Starting phenix.real_space_refine on Mon Apr 8 20:37:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/04_2024/8a3b_15110.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/04_2024/8a3b_15110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/04_2024/8a3b_15110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/04_2024/8a3b_15110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/04_2024/8a3b_15110.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/04_2024/8a3b_15110.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 84 5.16 5 C 9646 2.51 5 N 2219 2.21 5 O 2499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "G GLU 335": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14448 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "B" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "C" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "D" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "E" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "F" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "G" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Time building chain proxies: 7.13, per 1000 atoms: 0.49 Number of scatterers: 14448 At special positions: 0 Unit cell: (106.869, 105.778, 109.05, 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 84 16.00 O 2499 8.00 N 2219 7.00 C 9646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.59 Conformation dependent library (CDL) restraints added in 2.6 seconds 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3500 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 7 sheets defined 79.1% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 99 through 108 removed outlier: 4.059A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 130 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.971A pdb=" N LEU A 252 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 295 Proline residue: A 288 - end of helix removed outlier: 3.616A pdb=" N PHE A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.507A pdb=" N LEU A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 349 Processing helix chain 'B' and resid 32 through 61 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 99 through 108 removed outlier: 4.030A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 108 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 131 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 206 through 236 Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.926A pdb=" N LEU B 252 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 254 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 295 Proline residue: B 288 - end of helix removed outlier: 3.609A pdb=" N PHE B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.698A pdb=" N LEU B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 349 removed outlier: 3.528A pdb=" N LYS B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 61 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 99 through 108 removed outlier: 4.104A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 108 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 131 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 146 Processing helix chain 'C' and resid 196 through 205 removed outlier: 3.546A pdb=" N ASN C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 236 removed outlier: 3.534A pdb=" N LYS C 211 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 249 through 255 removed outlier: 3.530A pdb=" N LEU C 252 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN C 254 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 295 removed outlier: 3.552A pdb=" N LEU C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.573A pdb=" N PHE C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.660A pdb=" N LEU C 329 " --> pdb=" O ASN C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 349 removed outlier: 3.602A pdb=" N LYS C 345 " --> pdb=" O LEU C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 61 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 99 through 108 removed outlier: 4.111A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE D 108 " --> pdb=" O TRP D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 131 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 147 Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 206 through 236 removed outlier: 3.745A pdb=" N LYS D 211 " --> pdb=" O HIS D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 249 through 255 removed outlier: 4.029A pdb=" N LEU D 252 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN D 254 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 295 removed outlier: 3.666A pdb=" N LEU D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) Proline residue: D 288 - end of helix removed outlier: 3.647A pdb=" N PHE D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 removed outlier: 3.829A pdb=" N GLN D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 removed outlier: 3.896A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 349 Processing helix chain 'E' and resid 32 through 61 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 99 through 131 removed outlier: 4.082A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE E 108 " --> pdb=" O TRP E 104 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 146 Processing helix chain 'E' and