Starting phenix.real_space_refine on Sun Dec 10 12:10:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/12_2023/8a3b_15110.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/12_2023/8a3b_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_15110/12_2023/8a3b_15110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/12_2023/8a3b_15110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/12_2023/8a3b_15110.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/12_2023/8a3b_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-1.21rc1-5172/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: 7.92, per 1000 atoms: 0.55 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: 5.52 Conformation dependent library (CDL) restraints added in 2.7 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: 1.41 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: 3.88 Time building geometry restraints manager: 5.97 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: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.140 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 38.560 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.490 ------------------------------------------------------------------------------- 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 : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.2698 time to fit residues: 174.8115 Evaluate side-chains 378 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4437 ------------------------------------------------------------------------------- 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: 1.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 100 ASN A 337 ASN C 337 ASN D 63 GLN D 134 HIS E 63 GLN E 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14791 Z= 0.236 Angle : 0.546 6.736 20048 Z= 0.277 Chirality : 0.040 0.223 2373 Planarity : 0.004 0.036 2394 Dihedral : 3.796 19.691 1904 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.64 % Allowed : 10.82 % Favored : 87.54 % 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: 2.23 (0.20), residues: 1750 helix: 2.13 (0.14), residues: 1309 sheet: None (None), residues: 0 loop : -0.53 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 104 HIS 0.005 0.001 HIS B 207 PHE 0.016 0.001 PHE A 54 TYR 0.019 0.001 TYR C 198 ARG 0.004 0.000 ARG E 261 *********************** 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 431 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 404 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 413 average time/residue: 0.2736 time to fit residues: 163.1423 Evaluate side-chains 390 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 379 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2015 time to fit residues: 5.7184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 159 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 141 optimal weight: 0.4980 chunk 157 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN F 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2000 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= 0.196 Angle : 0.522 9.000 20048 Z= 0.259 Chirality : 0.038 0.239 2373 Planarity : 0.003 0.033 2394 Dihedral : 3.726 19.524 1904 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.70 % Allowed : 13.25 % Favored : 85.05 % 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: 2.43 (0.20), residues: 1750 helix: 2.13 (0.14), residues: 1302 sheet: 3.56 (0.65), residues: 42 loop : -0.33 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 104 HIS 0.004 0.001 HIS G 207 PHE 0.016 0.001 PHE A 54 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 417 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 389 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 401 average time/residue: 0.2732 time to fit residues: 158.1595 Evaluate side-chains 395 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 385 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1312 time to fit residues: 4.7361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 151 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 337 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14791 Z= 0.218 Angle : 0.530 9.868 20048 Z= 0.261 Chirality : 0.038 0.208 2373 Planarity : 0.003 0.032 2394 Dihedral : 3.718 19.625 1904 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.40 % Allowed : 15.62 % Favored : 82.98 % 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: 2.40 (0.20), residues: 1750 helix: 2.11 (0.14), residues: 1302 sheet: 3.59 (0.64), residues: 42 loop : -0.32 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 85 HIS 0.005 0.001 HIS E 207 PHE 0.015 0.001 PHE G 67 TYR 0.024 0.001 TYR C 121 ARG 0.002 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 407 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 384 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 394 average time/residue: 0.2724 time to fit residues: 154.8923 Evaluate side-chains 387 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 380 time to evaluate : 1.585 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1703 time to fit residues: 4.1935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.0870 chunk 96 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 151 optimal weight: 0.8980 chunk 42 optimal weight: 0.0170 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 63 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2404 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= 0.160 Angle : 0.505 8.644 20048 Z= 0.249 Chirality : 0.037 0.211 2373 Planarity : 0.003 0.035 2394 Dihedral : 3.634 18.952 1904 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.46 % Allowed : 16.35 % Favored : 82.19 % 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: 2.46 (0.20), residues: 1750 helix: 2.18 (0.14), residues: 1295 sheet: 3.61 (0.62), residues: 42 loop : -0.38 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 104 HIS 0.005 0.001 HIS F 207 PHE 0.014 0.001 PHE G 67 TYR 0.023 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 412 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 388 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 395 average time/residue: 0.2760 time to fit residues: 158.2278 Evaluate side-chains 392 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 384 time to evaluate : 1.728 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1323 time to fit residues: 4.4460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 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 106 HIS B 207 HIS C 337 ASN E 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14791 Z= 0.221 Angle : 0.526 9.315 20048 Z= 0.256 Chirality : 0.038 0.207 2373 Planarity : 0.003 0.036 2394 Dihedral : 3.667 19.116 1904 