Starting phenix.real_space_refine on Sat Mar 16 12:09:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6s_23706/03_2024/7m6s_23706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6s_23706/03_2024/7m6s_23706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6s_23706/03_2024/7m6s_23706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6s_23706/03_2024/7m6s_23706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6s_23706/03_2024/7m6s_23706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6s_23706/03_2024/7m6s_23706.pdb" } resolution = 3.61 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9510 2.51 5 N 2390 2.21 5 O 2625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 14625 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2906 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Chain: "B" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2906 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2906 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Chain: "D" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2906 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Chain: "E" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2906 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.73, per 1000 atoms: 0.53 Number of scatterers: 14625 At special positions: 0 Unit cell: (93.5, 92.4, 140.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2625 8.00 N 2390 7.00 C 9510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 176 " distance=2.06 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 176 " distance=2.06 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 176 " distance=2.06 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 176 " distance=2.06 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 176 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 62 " " NAG B 802 " - " ASN B 62 " " NAG C 802 " - " ASN C 62 " " NAG D 802 " - " ASN D 62 " " NAG E 802 " - " ASN E 62 " Time building additional restraints: 5.52 Conformation dependent library (CDL) restraints added in 2.7 seconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 25 sheets defined 41.3% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 removed outlier: 3.637A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 removed outlier: 4.417A pdb=" N SER A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 117' Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.554A pdb=" N LEU A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'A' and resid 272 through 295 Processing helix chain 'A' and resid 305 through 341 removed outlier: 3.877A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 440 removed outlier: 4.153A pdb=" N LYS A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 4.442A pdb=" N PHE A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 42 removed outlier: 3.637A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 4.417A pdb=" N SER B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 117' Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.553A pdb=" N LEU B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 272 through 295 Processing helix chain 'B' and resid 305 through 341 removed outlier: 3.877A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 323 " --> pdb=" O PHE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 440 removed outlier: 4.152A pdb=" N LYS B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 4.443A pdb=" N PHE B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 42 removed outlier: 3.637A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 removed outlier: 4.417A pdb=" N SER C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 117' Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.554A pdb=" N LEU C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 268 Processing helix chain 'C' and resid 272 through 295 Processing helix chain 'C' and resid 305 through 341 removed outlier: 3.877A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 323 " --> pdb=" O PHE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 440 removed outlier: 4.152A pdb=" N LYS C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 4.443A pdb=" N PHE C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 42 removed outlier: 3.637A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 117 removed outlier: 4.418A pdb=" N SER D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 112 through 117' Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.554A pdb=" N LEU D 248 " --> pdb=" O MET D 244 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 268 Processing helix chain 'D' and resid 272 through 295 Processing helix chain 'D' and resid 305 through 341 removed outlier: 3.876A pdb=" N LEU D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 323 " --> pdb=" O PHE D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 440 removed outlier: 4.152A pdb=" N LYS D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 4.442A pdb=" N PHE D 425 " --> pdb=" O VAL D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 42 removed outlier: 3.637A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 removed outlier: 4.417A pdb=" N SER E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 117' Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.554A pdb=" N LEU E 248 " --> pdb=" O MET E 244 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 268 Processing helix chain 'E' and resid 272 through 295 Processing helix chain 'E' and resid 305 through 341 removed outlier: 3.877A pdb=" N LEU E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU E 323 " --> pdb=" O PHE E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 440 removed outlier: 4.153A pdb=" N LYS E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL E 416 " --> pdb=" O THR E 412 " (cutoff:3.500A) Proline residue: E 419 - end of helix removed outlier: 4.441A pdb=" N PHE E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 109 removed outlier: 3.885A pdb=" N LEU A 142 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 132 removed outlier: 3.575A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 109 removed outlier: 3.885A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 132 removed outlier: 3.576A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AB1, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'C' and resid 106 through 109 removed outlier: 3.885A pdb=" N LEU C 142 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.575A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB6, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AB7, first strand: chain 'D' and resid 106 through 109 removed outlier: 3.885A pdb=" N LEU D 142 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.575A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC2, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AC3, first strand: chain 'E' and resid 106 through 109 removed outlier: 3.884A pdb=" N LEU E 142 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL E 61 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLU E 193 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.575A pdb=" N VAL E 159 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE E 132 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ARG E 155 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AC6, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AC7, first strand: chain 'E' and resid 224 through 225 900 hydrogen bonds defined for protein. 2640 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: 4.65 Time building geometry restraints manager: 6.