resid 196 through 204 Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 237 through 240 Processing helix chain 'E' and resid 249 through 255 removed outlier: 3.924A pdb=" N LEU E 252 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN E 254 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 295 removed outlier: 3.654A pdb=" N LEU E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Proline residue: E 288 - end of helix removed outlier: 3.571A pdb=" N PHE E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 Processing helix chain 'E' and resid 325 through 338 removed outlier: 3.727A pdb=" N LEU E 329 " --> pdb=" O ASN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 349 removed outlier: 3.543A pdb=" N LYS E 345 " --> pdb=" O LEU E 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 61 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 99 through 108 removed outlier: 4.310A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE F 108 " --> pdb=" O TRP F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 146 Proline residue: F 123 - end of helix removed outlier: 4.234A pdb=" N ALA F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Proline residue: F 133 - end of helix Processing helix chain 'F' and resid 196 through 205 Processing helix chain 'F' and resid 206 through 236 removed outlier: 3.567A pdb=" N MET F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 240 Processing helix chain 'F' and resid 249 through 255 removed outlier: 3.843A pdb=" N LEU F 252 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN F 254 " --> pdb=" O VAL F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 295 removed outlier: 3.635A pdb=" N LEU F 274 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Proline residue: F 288 - end of helix removed outlier: 3.633A pdb=" N PHE F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 300 Processing helix chain 'F' and resid 325 through 338 removed outlier: 3.539A pdb=" N LEU F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 349 Processing helix chain 'G' and resid 32 through 61 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 99 through 108 removed outlier: 3.980A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE G 108 " --> pdb=" O TRP G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 131 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 146 Processing helix chain 'G' and resid 196 through 205 Processing helix chain 'G' and resid 206 through 236 removed outlier: 3.612A pdb=" N MET G 210 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 240 Processing helix chain 'G' and resid 249 through 253 removed outlier: 3.965A pdb=" N LEU G 252 " --> pdb=" O SER G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 295 removed outlier: 3.539A pdb=" N LEU G 274 " --> pdb=" O GLY G 270 " (cutoff:3.500A) Proline residue: G 288 - end of helix removed outlier: 3.520A pdb=" N PHE G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE G 295 " --> pdb=" O VAL G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 300 removed outlier: 3.767A pdb=" N GLN G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.531A pdb=" N LEU G 329 " --> pdb=" O ASN G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 349 removed outlier: 3.632A pdb=" N LYS G 345 " --> pdb=" O LEU G 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.332A pdb=" N GLN A 263 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 67 removed outlier: 4.320A pdb=" N GLN B 263 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 67 removed outlier: 4.343A pdb=" N GLN E 263 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.476A pdb=" N GLN G 263 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2892 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: 4.44 Time building geometry restraints manager: 6.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4221 1.34 - 1.46: 3513 1.46 - 1.58: 6952 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 14791 Sorted by residual: bond pdb=" N HIS G 134 " pdb=" CA HIS G 134 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.28e-02 6.10e+03 5.55e+00 bond pdb=" N LEU C 28 " pdb=" CA LEU C 28 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.34e+00 bond pdb=" N LEU A 28 " pdb=" CA LEU A 28 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N LEU B 28 " pdb=" CA LEU B 28 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N LEU G 28 " pdb=" CA LEU G 28 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 ... (remaining 14786 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.18: 339 107.18 - 113.91: 8562 113.91 - 120.64: 6486 120.64 - 127.38: 4520 127.38 - 134.11: 141 Bond angle restraints: 20048 Sorted by residual: angle pdb=" C ILE E 287 " pdb=" CA ILE E 287 " pdb=" CB ILE E 287 " ideal model delta sigma weight residual 113.70 110.12 3.58 9.50e-01 1.11e+00 1.42e+01 angle pdb=" C PHE B 295 " pdb=" N ILE B 296 " pdb=" CA ILE B 296 " ideal model delta sigma weight residual 120.24 122.45 -2.21 6.30e-01 2.52e+00 1.23e+01 angle pdb=" C PHE D 295 " pdb=" N ILE D 296 " pdb=" CA ILE D 296 " ideal model delta sigma weight residual 120.24 122.36 -2.12 6.30e-01 2.52e+00 1.14e+01 angle pdb=" N LYS G 148 " pdb=" CA LYS G 148 " pdb=" C LYS G 148 " ideal model delta sigma weight residual 113.43 109.36 4.07 1.26e+00 6.30e-01 1.04e+01 angle pdb=" N ALA A 131 " pdb=" CA