (ttm) cc_final: 0.7859 (ttm) REVERT: C 360 ASP cc_start: 0.7851 (t70) cc_final: 0.7007 (t0) REVERT: C 424 GLN cc_start: 0.7049 (tt0) cc_final: 0.6713 (tt0) REVERT: C 425 TYR cc_start: 0.7722 (m-80) cc_final: 0.7391 (m-80) REVERT: C 428 GLU cc_start: 0.6801 (mt-10) cc_final: 0.5921 (mp0) REVERT: D 6 ASP cc_start: 0.6122 (p0) cc_final: 0.5868 (p0) REVERT: D 98 LYS cc_start: 0.7402 (mttt) cc_final: 0.7102 (mttp) REVERT: D 122 SER cc_start: 0.7994 (t) cc_final: 0.7729 (m) REVERT: D 180 ASP cc_start: 0.5990 (m-30) cc_final: 0.5441 (m-30) REVERT: D 212 MET cc_start: 0.8546 (ptt) cc_final: 0.8291 (ptt) REVERT: D 284 MET cc_start: 0.8113 (ttm) cc_final: 0.7859 (ttm) REVERT: D 360 ASP cc_start: 0.7854 (t70) cc_final: 0.7012 (t0) REVERT: D 424 GLN cc_start: 0.7047 (tt0) cc_final: 0.6711 (tt0) REVERT: D 425 TYR cc_start: 0.7728 (m-80) cc_final: 0.7395 (m-80) REVERT: D 428 GLU cc_start: 0.6812 (mt-10) cc_final: 0.5931 (mp0) outliers start: 16 outliers final: 16 residues processed: 174 average time/residue: 0.2703 time to fit residues: 74.1989 Evaluate side-chains 174 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 78 optimal weight: 5.9990 chunk 141 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 162 optimal weight: 0.1980 chunk 169 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 189 optimal weight: 0.0470 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 148 ASN C 148 ASN D 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17036 Z= 0.135 Angle : 0.484 5.878 23240 Z= 0.234 Chirality : 0.041 0.150 2348 Planarity : 0.004 0.049 3080 Dihedral : 6.497 63.739 2272 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.16 % Allowed : 13.31 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.47 (0.19), residues: 2000 helix: 1.04 (0.20), residues: 700 sheet: 0.99 (0.31), residues: 288 loop : -0.35 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.004 0.000 HIS C 235 PHE 0.010 0.001 PHE A 161 TYR 0.016 0.001 TYR A 236 ARG 0.004 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 1.896 Fit side-chains REVERT: A 6 ASP cc_start: 0.5921 (p0) cc_final: 0.5687 (p0) REVERT: A 98 LYS cc_start: 0.7204 (mttt) cc_final: 0.6948 (mttp) REVERT: A 122 SER cc_start: 0.7923 (t) cc_final: 0.7659 (m) REVERT: A 178 ASP cc_start: 0.5945 (t0) cc_final: 0.5664 (t0) REVERT: A 180 ASP cc_start: 0.5851 (m-30) cc_final: 0.5415 (m-30) REVERT: A 212 MET cc_start: 0.8434 (ptt) cc_final: 0.8197 (ptt) REVERT: A 360 ASP cc_start: 0.7860 (t70) cc_final: 0.7004 (t0) REVERT: A 425 TYR cc_start: 0.7699 (m-80) cc_final: 0.7378 (m-80) REVERT: A 428 GLU cc_start: 0.6689 (mt-10) cc_final: 0.5746 (mp0) REVERT: B 6 ASP cc_start: 0.5929 (p0) cc_final: 0.5694 (p0) REVERT: B 98 LYS cc_start: 0.7199 (mttt) cc_final: 0.6946 (mttp) REVERT: B 122 SER cc_start: 0.7921 (t) cc_final: 0.7660 (m) REVERT: B 178 ASP cc_start: 0.5939 (t0) cc_final: 0.5663 (t0) REVERT: B 180 ASP cc_start: 0.5853 (m-30) cc_final: 0.5415 (m-30) REVERT: B 212 MET cc_start: 0.8436 (ptt) cc_final: 0.8198 (ptt) REVERT: B 360 ASP cc_start: 0.7856 (t70) cc_final: 0.7000 (t0) REVERT: B 425 TYR cc_start: 0.7699 (m-80) cc_final: 0.7378 (m-80) REVERT: B 428 GLU cc_start: 0.6688 (mt-10) cc_final: 0.5746 (mp0) REVERT: C 6 ASP cc_start: 0.5931 (p0) cc_final: 0.5701 (p0) REVERT: C 98 LYS cc_start: 0.7200 (mttt) cc_final: 0.6947 (mttp) REVERT: C 122 SER cc_start: 0.7922 (t) cc_final: 0.7641 (m) REVERT: C 178 ASP cc_start: 0.5963 (t0) cc_final: 0.5655 (t0) REVERT: C 180 ASP cc_start: 0.5822 (m-30) cc_final: 0.5386 (m-30) REVERT: C 212 MET cc_start: 0.8436 (ptt) cc_final: 0.8200 (ptt) REVERT: C 360 ASP cc_start: 0.7851 (t70) cc_final: 0.6997 (t0) REVERT: C 424 GLN cc_start: 0.7019 (tt0) cc_final: 0.6675 (tt0) REVERT: C 425 TYR cc_start: 0.7618 (m-80) cc_final: 0.7264 (m-80) REVERT: C 428 GLU cc_start: 0.6558 (mt-10) cc_final: 0.5776 (mp0) REVERT: D 6 ASP cc_start: 0.5930 (p0) cc_final: 0.5697 (p0) REVERT: D 98 LYS cc_start: 0.7198 (mttt) cc_final: 0.6946 (mttp) REVERT: D 122 SER cc_start: 0.7923 (t) cc_final: 0.7642 (m) REVERT: D 178 ASP cc_start: 0.5961 (t0) cc_final: 0.5654 (t0) REVERT: D 180 ASP cc_start: 0.5820 (m-30) cc_final: 0.5385 (m-30) REVERT: D 212 MET cc_start: 0.8438 (ptt) cc_final: 0.8203 (ptt) REVERT: D 360 ASP cc_start: 0.7853 (t70) cc_final: 0.6998 (t0) REVERT: D 424 GLN cc_start: 0.7016 (tt0) cc_final: 0.6673 (tt0) REVERT: D 425 TYR cc_start: 0.7613 (m-80) cc_final: 0.7261 (m-80) REVERT: D 428 GLU cc_start: 0.6571 (mt-10) cc_final: 0.5784 (mp0) outliers start: 20 outliers final: 16 residues processed: 182 average time/residue: 0.2617 time to fit residues: 75.1792 Evaluate side-chains 186 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 132 optimal weight: 0.0060 chunk 199 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 158 optimal weight: 0.0670 chunk 16 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 overall best weight: 0.4934 ------------------------------------------------------------------------------- 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: 0.7385 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17036 Z= 0.142 Angle : 0.498 6.011 23240 Z= 0.240 Chirality : 0.041 0.149 2348 Planarity : 0.004 0.050 3080 Dihedral : 6.390 61.468 2272 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.62 % Allowed : 12.85 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.59 (0.19), residues: 2000 helix: 1.14 (0.20), residues: 704 sheet: 1.09 (0.31), residues: 288 loop : -0.30 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 183 HIS 0.005 0.000 HIS D 235 PHE 0.009 0.001 PHE A 136 TYR 0.016 0.001 TYR A 236 ARG 0.004 0.000 ARG B 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.964 Fit side-chains REVERT: A 6 ASP cc_start: 0.5938 (p0) cc_final: 0.5689 (p0) REVERT: A 61 MET cc_start: 0.6676 (tpp) cc_final: 0.6239 (mpp) REVERT: A 122 SER cc_start: 0.7892 (t) cc_final: 0.7611 (m) REVERT: A 178 ASP cc_start: 0.5890 (t0) cc_final: 0.5486 (t0) REVERT: A 180 ASP cc_start: 0.5624 (m-30) cc_final: 0.5174 (m-30) REVERT: A 202 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.6042 (t70) REVERT: A 360 ASP cc_start: 0.7876 (t70) cc_final: 0.7031 (t0) REVERT: A 425 TYR cc_start: 0.7675 (m-80) cc_final: 0.7284 (m-80) REVERT: A 428 GLU cc_start: 0.6552 (mt-10) cc_final: 0.5603 (mp0) REVERT: