Starting phenix.real_space_refine on Sun Mar 17 10:52:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el9_28225/03_2024/8el9_28225_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el9_28225/03_2024/8el9_28225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el9_28225/03_2024/8el9_28225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el9_28225/03_2024/8el9_28225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el9_28225/03_2024/8el9_28225_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el9_28225/03_2024/8el9_28225_updated.pdb" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 64 atoms to isotropic. 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 10420 2.51 5 N 2899 2.21 5 O 4042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 461": "OE1" <-> "OE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17429 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 497, 3997 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 497, 3997 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4102 Chain: "B" Number of atoms: 4009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 497, 3997 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 497, 3997 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4102 Chain: "C" Number of atoms: 4018 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4111 Chain: "D" Number of atoms: 4014 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4002 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 498, 4002 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4107 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: 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: 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: 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: "A" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 257 Classifications: {'water': 257} Link IDs: {None: 256} Chain: "B" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 260 Classifications: {'water': 260} Link IDs: {None: 259} Chain: "C" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 244 Classifications: {'water': 244} Link IDs: {None: 243} Chain: "D" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 254 Classifications: {'water': 254} Link IDs: {None: 253} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLY A 121 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 121 " occ=0.50 residue: pdb=" N AGLY B 121 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 121 " occ=0.50 residue: pdb=" N AGLY C 121 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY C 121 " occ=0.50 residue: pdb=" N AGLY D 121 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY D 121 " occ=0.50 Time building chain proxies: 17.47, per 1000 atoms: 1.00 Number of scatterers: 17429 At special positions: 0 Unit cell: (85.32, 113.4, 109.08, 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 4042 8.00 N 2899 7.00 C 10420 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: 8.23 Conformation dependent library (CDL) restraints added in 6.1 seconds 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 5 sheets defined 33.6% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.536A pdb=" N HIS A 63 " --> pdb=" O ASP A 59 " (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 199 removed outlier: 4.360A pdb=" N HIS A 194 " --> pdb=" O GLU A 191 " (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 247 through 256 removed outlier: 3.674A pdb=" N GLN A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 290 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: 3.891A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Proline residue: A 359 - end of helix removed outlier: 3.550A 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: 5.165A 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 500 Processing helix chain 'B' and resid 11 through 18 Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.621A pdb=" N HIS B 63 " --> pdb=" O ASP B 59 " (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 167 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 190 through 199 removed outlier: 4.360A pdb=" N HIS B 194 " --> pdb=" O GLU B 191 " (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 247 through 256 removed outlier: 3.583A pdb=" N GLN B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.751A pdb=" N GLU B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 290' 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: 3.847A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix removed outlier: 3.536A 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: 5.093A 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 500 Processing helix chain 'C' and resid 11 through 19 Processing helix chain 'C' and resid 55 through 66 removed outlier: 3.599A pdb=" N HIS C 63 " --> pdb=" O ASP C 59 " (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 167 Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 179 through 188 Processing helix chain 'C' and resid 190 through 199 removed outlier: 4.368A pdb=" N HIS C 194 " --> pdb=" O GLU C 191 " (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 247 through 256 removed outlier: 3.722A pdb=" N GLN C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) 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: 