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.46 % Allowed : 17.57 % Favored : 80.97 % 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: 2.40 (0.20), residues: 1750 helix: 2.14 (0.14), residues: 1295 sheet: 3.48 (0.62), residues: 42 loop : -0.39 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 104 HIS 0.004 0.001 HIS F 207 PHE 0.014 0.001 PHE G 243 TYR 0.023 0.002 TYR C 121 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 413 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 389 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 400 average time/residue: 0.2700 time to fit residues: 155.8435 Evaluate side-chains 400 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 387 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1533 time to fit residues: 5.7992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.2980 chunk 96 optimal weight: 0.0570 chunk 123 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 0.0370 chunk 105 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 G 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14791 Z= 0.152 Angle : 0.518 10.373 20048 Z= 0.249 Chirality : 0.037 0.198 2373 Planarity : 0.003 0.037 2394 Dihedral : 3.578 18.291 1904 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.16 % Allowed : 18.24 % Favored : 80.61 % 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: 2.25 (0.20), residues: 1750 helix: 2.14 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.43 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 104 HIS 0.004 0.001 HIS F 207 PHE 0.016 0.001 PHE C 234 TYR 0.022 0.001 TYR B 198 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 409 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 390 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 397 average time/residue: 0.2665 time to fit residues: 153.1486 Evaluate side-chains 387 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 382 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1229 time to fit residues: 3.2535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 107 optimal weight: 0.2980 chunk 114 optimal weight: 0.7980 chunk 83 optimal weight: 0.0050 chunk 15 optimal weight: 0.9980 chunk 132 optimal weight: 0.0470 chunk 153 optimal weight: 1.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14791 Z= 0.150 Angle : 0.516 9.045 20048 Z= 0.249 Chirality : 0.036 0.192 2373 Planarity : 0.003 0.036 2394 Dihedral : 3.513 17.340 1904 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.61 % Allowed : 18.42 % Favored : 80.97 % 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: 2.34 (0.20), residues: 1750 helix: 2.21 (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 0.005 0.001 HIS C 207 PHE 0.015 0.001 PHE C 108 TYR 0.019 0.001 TYR C 121 ARG 0.001 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 398 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 388 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 393 average time/residue: 0.2736 time to fit residues: 156.2745 Evaluate side-chains 386 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 382 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1332 time to fit residues: 3.3567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 157 optimal weight: 0.0010 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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** F 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2836 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 : 0.527 10.286 20048 Z= 0.251 Chirality : 0.037 0.253 2373 Planarity : 0.003 0.036 2394 Dihedral : 3.499 16.523 1904 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.30 % Allowed : 19.27 % 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: 2.34 (0.20), residues: 1750 helix: 2.17 (0.14), residues: 1309 sheet: None (None), residues: 0 loop : -0.34 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 104 HIS 0.005 0.001 HIS F 207 PHE 0.013 0.001 PHE F 295 TYR 0.028 0.001 TYR F 198 ARG 0.001 0.000 ARG F 29 *********************** 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 398 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 393 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 394 average time/residue: 0.2753 time to fit residues: 158.4553 Evaluate side-chains 388 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 387 time to evaluate : 1.786 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1251 time to fit residues: 2.4464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 107 optimal weight: 0.2980 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** B 337 ASN C 63 GLN D 100 ASN F 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2880 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= 0.177 Angle : 0.536 10.293 20048 Z= 0.255 Chirality : 0.037 0.272 2373 Planarity : 0.003 0.037 2394 Dihedral : 3.511 16.356 1904 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.36 % Allowed : 20.06 % Favored : 79.57 % 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: 2.31 (0.20), residues: 1750 helix: 2.15 (0.14), residues: 1309 sheet: None (None), residues: 0 loop : -0.36 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 104 HIS 0.005 0.001 HIS F 207 PHE 0.017 0.001 PHE D 109 TYR 0.028 0.001 TYR F 198 ARG 0.001 0.000 ARG G 75 ********************** 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 393 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 387 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 388 average time/residue: 0.2831 time to fit residues: 159.6035 Evaluate side-chains 388 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 384 time to evaluate : 1.605 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2118 time to fit residues: 3.5851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.153300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.138311 restraints weight = 18571.091| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.96 r_work: 0.3587 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2899 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= 0.218 Angle : 0.554 10.475 20048 Z= 0.264 Chirality : 0.038 0.300 2373 Planarity : 0.003 0.037 2394 Dihedral : 3.574 16.739 1904 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.43 % Allowed : 19.94 % Favored : 79.64 % 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: 2.24 (0.20), residues: 1750 helix: 2.10 (0.14), residues: 1309 sheet: None (None), residues: 0 loop : -0.37 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 104 HIS 0.005 0.001 HIS F 207 PHE 0.020 0.001 PHE C 234 TYR 0.027 0.002 TYR F 198 ARG 0.001 0.000 ARG G 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3637.61 seconds wall clock time: 66 minutes 46.66 seconds (4006.66 seconds total)