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4516 1.35 - 1.47: 3901 1.47 - 1.60: 6388 1.60 - 1.73: 0 1.73 - 1.85: 170 Bond restraints: 14975 Sorted by residual: bond pdb=" C ALA D 273 " pdb=" N PRO D 274 " ideal model delta sigma weight residual 1.335 1.366 -0.030 1.36e-02 5.41e+03 4.95e+00 bond pdb=" C ALA C 273 " pdb=" N PRO C 274 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.36e-02 5.41e+03 4.85e+00 bond pdb=" C ALA A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.36e-02 5.41e+03 4.77e+00 bond pdb=" C ILE B 253 " pdb=" N PRO B 254 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.36e-02 5.41e+03 4.73e+00 bond pdb=" C ILE C 253 " pdb=" N PRO C 254 " ideal model delta sigma weight residual 1.335 1.365 -0.029 1.36e-02 5.41e+03 4.66e+00 ... (remaining 14970 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.36: 343 105.36 - 112.58: 7257 112.58 - 119.81: 5599 119.81 - 127.04: 6849 127.04 - 134.27: 237 Bond angle restraints: 20285 Sorted by residual: angle pdb=" N LEU B 190 " pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " ideal model delta sigma weight residual 110.49 118.63 -8.14 1.69e+00 3.50e-01 2.32e+01 angle pdb=" N LEU A 190 " pdb=" CA LEU A 190 " pdb=" CB LEU A 190 " ideal model delta sigma weight residual 110.49 118.63 -8.14 1.69e+00 3.50e-01 2.32e+01 angle pdb=" N LEU E 190 " pdb=" CA LEU E 190 " pdb=" CB LEU E 190 " ideal model delta sigma weight residual 110.49 118.60 -8.11 1.69e+00 3.50e-01 2.30e+01 angle pdb=" N LEU C 190 " pdb=" CA LEU C 190 " pdb=" CB LEU C 190 " ideal model delta sigma weight residual 110.49 118.59 -8.10 1.69e+00 3.50e-01 2.30e+01 angle pdb=" N LEU D 190 " pdb=" CA LEU D 190 " pdb=" CB LEU D 190 " ideal model delta sigma weight residual 110.49 118.59 -8.10 1.69e+00 3.50e-01 2.29e+01 ... (remaining 20280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.22: 8185 14.22 - 28.44: 584 28.44 - 42.67: 181 42.67 - 56.89: 65 56.89 - 71.11: 20 Dihedral angle restraints: 9035 sinusoidal: 3755 harmonic: 5280 Sorted by residual: dihedral pdb=" N LEU B 190 " pdb=" C LEU B 190 " pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " ideal model delta harmonic sigma weight residual 122.80 131.30 -8.50 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" N LEU A 190 " pdb=" C LEU A 190 " pdb=" CA LEU A 190 " pdb=" CB LEU A 190 " ideal model delta harmonic sigma weight residual 122.80 131.29 -8.49 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" N LEU D 190 " pdb=" C LEU D 190 " pdb=" CA LEU D 190 " pdb=" CB LEU D 190 " ideal model delta harmonic sigma weight residual 122.80 131.28 -8.48 0 2.50e+00 1.60e-01 1.15e+01 ... (remaining 9032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2105 0.145 - 0.291: 155 0.291 - 0.436: 20 0.436 - 0.581: 0 0.581 - 0.727: 5 Chirality restraints: 2285 Sorted by residual: chirality pdb=" CG LEU C 279 " pdb=" CB LEU C 279 " pdb=" CD1 LEU C 279 " pdb=" CD2 LEU C 279 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CG LEU E 279 " pdb=" CB LEU E 279 " pdb=" CD1 LEU E 279 " pdb=" CD2 LEU E 279 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CG LEU A 279 " pdb=" CB LEU A 279 " pdb=" CD1 LEU A 279 " pdb=" CD2 LEU A 279 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 2282 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 148 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C GLY C 148 " -0.075 2.00e-02 2.50e+03 pdb=" O GLY C 148 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN C 149 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 148 " -0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C GLY D 148 " 0.075 2.00e-02 2.50e+03 pdb=" O GLY D 148 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN D 149 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 148 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C GLY A 148 " -0.075 2.00e-02 2.50e+03 pdb=" O GLY A 148 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN A 149 " 0.026 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3217 2.80 - 3.32: 13425 3.32 - 3.85: 23906 3.85 - 4.37: 26093 4.37 - 4.90: 45628 Nonbonded interactions: 112269 Sorted by model distance: nonbonded pdb=" O SER A 291 " pdb=" OG SER A 294 " model vdw 2.269 2.440 nonbonded pdb=" O SER B 291 " pdb=" OG SER B 294 " model vdw 2.269 2.440 nonbonded pdb=" O SER D 291 " pdb=" OG SER D 294 " model vdw 2.269 2.440 nonbonded pdb=" O SER E 291 " pdb=" OG SER E 294 " model vdw 2.270 2.440 nonbonded pdb=" O SER C 291 " pdb=" OG SER C 294 " model vdw 2.270 2.440 ... (remaining 112264 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 32 through 440) selection = (chain 'B' and resid 32 through 440) selection = (chain 'C' and resid 32 through 440) selection = (chain 'D' and resid 32 through 440) selection = (chain 'E' and resid 32 through 440) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.570 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 39.310 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.070 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 0.008 0.065 14975 Z= 0.528 Angle : 1.487 15.404 20285 Z= 0.807 Chirality : 0.090 0.727 2285 Planarity : 0.009 0.054 2535 Dihedral : 12.299 71.110 5590 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.20), residues: 1765 helix: 2.88 (0.19), residues: 680 sheet: 1.88 (0.26), residues: 410 loop : -0.93 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 263 HIS 0.005 0.002 HIS B 239 PHE 0.037 0.005 PHE B 87 TYR 0.071 0.005 TYR A 152 ARG 0.013 0.002 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7849 (mmt) cc_final: 0.6873 (mmm) REVERT: A 266 PHE cc_start: 0.7702 (m-80) cc_final: 0.7252 (m-80) REVERT: A 290 GLN cc_start: 0.9027 (tt0) cc_final: 0.8813 (tm-30) REVERT: B 42 MET cc_start: 0.8294 (ptp) cc_final: 0.8075 (ttp) REVERT: B 266 PHE cc_start: 0.7857 (m-80) cc_final: 0.7397 (m-80) REVERT: C 80 MET cc_start: 0.8052 (mmt) cc_final: 0.7197 (mmm) REVERT: C 266 PHE cc_start: 0.7835 (m-80) cc_final: 0.7384 (m-80) REVERT: D 80 MET cc_start: 0.8044 (mmt) cc_final: 0.7559 (mmm) REVERT: D 266 PHE cc_start: 0.7728 (m-80) cc_final: 0.7328 (m-80) REVERT: D 314 CYS cc_start: 0.9323 (m) cc_final: 0.9047 (p) REVERT: E 266 PHE cc_start: 0.7833 (m-80) cc_final: 0.7409 (m-80) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.2099 time to fit residues: 95.9464 Evaluate side-chains 171 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14975 Z= 0.198 Angle : 0.723 11.944 20285 Z= 0.359 Chirality : 0.046 0.163 2285 Planarity : 0.004 0.038 2535 Dihedral : 4.330 18.350 2055 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.68 % Allowed : 15.84 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.19), residues: 1765 helix: 2.68 (0.18), residues: 680 sheet: 1.76 (0.25), residues: 420 loop : -1.38 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 267 HIS 0.002 0.001 HIS A 133 PHE 0.023 0.002 PHE C 422 TYR 0.022 0.002 TYR A 325 ARG 0.005 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8049 (mp10) cc_final: 0.7716 (mp10) REVERT: A 266 PHE cc_start: 0.7817 (m-80) cc_final: 0.7329 (m-80) REVERT: A 290 GLN cc_start: 0.9007 (tt0) cc_final: 0.8759 (tm-30) REVERT: B 266 PHE cc_start: 0.8012 (m-80) cc_final: 0.7682 (m-80) REVERT: C 109 LEU cc_start: 0.8601 (mt) cc_final: 0.8352 (mp) REVERT: C 266 PHE cc_start: 0.7740 (m-80) cc_final: 0.7309 (m-80) REVERT: D 109 LEU cc_start: 0.8634 (mt) cc_final: 0.8301 (mp) REVERT: D 266 PHE cc_start: 0.8088 (m-80) cc_final: 0.7710 (m-80) REVERT: D 267 TRP cc_start: 0.6454 (m100) cc_final: 0.6021 (m100) REVERT: E 109 LEU cc_start: 0.8846 (mt) cc_final: 0.8453 (mp) outliers start: 27 outliers final: 13 residues processed: 199 average time/residue: 0.2298 time to fit residues: 73.3997 Evaluate side-chains 164 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 174 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 157 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 127 optimal weight: 0.0670 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14975 Z= 0.211 Angle : 0.702 11.509 20285 Z= 0.340 Chirality : 0.044 0.165 2285 Planarity : 0.003 0.031 2535 Dihedral : 4.095 16.394 2055 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.48 % Allowed : 16.40 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.19), residues: 1765 helix: 2.59 (0.19), residues: 680 sheet: 1.82 (0.27), residues: 390 loop : -1.35 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 267 HIS 0.003 