B 6 ASP cc_start: 0.5944 (p0) cc_final: 0.5695 (p0) REVERT: B 61 MET cc_start: 0.6677 (tpp) cc_final: 0.6241 (mpp) REVERT: B 122 SER cc_start: 0.7891 (t) cc_final: 0.7612 (m) REVERT: B 178 ASP cc_start: 0.5881 (t0) cc_final: 0.5479 (t0) REVERT: B 180 ASP cc_start: 0.5627 (m-30) cc_final: 0.5169 (m-30) REVERT: B 202 ASP cc_start: 0.6239 (OUTLIER) cc_final: 0.6033 (t70) REVERT: B 212 MET cc_start: 0.8373 (ptt) cc_final: 0.8173 (ptt) REVERT: B 360 ASP cc_start: 0.7873 (t70) cc_final: 0.7024 (t0) REVERT: B 425 TYR cc_start: 0.7674 (m-80) cc_final: 0.7283 (m-80) REVERT: B 428 GLU cc_start: 0.6554 (mt-10) cc_final: 0.5605 (mp0) REVERT: C 6 ASP cc_start: 0.5946 (p0) cc_final: 0.5700 (p0) REVERT: C 61 MET cc_start: 0.6667 (tpp) cc_final: 0.6232 (mpp) REVERT: C 122 SER cc_start: 0.7885 (t) cc_final: 0.7599 (m) REVERT: C 180 ASP cc_start: 0.5631 (m-30) cc_final: 0.5174 (m-30) REVERT: C 202 ASP cc_start: 0.6248 (OUTLIER) cc_final: 0.6045 (t70) REVERT: C 360 ASP cc_start: 0.7866 (t70) cc_final: 0.7019 (t0) REVERT: C 424 GLN cc_start: 0.7045 (tt0) cc_final: 0.6698 (tt0) REVERT: C 425 TYR cc_start: 0.7591 (m-80) cc_final: 0.7253 (m-80) REVERT: C 428 GLU cc_start: 0.6505 (mt-10) cc_final: 0.5728 (mp0) REVERT: D 6 ASP cc_start: 0.5945 (p0) cc_final: 0.5698 (p0) REVERT: D 61 MET cc_start: 0.6667 (tpp) cc_final: 0.6228 (mpp) REVERT: D 122 SER cc_start: 0.7888 (t) cc_final: 0.7601 (m) REVERT: D 180 ASP cc_start: 0.5638 (m-30) cc_final: 0.5185 (m-30) REVERT: D 202 ASP cc_start: 0.6243 (OUTLIER) cc_final: 0.6039 (t70) REVERT: D 360 ASP cc_start: 0.7868 (t70) cc_final: 0.7021 (t0) REVERT: D 424 GLN cc_start: 0.7043 (tt0) cc_final: 0.6696 (tt0) REVERT: D 425 TYR cc_start: 0.7585 (m-80) cc_final: 0.7248 (m-80) REVERT: D 428 GLU cc_start: 0.6520 (mt-10) cc_final: 0.5738 (mp0) outliers start: 28 outliers final: 16 residues processed: 188 average time/residue: 0.2490 time to fit residues: 74.7563 Evaluate side-chains 184 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 5.9990 chunk 146 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 66 optimal weight: 0.0770 chunk 163 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 9 optimal weight: 0.0770 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3272 r_free = 0.3272 target = 0.118220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.105936 restraints weight = 21504.165| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 0.88 r_work: 0.3018 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17036 Z= 0.146 Angle : 0.508 8.476 23240 Z= 0.244 Chirality : 0.041 0.159 2348 Planarity : 0.004 0.049 3080 Dihedral : 6.273 61.290 2272 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.87 % Allowed : 13.66 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.19), residues: 2000 helix: 1.22 (0.20), residues: 700 sheet: 1.17 (0.31), residues: 288 loop : -0.26 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 183 HIS 0.005 0.000 HIS B 235 PHE 0.015 0.001 PHE B 57 TYR 0.016 0.001 TYR A 236 ARG 0.003 0.000 ARG B 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.48 seconds wall clock time: 59 minutes 34.51 seconds (3574.51 seconds total)