Starting phenix.real_space_refine on Wed Feb 14 01:44:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izb_35838/02_2024/8izb_35838_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izb_35838/02_2024/8izb_35838.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izb_35838/02_2024/8izb_35838_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izb_35838/02_2024/8izb_35838_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izb_35838/02_2024/8izb_35838_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izb_35838/02_2024/8izb_35838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izb_35838/02_2024/8izb_35838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izb_35838/02_2024/8izb_35838_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izb_35838/02_2024/8izb_35838_updated.pdb" } resolution = 3.06 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= 0.056 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 59 5.16 5 C 5315 2.51 5 N 1416 2.21 5 O 1531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8322 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1954 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2246 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "R" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {'CLR': 2, 'UBL': 1} Inner-chain residues flagged as termini: ['pdbres="SER R 502 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.02, per 1000 atoms: 0.60 Number of scatterers: 8322 At special positions: 0 Unit cell: (79.18, 102.72, 133.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 1 15.00 O 1531 8.00 N 1416 7.00 C 5315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 91 " - pdb=" SG CYS R 168 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.6 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 10 sheets defined 38.5% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.520A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.646A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.527A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 16 through 51 removed outlier: 3.989A pdb=" N VAL R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 56 through 70 Processing helix chain 'R' and resid 72 through 81 removed outlier: 3.574A pdb=" N TYR R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR R 79 " --> pdb=" O ARG R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 121 removed outlier: 3.569A pdb=" N PHE R 93 " --> pdb=" O GLY R 89 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR R 96 " --> pdb=" O MET R 92 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS R 98 " --> pdb=" O CYS R 94 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR R 99 " --> pdb=" O PHE R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 125 No H-bonds generated for 'chain 'R' and resid 123 through 125' Processing helix chain 'R' and resid 129 through 131 No H-bonds generated for 'chain 'R' and resid 129 through 131' Processing helix chain 'R' and resid 135 through 154 removed outlier: 4.172A pdb=" N VAL R 150 " --> pdb=" O CYS R 146 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU R 151 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N PHE R 152 " --> pdb=" O ALA R 148 " (cutoff:3.500A) Proline residue: R 153 - end of helix Processing helix chain 'R' and resid 169 through 171 No H-bonds generated for 'chain 'R' and resid 169 through 171' Processing helix chain 'R' and resid 179 through 193 Processing helix chain 'R' and resid 195 through 211 Processing helix chain 'R' and resid 224 through 257 Proline residue: R 245 - end of helix Proline residue: R 251 - end of helix removed outlier: 3.608A pdb=" N LEU R 255 " --> pdb=" O PRO R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 292 removed outlier: 3.679A pdb=" N ARG R 268 " --> pdb=" O CYS R 264 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER R 285 " --> pdb=" O ALA R 281 