0.001 HIS D 225 PHE 0.016 0.001 PHE E 422 TYR 0.029 0.002 TYR E 325 ARG 0.006 0.000 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8139 (mp10) cc_final: 0.7771 (mp10) REVERT: A 164 MET cc_start: 0.7328 (ptt) cc_final: 0.7032 (ptp) REVERT: A 266 PHE cc_start: 0.7933 (m-80) cc_final: 0.7528 (m-80) REVERT: A 290 GLN cc_start: 0.9084 (tt0) cc_final: 0.8806 (tm-30) REVERT: B 266 PHE cc_start: 0.8017 (m-80) cc_final: 0.7648 (m-80) REVERT: C 109 LEU cc_start: 0.8655 (mt) cc_final: 0.8393 (mp) REVERT: C 266 PHE cc_start: 0.7782 (m-80) cc_final: 0.7345 (m-80) REVERT: D 90 GLN cc_start: 0.8617 (mp10) cc_final: 0.8333 (mp10) REVERT: D 109 LEU cc_start: 0.8604 (mt) cc_final: 0.8270 (mp) REVERT: D 266 PHE cc_start: 0.8112 (m-80) cc_final: 0.7769 (m-80) REVERT: D 267 TRP cc_start: 0.6442 (m100) cc_final: 0.6026 (m100) REVERT: D 314 CYS cc_start: 0.9372 (m) cc_final: 0.8963 (p) REVERT: E 102 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.6160 (t80) REVERT: E 267 TRP cc_start: 0.6499 (m100) cc_final: 0.6267 (m100) outliers start: 40 outliers final: 22 residues processed: 184 average time/residue: 0.2052 time to fit residues: 60.3411 Evaluate side-chains 170 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 261 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 159 optimal weight: 0.0270 chunk 169 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN B 210 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14975 Z= 0.188 Angle : 0.674 11.680 20285 Z= 0.324 Chirality : 0.044 0.255 2285 Planarity : 0.003 0.023 2535 Dihedral : 3.978 17.013 2055 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.05 % Allowed : 16.83 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.19), residues: 1765 helix: 2.52 (0.19), residues: 680 sheet: 1.62 (0.27), residues: 390 loop : -1.37 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 267 HIS 0.002 0.001 HIS D 225 PHE 0.038 0.001 PHE E 266 TYR 0.022 0.002 TYR D 325 ARG 0.009 0.000 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8255 (mp10) cc_final: 0.7874 (mp10) REVERT: A 266 PHE cc_start: 0.8044 (m-80) cc_final: 0.7649 (m-80) REVERT: A 290 GLN cc_start: 0.9076 (tt0) cc_final: 0.8873 (tm-30) REVERT: B 263 TRP cc_start: 0.7485 (m-10) cc_final: 0.7044 (m-10) REVERT: B 266 PHE cc_start: 0.8086 (m-80) cc_final: 0.7686 (m-80) REVERT: B 267 TRP cc_start: 0.6745 (m100) cc_final: 0.6486 (m100) REVERT: C 266 PHE cc_start: 0.7976 (m-80) cc_final: 0.7404 (m-80) REVERT: D 263 TRP cc_start: 0.7557 (m-10) cc_final: 0.6742 (m-10) REVERT: D 266 PHE cc_start: 0.8193 (m-80) cc_final: 0.7717 (m-80) REVERT: D 267 TRP cc_start: 0.6445 (m100) cc_final: 0.5956 (m100) REVERT: D 314 CYS cc_start: 0.9380 (m) cc_final: 0.8959 (p) REVERT: E 102 TYR cc_start: 0.6493 (OUTLIER) cc_final: 0.6085 (t80) REVERT: E 267 TRP cc_start: 0.6457 (m100) cc_final: 0.6053 (m100) outliers start: 33 outliers final: 25 residues processed: 178 average time/residue: 0.2281 time to fit residues: 65.0976 Evaluate side-chains 172 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 261 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.0970 chunk 96 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.0970 chunk 151 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 overall best weight: 1.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14975 Z= 0.175 Angle : 0.674 11.393 20285 Z= 0.320 Chirality : 0.044 0.198 2285 Planarity : 0.003 0.033 2535 Dihedral : 3.881 17.383 2055 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.30 % Allowed : 17.14 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 1765 helix: 2.57 (0.19), residues: 680 sheet: 1.46 (0.26), residues: 390 loop : -1.47 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 267 HIS 0.003 0.001 HIS E 225 PHE 0.045 0.001 PHE E 266 TYR 0.023 0.001 TYR A 325 ARG 0.002 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.7526 (m-10) cc_final: 0.6925 (m100) REVERT: A 266 PHE cc_start: 0.8080 (m-80) cc_final: 0.7671 (m-80) REVERT: B 263 TRP cc_start: 