3.838A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Proline residue: C 359 - end of helix 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 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: 5.145A 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 501 Processing helix chain 'D' and resid 11 through 19 Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.655A 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 199 removed outlier: 4.344A pdb=" N HIS D 194 " --> pdb=" O GLU D 191 " (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 247 through 256 removed outlier: 3.706A pdb=" N GLN D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) 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: 3.837A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) Proline residue: D 359 - end of helix removed outlier: 3.544A 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: 5.157A 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 501 Processing sheet with id= A, first strand: chain 'A' and resid 141 through 148 removed outlier: 7.159A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE A 279 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 315 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TRP A 277 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A 317 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 141 through 148 removed outlier: 7.144A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B 279 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS B 315 " --> pdb=" O TRP B 277 " (cutoff:3.500A) removed outlier: 6.392A 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: 7.154A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE C 234 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 229 through 232 Processing sheet with id= E, first strand: chain 'D' and resid 141 through 148 removed outlier: 7.171A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE D 279 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS D 315 " --> pdb=" O TRP D 277 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP D 277 " --> pdb=" O LYS D 315 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1366 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: 4.91 Time building geometry restraints manager: 8.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 7281 1.39 - 1.56: 9529 1.56 - 1.73: 20 1.73 - 1.90: 96 1.90 - 2.06: 16 Bond restraints: 16942 Sorted by residual: bond pdb=" CA GLN D 395 " pdb=" CB GLN D 395 " ideal model delta sigma weight residual 1.537 1.519 0.017 1.45e-02 4.76e+03 1.42e+00 bond pdb=" N GLY D 314 " pdb=" CA GLY D 314 " ideal model delta sigma weight residual 1.458 1.447 0.010 9.20e-03 1.18e+04 1.29e+00 bond pdb=" CA GLN B 395 " pdb=" C GLN B 395 " ideal model delta sigma weight residual 1.524 1.517 0.008 7.00e-03 2.04e+04 1.16e+00 bond pdb=" C GLN B 395 " pdb=" O GLN B 395 " ideal model delta sigma weight residual 1.233 1.247 -0.014 1.32e-02 5.74e+03 1.06e+00 bond pdb=" CA TYR D 358 " pdb=" C TYR D 358 " ideal model delta sigma weight residual 1.524 1.536 -0.013 1.26e-02 6.30e+03 9.98e-01 ... (remaining 16937 not shown) Histogram of bond angle deviations from ideal: 88.98 - 106.67: 734 106.67 - 124.37: 21776 124.37 - 142.07: 605 142.07 - 159.76: 0 159.76 - 177.46: 8 Bond angle restraints: 23123 Sorted by residual: angle pdb=" C ASP C 389 " pdb=" CA ASP C 389 " pdb=" CB ASP C 389 " ideal model delta sigma weight residual 115.89 109.79 6.10 1.32e+00 5.74e-01 2.14e+01 angle pdb=" C MET B 394 " pdb=" N GLN B 395 " pdb=" CA GLN B 395 " ideal model delta sigma weight residual 122.44 117.97 4.47 1.19e+00 7.06e-01 1.41e+01 angle pdb=" N GLY D 314 " pdb=" CA GLY D 314 " pdb=" C GLY D 314 " ideal model delta sigma weight residual 111.16 117.00 -5.84 1.76e+00 3.23e-01 1.10e+01 angle pdb=" C VAL D 313 " pdb=" N GLY D 314 " pdb=" CA GLY D 314 " ideal model delta sigma weight residual 122.16 119.76 2.40 7.70e-01 1.69e+00 9.71e+00 angle pdb=" N GLY C 216 " pdb=" CA GLY C 216 " pdb=" C GLY C 216 " ideal model delta sigma weight residual 113.18 105.94 7.24 2.37e+00 1.78e-01 9.33e+00 ... (remaining 23118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.52: 8817 20.52 - 41.03: 849 41.03 - 61.55: 171 61.55 - 82.06: 55 82.06 - 102.58: 9 Dihedral angle restraints: 9901 sinusoidal: 4091 harmonic: 5810 Sorted by residual: dihedral pdb=" CA HIS A 372 " pdb=" C HIS A 372 " pdb=" N ILE A 373 " pdb=" CA ILE A 373 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA HIS D 372 " pdb=" C HIS D 372 " pdb=" N ILE D 373 " pdb=" CA ILE D 373 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA HIS B 372 " pdb=" C HIS B 372 " pdb=" N ILE B 373 " pdb=" CA ILE B 373 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 9898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1446 0.036 - 0.073: 607 0.073 - 0.109: 225 0.109 - 0.145: 52 0.145 - 0.181: 4 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CA ILE D 373 " pdb=" N ILE D 373 " pdb=" C ILE D 373 " pdb=" CB ILE D 373 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA ILE B 373 " pdb=" N ILE B 373 " pdb=" C ILE B 373 " pdb=" CB ILE B 373 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CA ILE A 373 " pdb=" N ILE A 373 " pdb=" C ILE A 373 " pdb=" CB ILE A 373 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 2331 not