Starting phenix.real_space_refine on Sat Sep 28 01:48:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el9_28225/09_2024/8el9_28225.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el9_28225/09_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_28225/09_2024/8el9_28225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el9_28225/09_2024/8el9_28225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el9_28225/09_2024/8el9_28225.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el9_28225/09_2024/8el9_28225.cif" } 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. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 18.52, per 1000 atoms: 1.06 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 - 3.00 Amino acid : True - 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: 4.22 Conformation dependent library (CDL) restraints added in 3.7 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... Secondary structure from input PDB file: 76 helices and 8 sheets defined 39.0% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 54 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 97 through 101 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.674A pdb=" N GLN A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.543A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 348 through 366 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 369 through 373 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 471 through 486 Processing helix chain 'A' and resid 486 through 501 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 54 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 97 through 101 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.558A pdb=" N ILE B 205 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 257 removed outlier: 3.583A pdb=" N GLN B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 285 through 291 removed outlier: 3.751A pdb=" N GLU B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 366 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 369 through 373 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 471 through 486 Processing helix chain 'B' and resid 486 through 501 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 54 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 97 through 101 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 192 through 200 Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.593A pdb=" N ILE C 205 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.722A pdb=" N GLN C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 348 through 366 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 369 through 373 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 486 through 502 removed outlier: 3.546A pdb=" N ALA C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 54 through 65 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 160 through 169 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 192 through 200 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.549A pdb=" N ILE D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 257 removed outlier: 3.706A pdb=" N GLN D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 348 through 366 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 369 through 373 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 440 through 450 Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 486 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.567A pdb=" N ARG C 430 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 423 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.387A pdb=" N TRP A 277 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 315 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE A 279 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE A 82 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 removed outlier: 4.098A pdb=" N ILE A 423 " --> pdb=" O VAL D 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 44 removed outlier: 4.063A pdb=" N ILE D 423 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 343 through 345 removed outlier: 5.963A pdb=" N ILE B 281 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE B 82 " --> pdb=" O ASN B 319 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 423 through 424 removed outlier: 3.859A pdb=" N ILE C 423 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 345 removed outlier: 8.334A pdb=" N GLY C 214 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR C 238 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLY C 216 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N TYR C 236 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N HIS C 218 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE C 234 " --> pdb=" O HIS C 218 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE C 82 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 15.274A pdb=" N ASN C 142 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 14.411A pdb=" N LYS C 221 " --> pdb=" O ASN C 142 " (cutoff:3.500A) removed outlier: 13.452A pdb=" N ASP C 144 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 11.940A pdb=" N THR C 219 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 146 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N SER C 217 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 345 removed outlier: 6.448A pdb=" N TRP D 277 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS D 315 " --> pdb=" O TRP D 277 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE D 279 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE D 82 " --> pdb=" O ASN D 319 " (cutoff:3.500A) 663 hydrogen bonds defined for protein. 1847 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: 5.91 Time building geometry restraints manager: 4.92 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: 0.00 - 1.62: 22464 1.62 - 3.24: 505 3.24 - 4.86: 109 4.86 - 6.48: 41 6.48 - 8.10: 4 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: 1464 2.74 - 3.28: 17108 3.28 - 3.82: 35033 3.82 - 4.36: 44663 4.36 - 4.90: 67684 Nonbonded interactions: 165952 Sorted by model distance: nonbonded pdb=" O LYS A 273 " pdb=" O HOH A 701 " model vdw 2.197 3.040 nonbonded pdb=" O HOH D 747 " pdb=" O HOH D 872 " model vdw 2.223 3.040 nonbonded pdb=" O HOH B 715 " pdb=" O HOH B 737 " model vdw 2.229 3.040 nonbonded pdb=" O HOH C 765 " pdb=" O HOH C 876 " model vdw 2.234 3.040 nonbonded pdb=" O HOH D 713 " pdb=" O HOH D 779 " model vdw 2.245 3.040 ... (remaining 165947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 14.