0.7465 (m-10) cc_final: 0.6800 (m-10) REVERT: B 266 PHE cc_start: 0.8122 (m-80) cc_final: 0.7636 (m-80) REVERT: B 267 TRP cc_start: 0.6692 (m100) cc_final: 0.6483 (m100) REVERT: B 322 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9227 (mm) REVERT: C 266 PHE cc_start: 0.7870 (m-80) cc_final: 0.7364 (m-80) REVERT: D 42 MET cc_start: 0.8382 (ttp) cc_final: 0.7802 (mtp) REVERT: D 263 TRP cc_start: 0.7586 (m-10) cc_final: 0.6753 (m-10) REVERT: D 266 PHE cc_start: 0.8283 (m-80) cc_final: 0.7774 (m-80) REVERT: D 267 TRP cc_start: 0.6473 (m100) cc_final: 0.6008 (m100) REVERT: D 287 MET cc_start: 0.8765 (ttm) cc_final: 0.8519 (ttm) REVERT: E 102 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.6089 (t80) REVERT: E 267 TRP cc_start: 0.6412 (m100) cc_final: 0.5974 (m100) outliers start: 37 outliers final: 22 residues processed: 173 average time/residue: 0.2117 time to fit residues: 58.4729 Evaluate side-chains 167 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14975 Z= 0.360 Angle : 0.762 11.835 20285 Z= 0.378 Chirality : 0.046 0.233 2285 Planarity : 0.004 0.032 2535 Dihedral : 4.447 20.111 2055 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.23 % Allowed : 18.32 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1765 helix: 1.97 (0.18), residues: 715 sheet: 1.01 (0.26), residues: 415 loop : -2.07 (0.19), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 267 HIS 0.004 0.001 HIS C 133 PHE 0.041 0.002 PHE C 422 TYR 0.015 0.002 TYR C 433 ARG 0.003 0.001 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 140 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 PHE cc_start: 0.8271 (m-80) cc_final: 0.7873 (m-80) REVERT: B 266 PHE cc_start: 0.8346 (m-80) cc_final: 0.7883 (m-80) REVERT: B 267 TRP cc_start: 0.6958 (m100) cc_final: 0.6607 (m100) REVERT: C 263 TRP cc_start: 0.7441 (m-10) cc_final: 0.7052 (m-10) REVERT: C 266 PHE cc_start: 0.8138 (m-80) cc_final: 0.7640 (m-80) REVERT: C 422 PHE cc_start: 0.9093 (t80) cc_final: 0.8883 (t80) REVERT: D 90 GLN cc_start: 0.8761 (mp10) cc_final: 0.8543 (mp10) REVERT: D 263 TRP cc_start: 0.7640 (m-10) cc_final: 0.6866 (m-10) REVERT: D 266 PHE cc_start: 0.8664 (m-80) cc_final: 0.8181 (m-80) REVERT: D 267 TRP cc_start: 0.6678 (m100) cc_final: 0.6328 (m100) REVERT: E 102 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.6358 (t80) REVERT: E 263 TRP cc_start: 0.7876 (m-10) cc_final: 0.7166 (m-10) REVERT: E 267 TRP cc_start: 0.6515 (m100) cc_final: 0.6251 (m100) REVERT: E 290 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8751 (tm-30) REVERT: E 322 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9436 (mm) outliers start: 52 outliers final: 31 residues processed: 182 average time/residue: 0.2090 time to fit residues: 61.0293 Evaluate side-chains 169 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 0.0270 chunk 94 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN C 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14975 Z= 0.171 Angle : 0.700 12.612 20285 Z= 0.332 Chirality : 0.044 0.204 2285 Planarity : 0.003 0.027 2535 Dihedral : 4.107 17.451 2055 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.49 % Allowed : 20.81 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 1765 helix: 2.27 (0.19), residues: 700 sheet: 0.93 (0.26), residues: 415 loop : -1.95 (0.19), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 267 HIS 0.002 0.001 HIS C 133 PHE 0.018 0.001 PHE B 319 TYR 0.014 0.001 TYR D 433 ARG 0.003 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8976 (mmm) cc_final: 0.8771 (mmm) REVERT: A 263 TRP cc_start: 0.7413 (m-10) cc_final: 0.6825 (m-10) REVERT: A 266 PHE cc_start: 0.8297 (m-80) cc_final: 0.7860 (m-80) REVERT: B 80 MET cc_start: 0.8343 (mmm) cc_final: 0.8115 (tpt) REVERT: B 263 TRP cc_start: 0.7486 (m-10) cc_final: 0.6546 (m100) REVERT: B 266 PHE cc_start: 0.8334 (m-80) cc_final: 0.7868 (m-80) REVERT: B 267 TRP cc_start: 0.6670 (m100) cc_final: 0.6387 (m100) REVERT: C 263 TRP cc_start: 0.7306 (m-10) cc_final: 