shown) Planarity restraints: 3067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 346 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO C 347 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 347 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 347 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 346 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO B 347 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 347 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 346 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 347 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " 0.026 5.00e-02 4.00e+02 ... (remaining 3064 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1471 2.74 - 3.28: 17244 3.28 - 3.82: 35167 3.82 - 4.36: 44946 4.36 - 4.90: 67714 Nonbonded interactions: 166542 Sorted by model distance: nonbonded pdb=" O LYS A 273 " pdb=" O HOH A 701 " model vdw 2.197 2.440 nonbonded pdb=" O HOH D 747 " pdb=" O HOH D 872 " model vdw 2.223 2.440 nonbonded pdb=" O HOH B 715 " pdb=" O HOH B 737 " model vdw 2.229 2.440 nonbonded pdb=" O HOH C 765 " pdb=" O HOH C 876 " model vdw 2.234 2.440 nonbonded pdb=" O HOH D 713 " pdb=" O HOH D 779 " model vdw 2.245 2.440 ... (remaining 166537 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' and (resid 5 through 18 or resid 20 through 120 or resid 122 through \ 501 or resid 601 through 602)) selection = (chain 'B' and (resid 5 through 18 or resid 20 through 120 or resid 122 through \ 501 or resid 601 through 602)) selection = (chain 'C' and (resid 5 through 18 or resid 20 through 120 or resid 122 through \ 394 or (resid 395 and (name N or name CA or name C or name O or name CB )) or re \ sid 396 through 501 or resid 601 through 602)) selection = (chain 'D' and (resid 5 through 18 or resid 20 through 120 or resid 122 through \ 501 or resid 601 through 602)) } 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=0.50 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: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 15.140 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 59.980 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.150 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:14.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16942 Z= 0.200 Angle : 0.652 8.096 23123 Z= 0.337 Chirality : 0.046 0.181 2334 Planarity : 0.005 0.048 3067 Dihedral : 17.091 102.575 6177 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.23 % Allowed : 13.43 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 1998 helix: 0.50 (0.19), residues: 702 sheet: 0.65 (0.31), residues: 290 loop : -0.41 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 183 HIS 0.005 0.001 HIS A 218 PHE 0.012 0.002 PHE C 473 TYR 0.031 0.002 TYR C 236 ARG 0.009 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 2.006 Fit side-chains REVERT: A 499 LYS cc_start: 0.7604 (mtpp) cc_final: 0.7368 (mtmm) REVERT: C 476 LYS cc_start: 0.8140 (mmpt) cc_final: 0.7801 (mttt) outliers start: 19 outliers final: 18 residues processed: 199 average time/residue: 1.4904 time to fit residues: 328.0373 Evaluate side-chains 190 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 0.0370 chunk 79 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 449 ASN B 372 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 102 HIS D 372 HIS D 449 ASN D 501 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16942 Z= 0.196 Angle : 0.623 7.381 23123 Z= 0.319 Chirality : 0.046 0.175 2334 Planarity : 0.005 0.050 3067 Dihedral : 8.827 103.848 2298 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.46 % Allowed : 13.08 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.13 (0.18), residues: 1998 helix: 0.47 (0.19), residues: 702 sheet: 0.88 (0.31), residues: 300 loop : -0.36 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 183 HIS 0.007 0.001 HIS A 218 PHE 0.018 0.002 PHE A 136 TYR 0.028 0.002 TYR A 236 ARG 0.006 0.001 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 1.971 Fit side-chains REVERT: B 236 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8610 (p90) REVERT: B 499 LYS cc_start: 0.8076 (mtpm) cc_final: 0.7719 (mtpp) outliers start: 23 outliers final: 15 residues processed: 197 average time/residue: 1.4733 time to fit residues: 321.7239 Evaluate side-chains 188 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 49 optimal weight: 0.0040 chunk 178 optimal weight: 0.0070 chunk 192 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 372 HIS A 449 ASN B 372 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 372 HIS D 449 ASN D 501 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16942 Z= 0.144 Angle : 0.542 6.920 23123 Z= 0.274 Chirality : 0.044 0.169 2334 Planarity : 0.004 0.045 3067 Dihedral : 7.876 95.463 2286 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.75 % Allowed : 12.84 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.33 (0.18), residues: 1998 helix: 0.47 (0.19), residues: 704 sheet: 1.38 (0.32), residues: 294 loop : -0.24 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.004 0.001 HIS A 218 PHE 0.014 0.001 PHE B 136 TYR 0.022 0.001 TYR A 236 ARG 0.006 0.000 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 2.146 Fit side-chains REVERT: B 236 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8597 (p90) REVERT: B 499 