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS R 286 " --> pdb=" O SER R 282 " (cutoff:3.500A) Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 297 through 303 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.176A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.745A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.822A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.736A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.945A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.570A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.530A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.595A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 8 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.253A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1089 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: 2.41 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1340 1.31 - 1.43: 2360 1.43 - 1.56: 4716 1.56 - 1.68: 5 1.68 - 1.81: 82 Bond restraints: 8503 Sorted by residual: bond pdb=" CAM UBL R 501 " pdb=" CAN UBL R 501 " ideal model delta sigma weight residual 1.599 1.554 0.045 2.00e-02 2.50e+03 4.98e+00 bond pdb=" CAN UBL R 501 " pdb=" CAO UBL R 501 " ideal model delta sigma weight residual 1.525 1.559 -0.034 2.00e-02 2.50e+03 2.94e+00 bond pdb=" C5 CLR R 503 " pdb=" C6 CLR R 503 " ideal model delta sigma weight residual 1.332 1.299 0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C SER R 502 " pdb=" O SER R 502 " ideal model delta sigma weight residual 1.231 1.264 -0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" CAZ UBL R 501 " pdb=" CBA UBL R 501 " ideal model delta sigma weight residual 1.523 1.556 -0.033 2.00e-02 2.50e+03 2.65e+00 ... (remaining 8498 not shown) Histogram of bond angle deviations from ideal: 100.43 - 110.91: 3146 110.91 - 121.38: 6285 121.38 - 131.86: 2083 131.86 - 142.34: 18 142.34 - 152.81: 1 Bond angle restraints: 11533 Sorted by residual: angle pdb=" CAR UBL R 501 " pdb=" CAS UBL R 501 " pdb=" CAT UBL R 501 " ideal model delta sigma weight residual 119.99 152.81 -32.82 3.00e+00 1.11e-01 1.20e+02 angle pdb=" C13 CLR R 504 " pdb=" C17 CLR R 504 " pdb=" C20 CLR R 504 " ideal model delta sigma weight residual 119.60 111.25 8.35 3.00e+00 1.11e-01 7.74e+00 angle pdb=" CAS UBL R 501 " pdb=" CAT UBL R 501 " pdb=" CAU UBL R 501 " ideal model delta sigma weight residual 120.00 112.18 7.82 3.00e+00 1.11e-01 6.79e+00 angle pdb=" C13 CLR R 503 " pdb=" C17 CLR R 503 " pdb=" C20 CLR R 503 " ideal model delta sigma weight residual 119.60 112.23 7.37 3.00e+00 1.11e-01 6.04e+00 angle pdb=" C23 CLR R 503 " pdb=" C24 CLR R 503 " pdb=" C25 CLR R 503 " ideal model delta sigma weight residual 115.14 109.47 5.67 3.00e+00 1.11e-01 3.58e+00 ... (remaining 11528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.38: 5098 32.38 - 64.76: 53 64.76 - 97.14: 1 97.14 - 129.52: 0 129.52 - 161.89: 1 Dihedral angle restraints: 5153 sinusoidal: 2097 harmonic: 3056 Sorted by residual: dihedral pdb=" CAI UBL R 501 " pdb=" CAG UBL R 501 " pdb=" CAH UBL R 501 " pdb=" OAF UBL R 501 " ideal model delta sinusoidal sigma weight residual 137.75 -60.36 -161.89 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -161.70 -18.30 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1234 0.095 - 0.189: 60 0.189 - 0.284: 1 0.284 - 0.378: 3 0.378 - 0.473: 2 Chirality restraints: 1300 Sorted by residual: chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" C10 CLR R 503 " pdb=" C1 CLR R 503 " pdb=" C5 CLR R 503 " pdb=" C9 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.85 -2.51 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1297 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO B 236 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 288 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO R 289 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO R 289 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 