0.7050 (m-10) REVERT: C 266 PHE cc_start: 0.8107 (m-80) cc_final: 0.7653 (m-80) REVERT: D 90 GLN cc_start: 0.8731 (mp10) cc_final: 0.8517 (mp10) REVERT: D 263 TRP cc_start: 0.7472 (m-10) cc_final: 0.6757 (m-10) REVERT: D 266 PHE cc_start: 0.8656 (m-80) cc_final: 0.8165 (m-80) REVERT: D 267 TRP cc_start: 0.6478 (m100) cc_final: 0.6117 (m100) REVERT: E 102 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.6434 (t80) REVERT: E 187 MET cc_start: 0.8873 (mmm) cc_final: 0.8638 (mmm) REVERT: E 263 TRP cc_start: 0.7740 (m-10) cc_final: 0.7120 (m-10) REVERT: E 267 TRP cc_start: 0.6175 (m100) cc_final: 0.5854 (m100) REVERT: E 290 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8703 (tm-30) REVERT: E 322 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9376 (mm) outliers start: 24 outliers final: 13 residues processed: 169 average time/residue: 0.2143 time to fit residues: 57.9572 Evaluate side-chains 156 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 0.0040 chunk 132 optimal weight: 2.9990 chunk 153 optimal weight: 0.0040 overall best weight: 0.8010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 ASN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14975 Z= 0.165 Angle : 0.706 13.223 20285 Z= 0.333 Chirality : 0.044 0.219 2285 Planarity : 0.003 0.030 2535 Dihedral : 3.948 16.947 2055 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.18 % Allowed : 22.11 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 1765 helix: 2.30 (0.19), residues: 700 sheet: 0.88 (0.26), residues: 415 loop : -1.89 (0.20), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 267 HIS 0.002 0.001 HIS C 133 PHE 0.040 0.001 PHE E 422 TYR 0.014 0.001 TYR D 433 ARG 0.002 0.000 ARG E 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.737 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.7831 (mmm) cc_final: 0.7613 (tpt) REVERT: A 263 TRP cc_start: 0.7306 (m-10) cc_final: 0.6889 (m-10) REVERT: A 266 PHE cc_start: 0.8341 (m-80) cc_final: 0.7898 (m-80) REVERT: B 263 TRP cc_start: 0.7507 (m-10) cc_final: 0.6499 (m100) REVERT: B 266 PHE cc_start: 0.8293 (m-80) cc_final: 0.7896 (m-80) REVERT: B 267 TRP cc_start: 0.6565 (m100) cc_final: 0.6310 (m100) REVERT: C 201 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: C 263 TRP cc_start: 0.7258 (m-10) cc_final: 0.7008 (m-10) REVERT: C 266 PHE cc_start: 0.8078 (m-80) cc_final: 0.7677 (m-80) REVERT: D 80 MET cc_start: 0.7676 (tpt) cc_final: 0.7057 (mmm) REVERT: D 187 MET cc_start: 0.8744 (mmm) cc_final: 0.8461 (mmm) REVERT: D 263 TRP cc_start: 0.7390 (m-10) cc_final: 0.6661 (m-10) REVERT: D 266 PHE cc_start: 0.8649 (m-80) cc_final: 0.8078 (m-80) REVERT: D 267 TRP cc_start: 0.6361 (m100) cc_final: 0.5996 (m100) REVERT: E 187 MET cc_start: 0.8908 (mmm) cc_final: 0.8705 (mmm) REVERT: E 263 TRP cc_start: 0.7679 (m-10) cc_final: 0.7116 (m-10) outliers start: 19 outliers final: 13 residues processed: 163 average time/residue: 0.2143 time to fit residues: 55.5640 Evaluate side-chains 154 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 142 optimal weight: 0.0270 chunk 148 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** D 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14975 Z= 0.168 Angle : 0.742 14.229 20285 Z= 0.344 Chirality : 0.045 0.380 2285 Planarity : 0.003 0.042 2535 Dihedral : 3.941 18.812 2055 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.93 % Allowed : 23.29 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 1765 helix: 2.24 (0.19), residues: 700 sheet: 0.82 (0.26), residues: 415 loop : -1.86 (0.20), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 267 HIS 0.002 0.001 HIS A 225 PHE 0.027 0.001 PHE C 422 TYR 0.025 0.001 TYR B 325 ARG 0.002 0.000 ARG D 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7794 (mmm) cc_final: 0.7581 (tpt) REVERT: A 263 TRP cc_start: 0.7302 (m-10) cc_final: 0.6904 (m-10) REVERT: A 266 PHE cc_start: 0.8364 (m-80) cc_final: 0.7938 (m-80) REVERT: B 187 MET cc_start: 0.8504 (mmm) cc_final: 0.8122 (mmm) REVERT: B 