LYS cc_start: 0.7939 (mtpm) cc_final: 0.7588 (mtpp) outliers start: 28 outliers final: 18 residues processed: 201 average time/residue: 1.4488 time to fit residues: 322.8299 Evaluate side-chains 191 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 0.0000 chunk 189 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 372 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16942 Z= 0.171 Angle : 0.586 7.013 23123 Z= 0.297 Chirality : 0.045 0.167 2334 Planarity : 0.005 0.047 3067 Dihedral : 8.182 99.849 2282 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.98 % Allowed : 12.73 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.28 (0.18), residues: 1998 helix: 0.41 (0.19), residues: 706 sheet: 1.23 (0.32), residues: 290 loop : -0.20 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.006 0.001 HIS A 218 PHE 0.017 0.002 PHE A 136 TYR 0.024 0.002 TYR B 236 ARG 0.006 0.000 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 178 time to evaluate : 1.980 Fit side-chains REVERT: B 236 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.8676 (p90) REVERT: D 237 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7657 (mmtm) outliers start: 32 outliers final: 21 residues processed: 199 average time/residue: 1.4916 time to fit residues: 328.6667 Evaluate side-chains 195 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 237 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 449 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN C 235 HIS ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 449 ASN D 501 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16942 Z= 0.277 Angle : 0.707 9.052 23123 Z= 0.365 Chirality : 0.050 0.168 2334 Planarity : 0.006 0.051 3067 Dihedral : 8.963 106.616 2282 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.87 % Allowed : 13.08 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.01 (0.18), residues: 1998 helix: 0.31 (0.19), residues: 710 sheet: 0.88 (0.32), residues: 290 loop : -0.40 (0.18), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 183 HIS 0.008 0.002 HIS A 218 PHE 0.018 0.003 PHE A 132 TYR 0.031 0.003 TYR D 236 ARG 0.006 0.001 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 2.128 Fit side-chains REVERT: A 203 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7027 (mtm180) REVERT: B 236 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8634 (p90) REVERT: C 236 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8657 (p90) REVERT: D 237 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7330 (mmtm) outliers start: 30 outliers final: 19 residues processed: 194 average time/residue: 1.5410 time to fit residues: 329.4808 Evaluate side-chains 195 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 237 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 287 ASN A 449 ASN B 18 GLN B 287 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 ASN D 501 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16942 Z= 0.198 Angle : 0.625 8.295 23123 Z= 0.319 Chirality : 0.046 0.166 2334 Planarity : 0.005 0.050 3067 Dihedral : 8.596 103.180 2282 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.81 % Allowed : 12.96 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.13 (0.18), residues: 1998 helix: 0.40 (0.19), residues: 702 sheet: 0.97 (0.32), residues: 290 loop : -0.33 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 183 HIS 0.007 0.001 HIS A 218 PHE 0.018 0.002 PHE A 136 TYR 0.027 0.002 TYR D 236 ARG 0.006 0.001 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 2.109 Fit side-chains REVERT: A 236 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8660 (p90) REVERT: B 236 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.8670 (p90) REVERT: D 236 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.8659 (p90) REVERT: D 237 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7760 (mmtm) outliers start: 29 outliers final: 20 residues processed: 199 average time/residue: 1.5291 time to fit residues: 336.5912 Evaluate side-chains 199 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 237 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 159 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 287 ASN A 449 ASN B 287 ASN B 372 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 501 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16942 Z= 0.186 Angle : 0.612 8.704 23123 Z= 0.312 Chirality : 0.046 0.164 2334 Planarity : 0.005 0.048 3067 Dihedral : 8.518 101.714 2282 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.98 % Allowed : 12.61 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 1998 helix: 0.39 (0.19), residues: 706 sheet: 1.02 (0.32), residues: 290 loop : -0.28 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.006 0.001 HIS A 218 PHE 0.017 0.002 PHE A 136 TYR 0.027 0.002 TYR D 236 ARG 0.007 0.001 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 1.861 Fit side-chains REVERT: A 203 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.6933 (mtm180) REVERT: A 236 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.8655 (p90) REVERT: B 236 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.8644 (p90) REVERT: D 236 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8653 (p90) REVERT: D 237 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7740 (mmtm) outliers start: 32 