289 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " -0.016 5.00e-02 4.00e+02 2.43e-02 9.48e-01 pdb=" N PRO C 55 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.014 5.00e-02 4.00e+02 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1421 2.77 - 3.30: 7930 3.30 - 3.83: 13871 3.83 - 4.37: 17255 4.37 - 4.90: 29493 Nonbonded interactions: 69970 Sorted by model distance: nonbonded pdb=" OG SER A 205 " pdb=" O ASP B 118 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.262 2.440 nonbonded pdb=" O CYS R 204 " pdb=" OG1 THR R 208 " model vdw 2.273 2.440 nonbonded pdb=" OD2 ASP A 381 " pdb=" NH1 ARG A 385 " model vdw 2.285 2.520 nonbonded pdb=" O LEU R 97 " pdb=" ND2 ASN R 101 " model vdw 2.300 2.520 ... (remaining 69965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.410 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: 1.910 Check model and map are aligned: 0.170 Set scattering table: 0.080 Process input model: 25.780 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.002 0.045 8503 Z= 0.134 Angle : 0.541 32.823 11533 Z= 0.232 Chirality : 0.047 0.473 1300 Planarity : 0.003 0.042 1457 Dihedral : 9.628 161.895 3170 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.68 % Allowed : 4.17 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1031 helix: 1.14 (0.26), residues: 387 sheet: 0.68 (0.32), residues: 230 loop : 0.18 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.002 0.000 HIS B 91 PHE 0.013 0.001 PHE R 119 TYR 0.007 0.001 TYR N 60 ARG 0.003 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 245 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7609 (tp30) REVERT: A 20 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7524 (ttp-110) REVERT: A 34 LYS cc_start: 0.8475 (tttt) cc_final: 0.8259 (tttp) REVERT: A 35 GLN cc_start: 0.7932 (tp40) cc_final: 0.7439 (mm-40) REVERT: A 53 LYS cc_start: 0.8725 (pttp) cc_final: 0.8330 (pttt) REVERT: A 211 LYS cc_start: 0.8532 (mtmt) cc_final: 0.7973 (mttp) REVERT: A 221 MET cc_start: 0.8789 (ttp) cc_final: 0.8558 (ttp) REVERT: A 307 LYS cc_start: 0.9009 (mttt) cc_final: 0.8569 (mtmm) REVERT: A 358 TYR cc_start: 0.8896 (m-80) cc_final: 0.8495 (m-80) REVERT: A 381 ASP cc_start: 0.8918 (t70) cc_final: 0.8651 (t0) REVERT: B 101 MET cc_start: 0.8493 (mtp) cc_final: 0.8275 (mtp) REVERT: B 217 MET cc_start: 0.6948 (ppp) cc_final: 0.5928 (ppp) REVERT: B 219 ARG cc_start: 0.7553 (mtp85) cc_final: 0.7350 (mmp80) REVERT: B 254 ASP cc_start: 0.8289 (t70) cc_final: 0.7894 (t0) REVERT: C 38 MET cc_start: 0.8554 (ttp) cc_final: 0.8306 (ttm) REVERT: N 70 ILE cc_start: 0.8776 (tt) cc_final: 0.8336 (tt) REVERT: N 73 ASP cc_start: 0.7293 (t0) cc_final: 0.6955 (t0) REVERT: N 108 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: N 120 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8177 (mm-40) REVERT: R 21 ILE cc_start: 0.8703 (mt) cc_final: 0.8480 (mt) REVERT: R 113 SER cc_start: 0.9003 (t) cc_final: 0.8766 (m) REVERT: R 147 LEU cc_start: 0.8235 (tp) cc_final: 0.7846 (mp) REVERT: R 227 LYS cc_start: 0.7785 (mttt) cc_final: 0.7464 (tttt) REVERT: R 250 PHE cc_start: 0.8574 (t80) cc_final: 0.8358 (t80) REVERT: R 294 PHE cc_start: 0.8633 (m-80) cc_final: 0.8341 (m-10) outliers start: 6 outliers final: 2 residues processed: 250 average time/residue: 0.2622 time to fit residues: 83.8950 Evaluate side-chains 168 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 299 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.3980 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 19 GLN A 213 GLN A 264 ASN A 279 ASN B 6 GLN B 91 HIS B 220 GLN B 259 GLN N 3 GLN N 31 ASN N 82 GLN R 226 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8503 Z= 0.295 Angle : 0.567 7.616 11533 Z= 0.299 Chirality : 0.044 0.172 1300 Planarity : 0.004 0.044 1457 Dihedral : 8.094 165.641 1302 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.93 % Allowed : 