ALA A 131 " pdb=" CB ALA A 131 " ideal model delta sigma weight residual 114.17 110.52 3.65 1.14e+00 7.69e-01 1.03e+01 ... (remaining 20043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 7899 16.40 - 32.79: 671 32.79 - 49.19: 154 49.19 - 65.59: 51 65.59 - 81.99: 24 Dihedral angle restraints: 8799 sinusoidal: 3437 harmonic: 5362 Sorted by residual: dihedral pdb=" CA GLU C 145 " pdb=" C GLU C 145 " pdb=" N LEU C 146 " pdb=" CA LEU C 146 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLU E 145 " pdb=" C GLU E 145 " pdb=" N LEU E 146 " pdb=" CA LEU E 146 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLU F 145 " pdb=" C GLU F 145 " pdb=" N LEU F 146 " pdb=" CA LEU F 146 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 8796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1693 0.029 - 0.058: 427 0.058 - 0.087: 185 0.087 - 0.117: 58 0.117 - 0.146: 10 Chirality restraints: 2373 Sorted by residual: chirality pdb=" CA ILE C 258 " pdb=" N ILE C 258 " pdb=" C ILE C 258 " pdb=" CB ILE C 258 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA LEU F 28 " pdb=" N LEU F 28 " pdb=" C LEU F 28 " pdb=" CB LEU F 28 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE A 258 " pdb=" N ILE A 258 " pdb=" C ILE A 258 " pdb=" CB ILE A 258 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 2370 not shown) Planarity restraints: 2394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 74 " 0.003 2.00e-02 2.50e+03 8.20e-03 1.68e+00 pdb=" CG TRP A 74 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 74 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 74 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 74 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 74 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 74 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 74 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 74 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 74 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 128 " -0.104 9.50e-02 1.11e+02 4.70e-02 1.58e+00 pdb=" NE ARG A 128 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 128 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 128 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 128 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 333 " 0.009 2.00e-02 2.50e+03 9.07e-03 1.44e+00 pdb=" CG PHE B 333 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 333 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 333 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 333 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 333 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 333 " 0.001 2.00e-02 2.50e+03 ... (remaining 2391 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 120 2.65 - 3.21: 13993 3.21 - 3.78: 22510 3.78 - 4.34: 30452 4.34 - 4.90: 51494 Nonbonded interactions: 118569 Sorted by model distance: nonbonded pdb=" OD1 ASP G 147 " pdb=" OG SER G 343 " model vdw 2.091 2.440 nonbonded pdb=" OD1 ASP B 147 " pdb=" OG SER B 343 " model vdw 2.129 2.440 nonbonded pdb=" O TYR F 232 " pdb=" OG SER F 235 " model vdw 2.195 2.440 nonbonded pdb=" O TYR G 232 " pdb=" OG SER G 235 " model vdw 2.258 2.440 nonbonded pdb=" O TYR E 232 " pdb=" OG SER E 235 " model vdw 2.259 2.440 ... (remaining 118564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.920 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: 4.100 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 38.370 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14791 Z= 0.166 Angle : 0.546 6.661 20048 Z= 0.333 Chirality : 0.034 0.146 2373 Planarity : 0.003 0.047 2394 Dihedral : 14.171 81.986 5299 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.20), residues: 1750 helix: 2.26 (0.14), residues: 1288 sheet: None (None), residues: 0 loop : -0.87 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 74 HIS 0.004 0.001 HIS G 134 PHE 0.020 0.001 PHE B 333 TYR 0.011 0.001 TYR B 111 ARG 0.008 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8616 (tp) cc_final: 0.8160 (tp) REVERT: A 50 ILE cc_start: 0.8141 (mt) cc_final: 0.7926 (tt) REVERT: A 51 SER cc_start: 0.7780 (m) cc_final: 0.7529 (p) REVERT: A 65 SER cc_start: 0.8337 (p) cc_final: 0.8082 (m) REVERT: A 83 TYR cc_start: 0.7661 (t80) cc_final: 0.7449 (t80) REVERT: A 118 ILE cc_start: 0.8312 (mm) cc_final: 0.8095 (mm) REVERT: A 233 TYR cc_start: 0.8254 (t80) cc_final: 0.7817 (t80) REVERT: B 36 LYS cc_start: 0.8330 (tppt) cc_final: 0.7907 (tppt) REVERT: B 48 LEU cc_start: 0.8583 (tp) cc_final: 0.8216 (tp) REVERT: B 203 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7525 (ttpt) REVERT: B 224 LEU cc_start: 0.8201 (tp) cc_final: 0.7893 (tp) REVERT: B 234 PHE cc_start: 0.8579 (t80) cc_final: 0.8290 (t80) REVERT: B 349 VAL cc_start: 0.6444 (t) cc_final: 0.6108 (m) REVERT: C 36 LYS cc_start: 0.8430 (tmtt) cc_final: 0.7844 (tmtt) REVERT: C 48 LEU cc_start: 0.8599 (tp) cc_final: 0.8226 (tp) REVERT: C 51 SER cc_start: 0.8097 (m) cc_final: 0.7852 (p) REVERT: C 198 TYR cc_start: 0.7460 (t80) cc_final: 0.7227 (t80) REVERT: C 221 VAL cc_start: 0.8457 (t) cc_final: 0.8121 (p) REVERT: C 234 PHE cc_start: 0.8524 (t80) cc_final: 0.8213 (t80) REVERT: D 36 LYS cc_start: 0.8370 (tmtt) cc_final: 0.7783 (tmtt) REVERT: D 37 MET cc_start: 0.6877 (tpt) cc_final: 0.6580 (tpt) REVERT: D 89 GLN cc_start: 0.7760 (mt0) cc_final: 0.7126 (mt0) REVERT: D 104 TRP cc_start: 0.6781 (t-100) cc_final: 0.6504 (t-100) REVERT: D 203 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7732 (tmmt) REVERT: D 221 VAL cc_start: 0.8207 (t) cc_final: 0.7975 (t) REVERT: E 51 SER cc_start: 0.7832 (m) cc_final: 0.7621 (p) REVERT: E 108 PHE cc_start: 0.8324 (m-80) cc_final: 0.7947 (m-80) REVERT: E 148 LYS cc_start: 0.6983 (mtpt) cc_final: 0.6747 (mtmt) REVERT: E 203 LYS cc_start: 0.8023 (tmmt) cc_final: 0.7809 (tmmt) REVERT: E 232 TYR cc_start: 0.7707 (t80) cc_final: 0.7357 (t80) REVERT: F 36 LYS cc_start: 0.8411 (tmtt) cc_final: 0.8076 (tmtt) REVERT: G 47 LEU cc_start: 0.8431 (mt) cc_final: 0.8159 (mp) REVERT: G 48 LEU cc_start: 0.8575 (tp) cc_final: 0.8055 (tp) REVERT: G 50 ILE cc_start: 0.8137 (mt) cc_final: 0.7876 (tt) REVERT: G 202 LYS cc_start: 0.7365 (mmtt) cc_final: 0.7109 (mmtt) REVERT: G 203 LYS cc_start: 0.7711 (tttt) cc_final: 0.7490 (tttt) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.2801 time to fit residues: 180.9863 Evaluate side-chains 377 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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: 3.9990 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN D 63 GLN D 134 HIS E 63 GLN E 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14791 Z= 0.245 Angle : 0.537 6.660 20048 Z= 0.274 Chirality : 0.039 0.215 2373 Planarity : 0.004 0.037 2394 Dihedral : 3.785 19.752 1904 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.58 % Allowed : 10.15 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.20), residues: 1750 helix: 2.19 (0.14), residues: 1309 sheet: None (None), residues: 0 loop : -0.54 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 74 HIS 0.005 0.001 HIS B 207 PHE 0.015 0.001 PHE A 54 TYR 0.016 0.001 TYR C 121 ARG 0.003 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 399 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8590 (tp) cc_final: 0.8164 (tp) REVERT: A 50 ILE cc_start: 0.8093 (mt) cc_final: 0.7878 (tt) REVERT: A 228 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8080 (mt) REVERT: A 231 SER cc_start: 0.8110 (t) cc_final: 0.7820 (p) REVERT: A 233 TYR cc_start: 0.8129 (t80) cc_final: 0.7782 (t80) REVERT: B 36 LYS cc_start: 0.8377 (tppt) cc_final: 0.7963 (tppt) REVERT: B 130 SER cc_start: 0.8003 (t) cc_final: 0.7752 (p) REVERT: B 224 LEU cc_start: 0.8138 (tp) cc_final: 0.7887 (tp) REVERT: B 349 VAL cc_start: 0.6660 (t) cc_final: 0.6265 (m) REVERT: C 36 LYS cc_start: 0.8448 (tmtt) cc_final: 0.7819 (tmtt) REVERT: C 48 LEU cc_start: 0.8585 (tp) cc_final: 0.8276 (tp) REVERT: C 65 SER cc_start: 0.8022 (p) cc_final: 0.7790 (m) REVERT: C 115 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8045 (tt) REVERT: C 234 PHE cc_start: 0.8332 (t80) cc_final: 0.7987 (t80) REVERT: D 36 LYS cc_start: 0.8327 (tmtt) cc_final: 0.7742 (tmtt) REVERT: D 37 MET cc_start: 0.6934 (tpt) cc_final: 0.6612 (tpt) REVERT: D 203 LYS cc_start: 0.8276 (tmmt) cc_final: 0.7776 (tmmt) REVERT: D 229 TYR cc_start: 0.7926 (t80) cc_final: 0.7681 (t80) REVERT: E 36 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8053 (tmtt) REVERT: E 50 ILE cc_start: 0.7805 (mt) cc_final: 0.7553 (tt) REVERT: E 51 SER cc_start: 0.7773 (m) cc_final: 0.7569 (p) REVERT: E 203 LYS cc_start: 0.7983 (tmmt) cc_final: 0.7767 (tmmt) REVERT: E 221 VAL cc_start: 0.8307 (t) cc_final: 0.8078 (t) REVERT: E 228 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7977 (mt) REVERT: E 293 THR cc_start: 0.8419 (m) cc_final: 0.8031 (m) REVERT: E 336 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6727 (tm-30) REVERT: F 36 LYS cc_start: 0.8369 (tmtt) cc_final: 0.8015 (tmtt) REVERT: F 115 LEU cc_start: 0.8306 (tp) cc_final: 0.8092 (tt) REVERT: G 50 ILE cc_start: 0.8123 (mt) cc_final: 0.7891 (tt) REVERT: G 115 LEU cc_start: 0.8151 (tp) cc_final: 0.7939 (tt) REVERT: G 122 LEU cc_start: 0.8031 (mt) cc_final: 0.7752 (mp) outliers start: 26 outliers final: 11 residues processed: 410 average time/residue: 0.2801 time to fit residues: 165.8981 Evaluate side-chains 397 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 382 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 261 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 0.0570 chunk 141 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN C 90 GLN C 337 ASN D 134 HIS ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS F 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14791 Z= 0.208 Angle : 0.505 6.573 20048 Z= 0.255 Chirality : 0.039 0.236 2373 Planarity : 0.003 0.034 2394 Dihedral : 3.762 19.847 1904 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.95 % Allowed : 12.22 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.20), residues: 1750 helix: 2.18 (0.14), residues: 1302 sheet: 3.64 (0.68), residues: 42 loop : -0.32 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 85 HIS 0.003 0.001 HIS G 207 PHE 0.014 0.001 PHE F 243 TYR 0.023 0.001 TYR C 121 ARG 0.003 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 389 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8078 (mt) cc_final: 0.7873 (tt) REVERT: A 115 LEU cc_start: 0.8200 (tp) cc_final: 0.7957 (tt) REVERT: A 228 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7996 (mt) REVERT: A 231 SER cc_start: 0.8132 (t) cc_final: 0.7843 (p) REVERT: A 233 TYR cc_start: 0.8140 (t80) cc_final: 0.7867 (t80) REVERT: B 36 LYS cc_start: 0.8378 (tppt) cc_final: 0.7948 (tppt) REVERT: B 130 SER cc_start: 0.7955 (t) cc_final: 0.7742 (p) REVERT: B 224 LEU cc_start: 0.8142 (tp) cc_final: 0.7934 (tp) REVERT: B 349 VAL cc_start: 0.6801 (t) cc_final: 0.6365 (m) REVERT: C 65 SER cc_start: 0.8019 (p) cc_final: 0.7809 (m) REVERT: C 115 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8025 (tt) REVERT: C 198 TYR cc_start: 0.7446 (t80) cc_final: 0.7223 (t80) REVERT: C 234 PHE cc_start: 0.8300 (t80) cc_final: 0.7957 (t80) REVERT: D 36 LYS cc_start: 0.8301 (tmtt) cc_final: 0.7743 (tmtt) REVERT: D 37 MET cc_start: 0.6912 (tpt) cc_final: 0.6615 (tpt) REVERT: D 203 LYS cc_start: 0.8267 (tmmt) cc_final: 0.7772 (tmmt) REVERT: E 36 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8082 (tmtt) REVERT: E 50 ILE cc_start: 0.7775 (mt) cc_final: 0.7559 (tt) REVERT: E 108 PHE cc_start: 0.8002 (m-80) cc_final: 0.7720 (m-80) REVERT: E 115 LEU cc_start: 0.8302 (tp) cc_final: 0.8022 (tt) REVERT: E 203 LYS cc_start: 0.7955 (tmmt) cc_final: 0.7662 (tmmt) REVERT: E 221 VAL cc_start: 0.8285 (t) cc_final: 0.8082 (t) REVERT: E 293 THR cc_start: 0.8282 (m) cc_final: 0.7948 (m) REVERT: E 336 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6790 (tm-30) REVERT: F 36 LYS cc_start: 0.8367 (tmtt) cc_final: 0.7963 (tmtt) REVERT: F 83 TYR cc_start: 0.7626 (t80) cc_final: 0.7410 (t80) REVERT: G 50 ILE cc_start: 0.8063 (mt) cc_final: 0.7844 (tt) REVERT: G 115 LEU cc_start: 0.8111 (tp) cc_final: 0.7889 (tt) outliers start: 32 outliers final: 14 residues processed: 398 average time/residue: 0.2955 time to fit residues: 171.9766 Evaluate side-chains 400 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 383 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 159 optimal weight: 0.0970 chunk 169 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 151 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN C 337 ASN E 63 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 263 GLN F 337 ASN G 134 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14791 Z= 0.163 Angle : 0.491 7.030 20048 Z= 0.247 Chirality : 0.037 0.202 2373 Planarity : 0.003 0.029 2394 Dihedral : 3.653 19.413 1904 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.19 % Allowed : 13.43 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.20), residues: 1750 helix: 2.22 (0.14), residues: 1302 sheet: 3.58 (0.64), residues: 42 loop : -0.23 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 104 HIS 0.008 0.001 HIS E 207 PHE 0.018 0.001 PHE F 108 TYR 0.023 0.001 TYR B 121 ARG 0.003 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 385 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8058 (mt) cc_final: 0.7854 (tt) REVERT: A 115 LEU cc_start: 0.8189 (tp) cc_final: 0.7901 (tt) REVERT: A 228 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7991 (mt) REVERT: A 231 SER cc_start: 0.8148 (t) cc_final: 0.7866 (m) REVERT: A 233 TYR cc_start: 0.8064 (t80) cc_final: 0.7780 (t80) REVERT: A 274 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7385 (mp) REVERT: B 36 LYS cc_start: 0.8370 (tppt) cc_final: 0.7945 (tppt) REVERT: B 52 LEU cc_start: 0.8666 (mm) cc_final: 0.8416 (mp) REVERT: B 224 LEU cc_start: 0.8132 (tp) cc_final: 0.7919 (tp) REVERT: B 228 ILE cc_start: 0.8303 (tp) cc_final: 0.8031 (tp) REVERT: B 349 VAL cc_start: 0.6888 (t) cc_final: 0.6440 (m) REVERT: C 198 TYR cc_start: 0.7399 (t80) cc_final: 0.7167 (t80) REVERT: C 234 PHE cc_start: 0.8238 (t80) cc_final: 0.7945 (t80) REVERT: D 36 LYS cc_start: 0.8314 (tmtt) cc_final: 0.7760 (tmtt) REVERT: D 37 MET cc_start: 0.6889 (tpt) cc_final: 0.6605 (tpt) REVERT: D 203 LYS cc_start: 0.8158 (tmmt) cc_final: 0.7754 (tmmt) REVERT: E 36 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8087 (tmtt) REVERT: E 108 PHE cc_start: 0.7979 (m-80) cc_final: 0.7522 (m-80) REVERT: E 115 LEU cc_start: 0.8280 (tp) cc_final: 0.7985 (tt) REVERT: E 203 LYS cc_start: 0.7946 (tmmt) cc_final: 0.7655 (ttpp) REVERT: E 221 VAL cc_start: 0.8255 (t) cc_final: 0.8040 (t) REVERT: E 234 PHE cc_start: 0.8236 (t80) cc_final: 0.8031 (t80) REVERT: F 36 LYS cc_start: 0.8364 (tmtt) cc_final: 0.7977 (tmtt) REVERT: F 83 TYR cc_start: 0.7636 (t80) cc_final: 0.7389 (t80) REVERT: F 271 ILE cc_start: 0.8413 (mm) cc_final: 0.8007 (tp) REVERT: G 50 ILE cc_start: 0.8028 (mt) cc_final: 0.7805 (tt) REVERT: G 115 LEU cc_start: 0.8114 (tp) cc_final: 0.7876 (tt) REVERT: G 122 LEU cc_start: 0.8033 (mt) cc_final: 0.7733 (mp) outliers start: 36 outliers final: 14 residues processed: 399 average time/residue: 0.2715 time to fit residues: 156.8340 Evaluate side-chains 403 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 386 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 0.0970 chunk 69 optimal weight: 0.8980 chunk 144 optimal weight: 0.0570 chunk 116 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14791 Z= 0.157 Angle : 0.488 8.136 20048 Z= 0.242 Chirality : 0.037 0.202 2373 Planarity : 0.003 0.036 2394 Dihedral : 3.599 18.646 1904 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.95 % Allowed : 14.77 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.20), residues: 1750 helix: 2.29 (0.14), residues: 1295 sheet: 3.68 (0.63), residues: 42 loop : -0.32 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 104 HIS 0.005 0.001 HIS F 207 PHE 0.016 0.001 PHE F 108 TYR 0.022 0.001 TYR B 121 ARG 