263 TRP cc_start: 0.7575 (m-10) cc_final: 0.6595 (m100) REVERT: B 266 PHE cc_start: 0.8268 (m-80) cc_final: 0.7832 (m-80) REVERT: B 267 TRP cc_start: 0.6456 (m100) cc_final: 0.6250 (m100) REVERT: C 187 MET cc_start: 0.8690 (mmm) cc_final: 0.8443 (mmm) REVERT: C 201 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: C 263 TRP cc_start: 0.7294 (m-10) cc_final: 0.7046 (m-10) REVERT: C 266 PHE cc_start: 0.8089 (m-80) cc_final: 0.7685 (m-80) REVERT: D 187 MET cc_start: 0.8869 (mmm) cc_final: 0.8467 (mmm) REVERT: D 263 TRP cc_start: 0.7239 (m-10) cc_final: 0.6511 (m-10) REVERT: D 266 PHE cc_start: 0.8672 (m-80) cc_final: 0.8175 (m-80) REVERT: D 267 TRP cc_start: 0.6250 (m100) cc_final: 0.5936 (m100) REVERT: E 187 MET cc_start: 0.8908 (mmm) cc_final: 0.8535 (mmm) REVERT: E 263 TRP cc_start: 0.7824 (m-10) cc_final: 0.7542 (m-10) outliers start: 15 outliers final: 12 residues processed: 161 average time/residue: 0.2168 time to fit residues: 55.6270 Evaluate side-chains 154 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 251 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 chunk 110 optimal weight: 2.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14975 Z= 0.197 Angle : 0.743 13.212 20285 Z= 0.350 Chirality : 0.045 0.249 2285 Planarity : 0.003 0.058 2535 Dihedral : 3.984 20.285 2055 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.99 % Allowed : 23.48 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 1765 helix: 2.24 (0.19), residues: 700 sheet: 0.73 (0.26), residues: 415 loop : -1.87 (0.20), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 267 HIS 0.002 0.001 HIS C 133 PHE 0.040 0.001 PHE B 422 TYR 0.022 0.001 TYR B 325 ARG 0.001 0.000 ARG A 400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8745 (mmm) cc_final: 0.8495 (mmm) REVERT: A 263 TRP cc_start: 0.7361 (m-10) cc_final: 0.6941 (m-10) REVERT: A 266 PHE cc_start: 0.8403 (m-80) cc_final: 0.7959 (m-80) REVERT: B 113 MET cc_start: 0.8966 (pmm) cc_final: 0.8717 (pmm) REVERT: B 187 MET cc_start: 0.8609 (mmm) cc_final: 0.8289 (mmm) REVERT: B 263 TRP cc_start: 0.7507 (m-10) cc_final: 0.6745 (m-10) REVERT: B 266 PHE cc_start: 0.8304 (m-80) cc_final: 0.7760 (m-80) REVERT: C 187 MET cc_start: 0.8744 (mmm) cc_final: 0.8502 (mmm) REVERT: C 263 TRP cc_start: 0.7247 (m-10) cc_final: 0.6922 (m-10) REVERT: C 266 PHE cc_start: 0.8131 (m-80) cc_final: 0.7729 (m-80) REVERT: D 187 MET cc_start: 0.8876 (mmm) cc_final: 0.8473 (mmm) REVERT: D 263 TRP cc_start: 0.7269 (m-10) cc_final: 0.6493 (m-10) REVERT: D 266 PHE cc_start: 0.8751 (m-80) cc_final: 0.8292 (m-80) REVERT: D 267 TRP cc_start: 0.6373 (m100) cc_final: 0.6045 (m100) REVERT: E 187 MET cc_start: 0.8939 (mmm) cc_final: 0.8587 (mmm) REVERT: E 263 TRP cc_start: 0.7784 (m-10) cc_final: 0.7325 (m-10) outliers start: 16 outliers final: 12 residues processed: 155 average time/residue: 0.2183 time to fit residues: 54.1635 Evaluate side-chains 151 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 251 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.057652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045335 restraints weight = 92832.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046575 restraints weight = 57115.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047425 restraints weight = 40976.989| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14975 Z= 0.262 Angle : 0.760 12.823 20285 Z= 0.362 Chirality : 0.045 0.275 2285 Planarity : 0.004 0.048 2535 Dihedral : 4.188 19.374 2055 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.18 % Allowed : 23.48 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1765 helix: 2.04 (0.19), residues: 720 sheet: 0.60 (0.25), residues: 415 loop : -2.10 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 267 HIS 0.003 0.001 HIS C 133 PHE 0.027 0.001 PHE C 422 TYR 0.022 0.002 TYR B 325 ARG 0.003 0.000 ARG B 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2521.59 seconds wall clock time: 46 minutes 49.00 seconds (2809.00 seconds total)