10.26 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1031 helix: 1.74 (0.25), residues: 393 sheet: 0.32 (0.31), residues: 237 loop : 0.30 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.032 0.002 PHE R 119 TYR 0.019 0.002 TYR R 47 ARG 0.005 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7796 (tp40) cc_final: 0.7317 (mm110) REVERT: A 211 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8168 (mttp) REVERT: A 213 GLN cc_start: 0.8391 (tt0) cc_final: 0.8171 (tt0) REVERT: A 307 LYS cc_start: 0.8965 (mttt) cc_final: 0.8599 (mtmm) REVERT: A 358 TYR cc_start: 0.9083 (m-80) cc_final: 0.8680 (m-80) REVERT: B 101 MET cc_start: 0.8797 (mtp) cc_final: 0.8430 (mtp) REVERT: B 196 THR cc_start: 0.8788 (m) cc_final: 0.8471 (p) REVERT: B 217 MET cc_start: 0.7555 (ppp) cc_final: 0.5984 (ppp) REVERT: B 219 ARG cc_start: 0.7651 (mtp85) cc_final: 0.7364 (mmp80) REVERT: B 254 ASP cc_start: 0.8427 (t70) cc_final: 0.8024 (t0) REVERT: C 20 LYS cc_start: 0.8411 (mttt) cc_final: 0.8149 (mtmm) REVERT: C 38 MET cc_start: 0.8440 (ttp) cc_final: 0.8217 (ttm) REVERT: N 70 ILE cc_start: 0.8758 (tt) cc_final: 0.8515 (tt) REVERT: N 73 ASP cc_start: 0.7342 (t0) cc_final: 0.6997 (t0) REVERT: N 76 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8580 (mmmm) REVERT: N 108 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8661 (m-80) REVERT: N 120 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7957 (mm-40) REVERT: R 45 TYR cc_start: 0.7470 (t80) cc_final: 0.7244 (t80) REVERT: R 92 MET cc_start: 0.8575 (mmp) cc_final: 0.8323 (mmm) REVERT: R 207 LYS cc_start: 0.8098 (mttm) cc_final: 0.7843 (mmtp) outliers start: 26 outliers final: 16 residues processed: 198 average time/residue: 0.2514 time to fit residues: 64.3824 Evaluate side-chains 168 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 299 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 chunk 63 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 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 23 ASN B 220 GLN B 259 GLN N 31 ASN R 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8503 Z= 0.156 Angle : 0.475 6.235 11533 Z= 0.247 Chirality : 0.041 0.154 1300 Planarity : 0.003 0.041 1457 Dihedral : 7.705 164.528 1302 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.27 % Allowed : 11.72 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1031 helix: 1.95 (0.26), residues: 399 sheet: 0.22 (0.31), residues: 222 loop : 0.21 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.028 0.002 PHE R 119 TYR 0.013 0.001 TYR N 60 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7699 (mtm180) cc_final: 0.6998 (mtm-85) REVERT: A 23 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7380 (t0) REVERT: A 35 GLN cc_start: 0.7641 (tp40) cc_final: 0.7008 (tt0) REVERT: A 211 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8262 (mttp) REVERT: A 213 GLN cc_start: 0.8254 (tt0) cc_final: 0.7955 (tt0) REVERT: A 307 LYS cc_start: 0.8925 (mttt) cc_final: 0.8648 (mtmm) REVERT: A 335 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8010 (m) REVERT: A 358 TYR cc_start: 0.9063 (m-80) cc_final: 0.8659 (m-80) REVERT: B 101 MET cc_start: 0.8624 (mtp) cc_final: 0.8320 (mtp) REVERT: B 219 ARG cc_start: 0.7576 (mtp85) cc_final: 0.7321 (mmp80) REVERT: B 254 ASP cc_start: 0.8389 (t70) cc_final: 0.8015 (t0) REVERT: C 38 MET cc_start: 0.8342 (ttp) cc_final: 0.8131 (ttm) REVERT: N 70 ILE cc_start: 0.8849 (tt) cc_final: 0.8574 (tt) REVERT: N 73 ASP cc_start: 0.7364 (t0) cc_final: 0.7052 (t0) REVERT: N 76 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8558 (mmmm) REVERT: N 108 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: R 92 MET cc_start: 0.8676 (mmp) cc_final: 0.8449 (mmm) REVERT: R 113 SER cc_start: 0.8943 (t) cc_final: 0.8594 (m) REVERT: R 183 VAL cc_start: 0.8818 (t) cc_final: 0.8614 (p) outliers start: 29 outliers final: 18 residues processed: 189 average time/residue: 