0.002 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 386 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8051 (mt) cc_final: 0.7839 (tt) REVERT: A 115 LEU cc_start: 0.8185 (tp) cc_final: 0.7916 (tt) REVERT: A 228 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7995 (mt) REVERT: A 231 SER cc_start: 0.8129 (t) cc_final: 0.7865 (m) REVERT: A 233 TYR cc_start: 0.8052 (t80) cc_final: 0.7799 (t80) REVERT: A 274 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7346 (mp) REVERT: B 36 LYS cc_start: 0.8407 (tppt) cc_final: 0.7969 (tppt) REVERT: B 224 LEU cc_start: 0.8126 (tp) cc_final: 0.7910 (tp) REVERT: B 228 ILE cc_start: 0.8303 (tp) cc_final: 0.8026 (tp) REVERT: B 349 VAL cc_start: 0.6902 (t) cc_final: 0.6462 (m) REVERT: C 198 TYR cc_start: 0.7367 (t80) cc_final: 0.7120 (t80) REVERT: C 234 PHE cc_start: 0.8229 (t80) cc_final: 0.7922 (t80) REVERT: D 36 LYS cc_start: 0.8318 (tmtt) cc_final: 0.7767 (tmtt) REVERT: D 37 MET cc_start: 0.6885 (tpt) cc_final: 0.6610 (tpt) REVERT: D 52 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8358 (mp) REVERT: D 203 LYS cc_start: 0.8130 (tmmt) cc_final: 0.7737 (tmmt) REVERT: E 36 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8106 (tmtt) REVERT: E 108 PHE cc_start: 0.7954 (m-80) cc_final: 0.7533 (m-80) REVERT: E 115 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7957 (tt) REVERT: E 203 LYS cc_start: 0.7940 (tmmt) cc_final: 0.7647 (tmmt) REVERT: F 36 LYS cc_start: 0.8363 (tmtt) cc_final: 0.8004 (tmtt) REVERT: F 83 TYR cc_start: 0.7599 (t80) cc_final: 0.7293 (t80) REVERT: F 271 ILE cc_start: 0.8403 (mm) cc_final: 0.8014 (tp) REVERT: G 50 ILE cc_start: 0.8016 (mt) cc_final: 0.7794 (tt) REVERT: G 115 LEU cc_start: 0.8084 (tp) cc_final: 0.7842 (tt) REVERT: G 122 LEU cc_start: 0.8028 (mt) cc_final: 0.7727 (mp) outliers start: 32 outliers final: 18 residues processed: 400 average time/residue: 0.2710 time to fit residues: 157.0888 Evaluate side-chains 401 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 378 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 274 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 163 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 337 ASN C 337 ASN E 89 GLN E 207 HIS G 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14791 Z= 0.198 Angle : 0.500 8.988 20048 Z= 0.247 Chirality : 0.037 0.208 2373 Planarity : 0.003 0.037 2394 Dihedral : 3.598 18.461 1904 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.95 % Allowed : 16.23 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.20), residues: 1750 helix: 2.28 (0.14), residues: 1295 sheet: 3.58 (0.64), residues: 42 loop : -0.32 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 104 HIS 0.017 0.002 HIS E 207 PHE 0.015 0.001 PHE F 108 TYR 0.023 0.001 TYR E 212 ARG 0.002 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 380 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8066 (mt) cc_final: 0.7866 (tt) REVERT: A 115 LEU cc_start: 0.8180 (tp) cc_final: 0.7920 (tt) REVERT: A 228 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8017 (mt) REVERT: A 231 SER cc_start: 0.8133 (t) cc_final: 0.7881 (m) REVERT: A 232 TYR cc_start: 0.7796 (t80) cc_final: 0.7581 (t80) REVERT: A 274 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7406 (mp) REVERT: B 198 TYR cc_start: 0.7657 (t80) cc_final: 0.7154 (t80) REVERT: B 224 LEU cc_start: 0.8118 (tp) cc_final: 0.7904 (tp) REVERT: B 228 ILE cc_start: 0.8303 (tp) cc_final: 0.8021 (tp) REVERT: B 349 VAL cc_start: 0.6725 (t) cc_final: 0.6397 (m) REVERT: C 52 LEU cc_start: 0.8545 (mp) cc_final: 0.8330 (mp) REVERT: C 198 TYR cc_start: 0.7399 (t80) cc_final: 0.7143 (t80) REVERT: C 234 PHE cc_start: 0.8232 (t80) cc_final: 0.7918 (t80) REVERT: D 36 LYS cc_start: 0.8317 (tmtt) cc_final: 0.7779 (tmtt) REVERT: D 37 MET cc_start: 0.6898 (tpt) cc_final: 0.6620 (tpt) REVERT: D 52 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8345 (mp) REVERT: D 203 LYS cc_start: 0.8135 (tmmt) cc_final: 0.7749 (tmmt) REVERT: E 36 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8116 (tmtt) REVERT: E 108 PHE cc_start: 0.7988 (m-80) cc_final: 0.7570 (m-80) REVERT: E 115 LEU cc_start: 0.8231 (tp) cc_final: 0.7974 (tt) REVERT: E 203 LYS cc_start: 0.7956 (tmmt) cc_final: 0.7646 (ttpp) REVERT: F 36 LYS cc_start: 0.8375 (tmtt) cc_final: 0.8026 (tmtt) REVERT: F 83 TYR cc_start: 0.7570 (t80) cc_final: 0.7342 (t80) REVERT: G 50 ILE cc_start: 0.8076 (mt) cc_final: 0.7845 (tt) REVERT: G 115 LEU cc_start: 0.8095 (tp) cc_final: 0.7858 (tt) outliers start: 32 outliers final: 20 residues processed: 394 average time/residue: 0.2840 time to fit residues: 164.0860 Evaluate side-chains 404 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 380 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 337 ASN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14791 Z= 0.203 Angle : 0.503 9.629 20048 Z= 0.248 Chirality : 0.037 0.196 2373 Planarity : 0.003 0.038 2394 Dihedral : 3.620 18.620 1904 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.19 % Allowed : 16.17 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.20), residues: 1750 helix: 2.22 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.39 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 104 HIS 0.017 0.002 HIS E 207 PHE 0.015 0.001 PHE F 108 TYR 0.021 0.001 TYR E 212 ARG 0.002 