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 49.940 Find NCS groups from input model: 0.920 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.900 ------------------------------------------------------------------------------- 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= 0.196 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 : 1.877 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: 1.4421 time to fit residues: 318.2316 Evaluate side-chains 190 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.868 ------------------------------------------------------------------------------- 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: 0.7980 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 372 HIS A 449 ASN B 331 GLN B 372 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 102 HIS D 331 GLN D 372 HIS D 449 ASN D 501 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0729 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= 0.193 Angle : 0.624 7.109 23123 Z= 0.324 Chirality : 0.046 0.169 2334 Planarity : 0.005 0.050 3067 Dihedral : 8.808 102.855 2298 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.34 % Allowed : 13.08 % Favored : 85.58 % 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: 0.29 (0.18), residues: 1998 helix: 0.69 (0.20), residues: 714 sheet: 1.02 (0.32), residues: 294 loop : -0.36 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.006 0.001 HIS A 218 PHE 0.018 0.002 PHE A 136 TYR 0.028 0.002 TYR C 236 ARG 0.005 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 211 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 2.098 Fit side-chains REVERT: B 236 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8731 (p90) REVERT: B 252 ARG cc_start: 0.8600 (ttp80) cc_final: 0.8341 (ttp80) REVERT: B 499 LYS cc_start: 0.8005 (mtpm) cc_final: 0.7659 (mtpp) outliers start: 21 outliers final: 11 residues processed: 203 average time/residue: 1.3976 time to fit residues: 316.0792 Evaluate side-chains 181 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU 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 D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 176 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN D 501 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0825 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= 0.208 Angle : 0.638 7.344 23123 Z= 0.331 Chirality : 0.047 0.168 2334 Planarity : 0.005 0.051 3067 Dihedral : 8.680 102.708 2282 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.87 % Allowed : 12.38 % Favored : 85.76 % 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: 0.75 (0.20), residues: 714 sheet: 1.01 (0.32), residues: 294 loop : -0.36 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 183 HIS 0.007 0.001 HIS A 218 PHE 0.017 0.002 PHE A 136 TYR 0.028 0.002 TYR A 236 ARG 0.007 0.001 ARG C 252 *********************** 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 205 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 1.993 Fit side-chains REVERT: B 236 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.8775 (p90) REVERT: B 252 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8314 (ttp80) REVERT: C 236 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.8721 (p90) REVERT: D 236 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8688 (p90) outliers start: 30 outliers final: 17 residues processed: 195 average time/residue: 1.4036 time to fit residues: 305.3590 Evaluate side-chains 184 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR 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 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 44 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR 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 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 85 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 169 optimal weight: 0.1980 chunk 51 optimal weight: 7.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16942 Z= 0.157 Angle : 0.565 6.468 23123 Z= 0.291 Chirality : 0.044 0.161 2334 Planarity : 0.005 0.048 3067 Dihedral : 8.117 97.094 2282 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.63 % Allowed : 12.73 % Favored : 85.64 % 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: 0.54 (0.19), residues: 1998 helix: 0.84 (0.20), residues: 718 sheet: 1.22 (0.32), residues: 294 loop : -0.19 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 183 HIS 0.004 0.001 HIS A 218 PHE 0.015 0.001 PHE B 136 TYR 0.023 0.001 TYR C 236 ARG 0.006 0.000 ARG A 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 200 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 1.937 Fit side-chains REVERT: B 252 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8296 (ttp80) REVERT: C 476 LYS cc_start: 0.8108 (mmpt) cc_final: 0.7799 (mttt) REVERT: D 237 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7947 (mmtm) outliers start: 26 outliers final: 15 residues processed: 191 average time/residue: 1.4123 time to fit residues: 300.3199 Evaluate side-chains 179 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 146 VAL Chi-restraints excluded: chain B residue 238 THR 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 237 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 170 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0913 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= 0.176 Angle : 0.596 6.842 23123 Z= 0.307 Chirality : 0.045 0.162 2334 Planarity : 0.005 0.049 3067 Dihedral : 8.363 99.809 2281 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.98 % Allowed : 12.26 % Favored : 85.76 % 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: 0.51 (0.19), residues: 1998 helix: 0.82 (0.20), residues: 718 sheet: 1.18 (0.32), residues: 294 loop : -0.21 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 183 HIS 0.005 0.001 HIS A 218 PHE 0.017 0.002 PHE A 136 TYR 0.022 0.002 TYR C 236 ARG 0.006 0.001 ARG B 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 200 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 1.835 Fit side-chains REVERT: D 237 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7885 (mmtm) outliers start: 32 outliers final: 22 residues processed: 191 average time/residue: 1.4510 time to fit residues: 308.8170 Evaluate side-chains 182 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 146 VAL Chi-restraints excluded: chain B residue 167 SER 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 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 C residue 361 THR Chi-restraints excluded: chain C residue 422 SER 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 237 LYS Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0935 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= 0.176 Angle : 0.595 6.786 23123 Z= 0.307 Chirality : 0.045 0.161 2334 Planarity : 0.005 0.049 3067 Dihedral : 8.356 99.995 2281 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.98 % Allowed : 12.38 % Favored : 85.64 % 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: 0.50 (0.19), residues: 1998 helix: 0.82 (0.20), residues: 718 sheet: 1.14 (0.32), residues: 294 loop : -0.21 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 183 HIS 0.005 0.001 HIS A 218 PHE 0.016 0.002 PHE A 136 TYR 0.025 0.002 TYR C 236 ARG 0.008 0.001 ARG B 252 *********************** 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 195 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 2.123 Fit side-chains REVERT: A 203 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.6444 (mtm180) REVERT: D 237 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7882 (mmtm) outliers start: 32 outliers final: 22 residues processed: 187 average time/residue: 1.4154 time to fit residues: 294.1864 Evaluate side-chains 