0.2476 time to fit residues: 61.2781 Evaluate side-chains 175 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 299 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.0570 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 32 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8503 Z= 0.247 Angle : 0.503 5.884 11533 Z= 0.264 Chirality : 0.042 0.157 1300 Planarity : 0.003 0.042 1457 Dihedral : 7.660 157.009 1302 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.85 % Allowed : 12.06 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1031 helix: 1.99 (0.26), residues: 399 sheet: 0.19 (0.32), residues: 216 loop : 0.13 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS R 274 PHE 0.030 0.002 PHE R 119 TYR 0.013 0.001 TYR R 47 ARG 0.005 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 155 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7722 (mtm180) cc_final: 0.7026 (mtm-85) REVERT: A 23 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7740 (t0) REVERT: A 35 GLN cc_start: 0.7610 (tp40) cc_final: 0.6974 (tt0) REVERT: A 211 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8237 (mttp) REVERT: A 213 GLN cc_start: 0.8325 (tt0) cc_final: 0.8041 (tt0) REVERT: A 307 LYS cc_start: 0.8958 (mttt) cc_final: 0.8631 (mtmm) REVERT: A 335 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8081 (m) REVERT: A 358 TYR cc_start: 0.9083 (m-80) cc_final: 0.8749 (m-80) REVERT: B 196 THR cc_start: 0.8604 (m) cc_final: 0.8177 (p) REVERT: B 219 ARG cc_start: 0.7657 (mtp85) cc_final: 0.7305 (mmp80) REVERT: B 254 ASP cc_start: 0.8398 (t70) cc_final: 0.8006 (t0) REVERT: C 20 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7683 (mtmt) REVERT: N 70 ILE cc_start: 0.8808 (tt) cc_final: 0.8552 (tt) REVERT: N 73 ASP cc_start: 0.7452 (t0) cc_final: 0.7085 (t0) REVERT: N 76 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8426 (mmmm) REVERT: N 108 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8528 (m-80) REVERT: R 102 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8009 (ttp) REVERT: R 127 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.6772 (m170) REVERT: R 183 VAL cc_start: 0.8677 (t) cc_final: 0.8472 (p) outliers start: 43 outliers final: 28 residues processed: 182 average time/residue: 0.2416 time to fit residues: 57.5379 Evaluate side-chains 181 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 94 CYS Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 299 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8503 Z= 0.265 Angle : 0.510 5.570 11533 Z= 0.267 Chirality : 0.043 0.157 1300 Planarity : 0.003 0.042 1457 Dihedral : 7.408 147.126 1300 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.62 % Allowed : 12.63 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1031 helix: 2.02 (0.26), residues: 398 sheet: 0.10 (0.32), residues: 217 loop : 0.05 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS R 274 PHE 0.030 0.002 PHE R 119 TYR 0.013 0.001 TYR R 47 ARG 0.005 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7673 (mtm180) cc_final: 0.6984 (mtm-85) REVERT: A 23 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7652 (t0) REVERT: A 35 GLN cc_start: 0.7600 (tp40) cc_final: 0.7011 (tt0) REVERT: A 211 LYS cc_start: 0.8644 (mtmt) cc_final: 0.8262 (mttp) REVERT: A 213 GLN cc_start: 0.8356 (tt0) cc_final: 0.8127 (tt0) REVERT: A 307 LYS cc_start: 0.8957 (mttt) cc_final: 0.8625 (mtmm) REVERT: A 335 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8111 (m) REVERT: A 358 TYR cc_start: 0.9083 (m-80) cc_final: 0.8752 (m-80) REVERT: B 219 ARG cc_start: 0.7723 (mtp85) cc_final: 0.7292 (mmp80) REVERT: B 254 ASP cc_start: 0.8430 (t70) cc_final: 0.8027 (t0) REVERT: N 70 ILE cc_start: 0.8800 (tt) cc_final: 0.8536 (tt) REVERT: N 73 ASP cc_start: 0.7557 (t0) cc_final: 0.7180 (t0) REVERT: N 76 LYS cc_start: 0.8804 (mmmm) cc_final: 0.8326 (mmmm) REVERT: R 102 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8053 (ttp) REVERT: R 127 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.6789 (m170) REVERT: R 183 VAL cc_start: 0.8694 (t) cc_final: 0.8493 (p) outliers start: 41 outliers final: 34 residues processed: 180 average time/residue: 0.2710 time to fit residues: 62.8923 Evaluate side-chains 182 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 94 CYS Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 299 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8503 Z= 0.173 Angle : 0.472 5.991 11533 Z= 0.249 Chirality : 0.041 0.155 1300 Planarity : 0.003 0.041 1457 Dihedral : 7.107 134.806 1300 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.17 % Allowed : 13.64 % 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: 1.29 (0.26), residues: 1031 helix: 2.11 (0.26), residues: 400 sheet: 0.13 (0.32), residues: 223 loop : 0.13 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS R 274 PHE 0.027 0.001 PHE R 119 TYR 0.013 0.001 TYR N 60 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7567 (tp40) cc_final: 0.6986 (tt0) REVERT: A 211 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8163 (mttp) REVERT: A 213 GLN cc_start: 0.8301 (tt0) cc_final: 0.8007 (tt0) REVERT: A 307 LYS cc_start: 0.8919 (mttt) cc_final: 0.8600 (mtmm) REVERT: A 335 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8048 (m) REVERT: A 358 TYR cc_start: 0.9087 (m-80) cc_final: 0.8743 (m-80) REVERT: B 17 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7818 (tm-30) REVERT: B 196 THR cc_start: 0.8549 (m) cc_final: 0.8058 (p) REVERT: B 219 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7275 (mmp80) REVERT: B 254 ASP cc_start: 0.8343 (t70) cc_final: 0.7925 (t0) REVERT: N 5 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7688 (mt0) REVERT: N 70 ILE cc_start: 0.8783 (tt) cc_final: 0.8507 (tt) REVERT: N 73 ASP cc_start: 0.7523 (t0) cc_final: 0.7112 (t0) REVERT: N 76 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8291 (mmmm) REVERT: R 127 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.6636 (m170) REVERT: R 183 VAL cc_start: 0.8691 (t) cc_final: 0.8484 (p) outliers start: 37 outliers final: 24 residues processed: 181 average time/residue: 0.2606 time to fit residues: 60.6306 Evaluate side-chains 176 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 94 CYS Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 32 GLN B 88 ASN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8503 Z= 0.233 Angle : 0.499 7.562 11533 Z= 0.259 Chirality : 0.042 0.162 1300 Planarity : 0.003 0.041 1457 Dihedral : 6.773 111.918 1298 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.28 % Allowed : 13.30 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1031 helix: 2.08 (0.26), residues: 401 sheet: 0.11 (0.32), residues: 223 loop : 0.13 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS R 274 PHE 0.029 0.002 PHE R 119 TYR 0.014 0.001 TYR N 60 ARG 0.006 0.000 ARG R 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7595 (mtm180) cc_final: 0.6920 (mtm-85) REVERT: A 35 GLN cc_start: 0.7580 (tp40) cc_final: 0.7007 (tt0) REVERT: A 211 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8190 (mttp) REVERT: A 213 GLN cc_start: 0.8333 (tt0) cc_final: 0.8047 (tt0) REVERT: A 307 LYS cc_start: 0.8922 (mttt) cc_final: 0.8555 (mtmm) REVERT: A 335 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8100 (m) REVERT: A 358 TYR cc_start: 0.9092 (m-80) cc_final: 0.8757 (m-80) REVERT: B 17 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7927 (tm-30) REVERT: B 219 ARG cc_start: 0.7753 (mtp85) cc_final: 0.7286 (mmp80) REVERT: B 254 ASP cc_start: 0.8243 (t70) cc_final: 0.7814 (t0) REVERT: N 5 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7692 (mt0) REVERT: N 70 ILE cc_start: 0.8791 (tt) cc_final: 0.8540 (tt) REVERT: N 73 ASP cc_start: 0.7626 (t0) cc_final: 0.7179 (t0) REVERT: N 76 LYS cc_start: 0.8812 (mmmm) cc_final: 