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 387 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8160 (tp) cc_final: 0.7913 (tt) REVERT: A 228 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7978 (mt) REVERT: A 231 SER cc_start: 0.8134 (t) cc_final: 0.7875 (m) REVERT: A 274 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7395 (mp) REVERT: B 135 LEU cc_start: 0.7416 (tp) cc_final: 0.6766 (tp) REVERT: B 198 TYR cc_start: 0.7651 (t80) cc_final: 0.7173 (t80) REVERT: B 224 LEU cc_start: 0.8102 (tp) cc_final: 0.7899 (tp) REVERT: B 228 ILE cc_start: 0.8288 (tp) cc_final: 0.7998 (tp) REVERT: B 349 VAL cc_start: 0.6826 (t) cc_final: 0.6519 (m) REVERT: C 234 PHE cc_start: 0.8237 (t80) cc_final: 0.7919 (t80) REVERT: D 36 LYS cc_start: 0.8344 (tmtt) cc_final: 0.7761 (tmtt) REVERT: D 37 MET cc_start: 0.6890 (tpt) cc_final: 0.6602 (tpt) REVERT: D 52 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8391 (mp) REVERT: D 203 LYS cc_start: 0.8127 (tmmt) cc_final: 0.7744 (tmmt) REVERT: E 36 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8108 (tmtt) REVERT: E 108 PHE cc_start: 0.7988 (m-80) cc_final: 0.7579 (m-80) REVERT: E 115 LEU cc_start: 0.8284 (tp) cc_final: 0.8020 (tt) REVERT: E 203 LYS cc_start: 0.7958 (tmmt) cc_final: 0.7655 (tmmt) REVERT: F 36 LYS cc_start: 0.8350 (tmtt) cc_final: 0.8042 (tmtt) REVERT: F 83 TYR cc_start: 0.7575 (t80) cc_final: 0.7340 (t80) REVERT: F 271 ILE cc_start: 0.8357 (mm) cc_final: 0.7962 (tp) REVERT: G 50 ILE cc_start: 0.8074 (mt) cc_final: 0.7845 (tt) REVERT: G 115 LEU cc_start: 0.8082 (tp) cc_final: 0.7850 (tt) outliers start: 36 outliers final: 23 residues processed: 404 average time/residue: 0.2745 time to fit residues: 160.3270 Evaluate side-chains 408 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 381 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 274 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.0670 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 0.0470 chunk 114 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN F 90 GLN F 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14791 Z= 0.161 Angle : 0.505 11.663 20048 Z= 0.246 Chirality : 0.037 0.190 2373 Planarity : 0.003 0.038 2394 Dihedral : 3.579 18.141 1904 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.88 % Allowed : 16.78 % Favored : 81.34 % 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: 2.39 (0.20), residues: 1750 helix: 2.24 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.39 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 104 HIS 0.016 0.001 HIS E 207 PHE 0.018 0.001 PHE A 234 TYR 0.021 0.001 TYR E 212 ARG 0.002 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 388 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7949 (mt) REVERT: A 231 SER cc_start: 0.8086 (t) cc_final: 0.7841 (m) REVERT: A 274 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7349 (mp) REVERT: B 135 LEU cc_start: 0.7305 (tp) cc_final: 0.6743 (tp) REVERT: B 198 TYR cc_start: 0.7640 (t80) cc_final: 0.7148 (t80) REVERT: B 228 ILE cc_start: 0.8277 (tp) cc_final: 0.7981 (tp) REVERT: B 349 VAL cc_start: 0.6814 (t) cc_final: 0.6484 (m) REVERT: C 198 TYR cc_start: 0.7398 (t80) cc_final: 0.7160 (t80) REVERT: C 234 PHE cc_start: 0.8218 (t80) cc_final: 0.7918 (t80) REVERT: D 36 LYS cc_start: 0.8349 (tmtt) cc_final: 0.7761 (tmtt) REVERT: D 37 MET cc_start: 0.6884 (tpt) cc_final: 0.6601 (tpt) REVERT: D 52 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8382 (mp) REVERT: D 203 LYS cc_start: 0.8101 (tmmt) cc_final: 0.7735 (tmmt) REVERT: E 36 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8097 (tmtt) REVERT: E 115 LEU cc_start: 0.8260 (tp) cc_final: 0.8020 (tt) REVERT: E 203 LYS cc_start: 0.7938 (tmmt) cc_final: 0.7633 (ttpp) REVERT: F 36 LYS cc_start: 0.8334 (tmtt) cc_final: 0.8021 (tmtt) REVERT: F 83 TYR cc_start: 0.7569 (t80) cc_final: 0.7307 (t80) REVERT: F 342 LYS cc_start: 0.7907 (tmtt) cc_final: 0.7527 (tptp) REVERT: G 50 ILE cc_start: 0.8073 (mt) cc_final: 0.7846 (tt) REVERT: G 115 LEU cc_start: 0.8089 (tp) cc_final: 0.7838 (tt) REVERT: G 122 LEU cc_start: 0.8030 (mt) cc_final: 0.7723 (mp) REVERT: G 211 LYS cc_start: 0.7603 (mtpt) cc_final: 0.7358 (ttpt) outliers start: 31 outliers final: 22 residues processed: 399 average time/residue: 0.2727 time to fit residues: 157.4794 Evaluate side-chains 414 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 388 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.0470 chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 156 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 337 ASN C 100 ASN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS G 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14791 Z= 0.181 Angle : 0.507 9.891 20048 Z= 0.248 Chirality : 0.037 0.191 2373 Planarity : 0.003 0.037 2394 Dihedral : 3.578 17.781 1904 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.95 % Allowed : 16.90 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.20), residues: 1750 helix: 2.24 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.42 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 104 HIS 0.005 0.001 HIS F 207 PHE 0.017 0.001 PHE F 108 TYR 0.020 0.001 TYR G 212 ARG 0.001 0.000 ARG G 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 391 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7942 (mt) REVERT: A 231 SER cc_start: 0.8081 (t) cc_final: 0.7842 (m) REVERT: A 234 PHE cc_start: 0.8293 (t80) cc_final: 0.7882 (t80) REVERT: A 274 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7386 (mp) REVERT: B 135 LEU cc_start: 0.7271 (tp) cc_final: 0.6740 (tp) REVERT: B 198 TYR cc_start: 0.7645 (t80) cc_final: 0.7157 (t80) REVERT: B 228 ILE cc_start: 0.8250 (tp) cc_final: 0.7953 (tp) REVERT: B 349 VAL cc_start: 0.6860 (t) cc_final: 0.6521 (m) REVERT: C 198 TYR cc_start: 0.7396 (t80) cc_final: 0.7142 (t80) REVERT: C 234 PHE cc_start: 0.8230 (t80) cc_final: 0.7904 (t80) REVERT: D 36 LYS cc_start: 0.8345 (tmtt) cc_final: 0.7741 (tmtt) REVERT: D 37 MET cc_start: 0.6880 (tpt) cc_final: 0.6611 (tpt) REVERT: D 52 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8389 (mp) REVERT: D 203 LYS cc_start: 0.8105 (tmmt) cc_final: 0.7740 (tmmt) REVERT: E 36 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8066 (tmtt) REVERT: E 115 LEU cc_start: 0.8272 (tp) cc_final: 0.8036 (tt) REVERT: E 203 LYS cc_start: 0.7880 (tmmt) cc_final: 0.7552 (ttpp) REVERT: F 36 LYS cc_start: 0.8355 (tmtt) cc_final: 0.8049 (tmtt) REVERT: F 83 TYR cc_start: 0.7581 (t80) cc_final: 0.7276 (t80) REVERT: F 271 ILE cc_start: 0.8336 (mm) cc_final: 0.7947 (tp) REVERT: F 342 LYS cc_start: 0.7864 (tmtt) cc_final: 0.7491 (tptp) REVERT: G 50 ILE cc_start: 0.8085 (mt) cc_final: 0.7851 (tt) REVERT: G 115 LEU cc_start: 0.8077 (tp) cc_final: 0.7856 (tt) REVERT: G 211 LYS cc_start: 0.7609 (mtpt) cc_final: 0.7350 (ttpt) outliers start: 32 outliers final: 24 residues processed: 403 average time/residue: 0.2751 time to fit residues: 160.1687 Evaluate side-chains 415 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 387 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 0.0470 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14791 Z= 0.189 Angle : 0.514 10.037 20048 Z= 0.250 Chirality : 0.037 0.245 2373 Planarity : 0.003 0.037 2394 Dihedral : 3.590 17.681 1904 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.76 % Allowed : 17.51 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.20), residues: 1750 helix: 2.22 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.42 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 104 HIS 0.006 0.001 HIS E 207 PHE 0.018 0.001 PHE F 108 TYR 0.022 0.001 TYR G 212 ARG 0.001 0.000 ARG F 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 390 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7936 (mt) REVERT: A 231 SER cc_start: 0.8073 (t) cc_final: 0.7832 (m) REVERT: A 274 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7382 (mp) REVERT: B 135 LEU cc_start: 0.7241 (tp) cc_final: 0.6717 (tp) REVERT: B 198 TYR cc_start: 0.7643 (t80) cc_final: 0.7224 (t80) REVERT: B 228 ILE cc_start: 0.8252 (tp) cc_final: 0.7952 (tp) REVERT: B 349 VAL cc_start: 0.6904 (t) cc_final: 0.6564 (m) REVERT: C 198 TYR cc_start: 0.7399 (t80) cc_final: 0.7146 (t80) REVERT: C 234 PHE cc_start: 0.8229 (t80) cc_final: 0.7907 (t80) REVERT: D 36 LYS cc_start: 0.8332 (tmtt) cc_final: 0.7718 (tmtt) REVERT: D 37 MET cc_start: 0.6881 (tpt) cc_final: 0.6611 (tpt) REVERT: D 52 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8392 (mp) REVERT: D 203 LYS cc_start: 0.8101 (tmmt) cc_final: 0.7741 (tmmt) REVERT: E 36 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8064 (tmtt) REVERT: E 115 LEU cc_start: 0.8227 (tp) cc_final: 0.7994 (tt) REVERT: E 203 LYS cc_start: 0.7875 (tmmt) cc_final: 0.7553 (ttpp) REVERT: F 36 LYS cc_start: 0.8357 (tmtt) cc_final: 0.8054 (tmtt) REVERT: F 83 TYR cc_start: 0.7565 (t80) cc_final: 0.7332 (t80) REVERT: F 271 ILE cc_start: 0.8366 (mm) cc_final: 0.7976 (tp) REVERT: F 342 LYS cc_start: 0.7873 (tmtt) cc_final: 0.7491 (tptp) REVERT: G 50 ILE cc_start: 0.8105 (mt) cc_final: 0.7854 (tt) REVERT: G 115 LEU cc_start: 0.8077 (tp) cc_final: 0.7841 (tt) REVERT: G 122 LEU cc_start: 0.8039 (mt) cc_final: 0.7737 (mp) REVERT: G 202 LYS cc_start: 0.7199 (mmtt) cc_final: 0.6962 (mmtt) REVERT: G 211 LYS cc_start: 0.7614 (mtpt) cc_final: 0.7356 (ttpt) outliers start: 29 outliers final: 24 residues processed: 403 average time/residue: 0.2667 time to fit residues: 155.8989 Evaluate side-chains 415 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 387 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 139 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 122 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 337 ASN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS F 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.152864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138221 restraints weight = 18724.017| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.90 r_work: 0.3601 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14791 Z= 0.164 Angle : 0.506 9.882 20048 Z= 0.246 Chirality : 0.037 0.275 2373 Planarity : 0.003 0.037 2394 Dihedral : 3.558 17.459 1904 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.88 % Allowed : 17.69 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.20), residues: 1750 helix: 2.25 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.42 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 104 HIS 0.006 0.001 HIS E 207 PHE 0.017 0.001 PHE F 108 TYR 0.021 0.001 TYR G 212 ARG 0.001 0.000 ARG F 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3675.17 seconds wall clock time: 68 minutes 0.68 seconds (4080.68 seconds total)