outliers final: 23 residues processed: 201 average time/residue: 1.5237 time to fit residues: 338.1394 Evaluate side-chains 202 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 237 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 112 optimal weight: 0.4980 chunk 56 optimal weight: 0.1980 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 148 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 287 ASN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN B 18 GLN B 287 ASN B 372 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 501 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16942 Z= 0.162 Angle : 0.574 7.187 23123 Z= 0.292 Chirality : 0.045 0.163 2334 Planarity : 0.005 0.047 3067 Dihedral : 8.245 98.297 2282 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.98 % Allowed : 12.55 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.32 (0.18), residues: 1998 helix: 0.54 (0.20), residues: 694 sheet: 1.16 (0.32), residues: 290 loop : -0.22 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.005 0.001 HIS A 218 PHE 0.015 0.002 PHE B 136 TYR 0.024 0.002 TYR D 236 ARG 0.007 0.000 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 2.010 Fit side-chains REVERT: B 236 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.8671 (p90) REVERT: D 236 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.8594 (p90) REVERT: D 237 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7883 (mmtm) outliers start: 32 outliers final: 23 residues processed: 197 average time/residue: 1.4889 time to fit residues: 324.8042 Evaluate side-chains 196 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 287 ASN A 449 ASN B 18 GLN B 331 GLN B 372 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 501 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16942 Z= 0.180 Angle : 0.600 7.379 23123 Z= 0.305 Chirality : 0.046 0.163 2334 Planarity : 0.005 0.048 3067 Dihedral : 8.366 100.367 2282 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.98 % Allowed : 12.55 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.30 (0.18), residues: 1998 helix: 0.53 (0.20), residues: 694 sheet: 1.15 (0.32), residues: 290 loop : -0.23 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.006 0.001 HIS A 218 PHE 0.018 0.002 PHE A 136 TYR 0.027 0.002 TYR D 236 ARG 0.007 0.000 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 172 time to evaluate : 1.991 Fit side-chains REVERT: A 203 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.6941 (mtm180) REVERT: A 394 MET cc_start: 0.5969 (mpt) cc_final: 0.5657 (mpt) REVERT: B 236 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8587 (p90) REVERT: D 236 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8636 (p90) REVERT: D 237 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7744 (mmtm) outliers start: 32 outliers final: 26 residues processed: 197 average time/residue: 1.4884 time to fit residues: 324.7774 Evaluate side-chains 201 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.8980 chunk 186 optimal weight: 0.0870 chunk 113 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 287 ASN A 449 ASN B 372 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 16942 Z= 0.214 Angle : 0.787 59.168 23123 Z= 0.441 Chirality : 0.046 0.163 2334 Planarity : 0.005 0.048 3067 Dihedral : 8.388 100.376 2282 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.93 % Allowed : 12.61 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.30 (0.18), residues: 1998 helix: 0.53 (0.20), residues: 694 sheet: 1.15 (0.32), residues: 290 loop : -0.24 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.006 0.001 HIS A 218 PHE 0.017 0.002 PHE A 136 TYR 0.027 0.002 TYR D 236 ARG 0.005 0.000 ARG C 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 1.610 Fit side-chains REVERT: A 203 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.6941 (mtm180) REVERT: A 394 MET cc_start: 0.5904 (mpt) cc_final: 0.5682 (mpt) REVERT: B 236 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.8587 (p90) REVERT: D 236 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8637 (p90) REVERT: D 237 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7744 (mmtm) outliers start: 31 outliers final: 25 residues processed: 195 average time/residue: 1.4705 time to fit residues: 317.0485 Evaluate side-chains 200 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 287 ASN A 449 ASN B 372 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.118013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.103450 restraints weight = 34438.009| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.07 r_work: 0.2991 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 16942 Z= 0.214 Angle : 0.787 59.168 23123 Z= 0.441 Chirality : 0.046 0.163 2334 Planarity : 0.005 0.048 3067 Dihedral : 8.388 100.376 2282 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.87 % Allowed : 12.67 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.30 (0.18), residues: 1998 helix: 0.53 (0.20), residues: 694 sheet: 1.15 (0.32), residues: 290 loop : -0.24 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.006 0.001 HIS A 218 PHE 0.017 0.002 PHE A 136 TYR 0.027 0.002 TYR D 236 ARG 0.005 0.000 ARG C 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6208.58 seconds wall clock time: 110 minutes 48.39 seconds (6648.39 seconds total)