183 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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 203 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 167 SER 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 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 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0937 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= 0.178 Angle : 0.599 6.848 23123 Z= 0.309 Chirality : 0.046 0.162 2334 Planarity : 0.005 0.049 3067 Dihedral : 8.391 100.506 2281 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: 0.50 (0.19), residues: 1998 helix: 0.83 (0.20), residues: 718 sheet: 1.14 (0.32), residues: 294 loop : -0.21 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 183 HIS 0.006 0.001 HIS A 218 PHE 0.017 0.002 PHE A 136 TYR 0.025 0.002 TYR C 236 ARG 0.007 0.001 ARG A 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 195 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.938 Fit side-chains REVERT: A 203 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.6445 (mtm180) REVERT: D 237 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7889 (mmtm) outliers start: 32 outliers final: 22 residues processed: 187 average time/residue: 1.4151 time to fit residues: 294.5760 Evaluate side-chains 182 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.986 ------------------------------------------------------------------------------- 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 203 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 167 SER 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 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 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0942 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= 0.179 Angle : 0.600 6.844 23123 Z= 0.310 Chirality : 0.046 0.161 2334 Planarity : 0.005 0.050 3067 Dihedral : 8.391 100.655 2281 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.87 % Allowed : 12.38 % Favored : 85.76 % 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: 0.49 (0.19), residues: 1998 helix: 0.83 (0.20), residues: 718 sheet: 1.12 (0.32), residues: 294 loop : -0.22 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 183 HIS 0.005 0.001 HIS A 218 PHE 0.016 0.002 PHE A 136 TYR 0.025 0.002 TYR C 236 ARG 0.007 0.001 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 193 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 2.056 Fit side-chains REVERT: A 203 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.6442 (mtm180) REVERT: D 237 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7878 (mmtm) outliers start: 30 outliers final: 23 residues processed: 186 average time/residue: 1.4287 time to fit residues: 295.6148 Evaluate side-chains 183 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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 203 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 167 SER 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 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 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 237 LYS Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 0.2980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16942 Z= 0.186 Angle : 0.607 7.248 23123 Z= 0.313 Chirality : 0.046 0.162 2334 Planarity : 0.005 0.050 3067 Dihedral : 8.428 101.115 2281 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.69 % Allowed : 12.61 % Favored : 85.70 % 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: 0.48 (0.19), residues: 1998 helix: 0.82 (0.20), residues: 718 sheet: 1.11 (0.32), residues: 294 loop : -0.22 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 183 HIS 0.006 0.001 HIS A 218 PHE 0.017 0.002 PHE A 136 TYR 0.026 0.002 TYR C 236 ARG 0.007 0.001 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 190 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 1.927 Fit side-chains REVERT: A 203 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.6443 (mtm180) REVERT: A 499 LYS cc_start: 0.7867 (mtpm) cc_final: 0.7521 (mtpp) REVERT: D 237 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7861 (mmtm) outliers start: 27 outliers final: 21 residues processed: 182 average time/residue: 1.4850 time to fit residues: 299.6293 Evaluate side-chains 183 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 203 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 167 SER 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 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 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.7980 chunk 186 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 372 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN C 235 HIS ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16942 Z= 0.212 Angle : 0.642 7.632 23123 Z= 0.333 Chirality : 0.047 0.163 2334 Planarity : 0.005 0.051 3067 Dihedral : 8.627 102.677 2281 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.69 % Allowed : 12.55 % Favored : 85.76 % 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: 0.39 (0.18), residues: 1998 helix: 0.78 (0.20), residues: 718 sheet: 0.98 (0.32), residues: 294 loop : -0.29 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 183 HIS 0.007 0.001 HIS A 218 PHE 0.017 0.002 PHE A 136 TYR 0.027 0.002 TYR A 236 ARG 0.007 0.001 ARG A 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 194 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 2.090 Fit side-chains REVERT: A 203 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.6441 (mtm180) REVERT: A 499 LYS cc_start: 0.7933 (mtpm) cc_final: 0.7568 (mtpp) REVERT: D 237 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7748 (mmtm) outliers start: 27 outliers final: 20 residues processed: 187 average time/residue: 1.4415 time to fit residues: 302.3835 Evaluate side-chains 184 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 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 167 SER 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 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 422 SER Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 237 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 A 501 ASN B 372 HIS B 407 ASN B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.113861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.099062 restraints weight = 34762.778| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.08 r_work: 0.2928 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16942 Z= 0.324 Angle : 0.762 9.927 23123 Z= 0.399 Chirality : 0.052 0.171 2334 Planarity : 0.006 0.052 3067 Dihedral : 9.153 106.572 2281 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.17 % Allowed : 13.25 % Favored : 85.58 % 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: 0.04 (0.18), residues: 1998 helix: 0.58 (0.19), residues: 718 sheet: 0.60 (0.31), residues: 290 loop : -0.49 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 183 HIS 0.008 0.002 HIS C 63 PHE 0.020 0.004 PHE A 132 TYR 0.030 0.003 TYR C 236 ARG 0.007 0.001 ARG A 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5899.91 seconds wall clock time: 105 minutes 12.83 seconds (6312.83 seconds total)