0.8246 (mmmm) REVERT: R 127 HIS cc_start: 0.7409 (OUTLIER) cc_final: 0.6732 (m170) REVERT: R 183 VAL cc_start: 0.8683 (t) cc_final: 0.8463 (p) outliers start: 38 outliers final: 34 residues processed: 177 average time/residue: 0.2600 time to fit residues: 59.5161 Evaluate side-chains 183 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 94 CYS Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 0.0970 chunk 55 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 32 GLN B 259 GLN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8503 Z= 0.165 Angle : 0.470 6.670 11533 Z= 0.245 Chirality : 0.041 0.168 1300 Planarity : 0.003 0.040 1457 Dihedral : 6.380 79.252 1298 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.72 % Allowed : 14.32 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1031 helix: 2.20 (0.26), residues: 400 sheet: 0.29 (0.32), residues: 216 loop : 0.13 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS R 274 PHE 0.027 0.001 PHE R 119 TYR 0.013 0.001 TYR N 60 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7616 (mtm180) cc_final: 0.6944 (mtm-85) REVERT: A 23 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7329 (t0) REVERT: A 35 GLN cc_start: 0.7547 (tp40) cc_final: 0.6973 (tt0) REVERT: A 211 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8154 (mttp) REVERT: A 213 GLN cc_start: 0.8275 (tt0) cc_final: 0.7978 (tt0) REVERT: A 307 LYS cc_start: 0.8889 (mttt) cc_final: 0.8553 (mtmm) REVERT: A 335 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8057 (m) REVERT: A 358 TYR cc_start: 0.9058 (m-80) cc_final: 0.8692 (m-80) REVERT: B 17 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7873 (tm-30) REVERT: B 219 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7289 (mmp80) REVERT: B 254 ASP cc_start: 0.8048 (t70) cc_final: 0.7639 (t0) REVERT: C 20 LYS cc_start: 0.8282 (ptpt) cc_final: 0.7637 (ptpp) REVERT: N 5 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7708 (mt0) REVERT: N 70 ILE cc_start: 0.8825 (tt) cc_final: 0.8564 (tt) REVERT: N 73 ASP cc_start: 0.7639 (t0) cc_final: 0.7274 (t0) REVERT: N 76 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8231 (mmmm) REVERT: R 92 MET cc_start: 0.8460 (mmm) cc_final: 0.8190 (mmm) REVERT: R 127 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.6590 (m170) REVERT: R 172 LEU cc_start: 0.8509 (mt) cc_final: 0.8115 (mp) REVERT: R 183 VAL cc_start: 0.8681 (t) cc_final: 0.8462 (p) REVERT: R 301 ARG cc_start: 0.7065 (mtm110) cc_final: 0.6832 (mtm-85) outliers start: 33 outliers final: 25 residues processed: 176 average time/residue: 0.2684 time to fit residues: 60.7894 Evaluate side-chains 182 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 32 GLN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8503 Z= 0.184 Angle : 0.478 6.233 11533 Z= 0.248 Chirality : 0.041 0.167 1300 Planarity : 0.003 0.040 1457 Dihedral : 6.318 74.834 1298 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.06 % Allowed : 14.32 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.26), residues: 1031 helix: 2.31 (0.26), residues: 395 sheet: 0.45 (0.32), residues: 219 loop : 0.17 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 281 HIS 0.002 0.001 HIS R 274 PHE 0.027 0.002 PHE R 119 TYR 0.014 0.001 TYR N 60 ARG 0.007 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7610 (mtm180) cc_final: 0.6945 (mtm-85) REVERT: A 23 ASN cc_start: 0.7590 (OUTLIER) cc_final: 0.7196 (t0) REVERT: A 35 GLN cc_start: 0.7564 (tp40) cc_final: 0.6989 (tt0) REVERT: A 211 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8156 (mttp) REVERT: A 213 GLN cc_start: 0.8271 (tt0) cc_final: 0.7972 (tt0) REVERT: A 307 LYS cc_start: 0.8905 (mttt) cc_final: 0.8567 (mtmm) REVERT: A 335 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8085 (m) REVERT: A 358 TYR cc_start: 0.9055 (m-80) cc_final: 0.8689 (m-80) REVERT: B 17 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 78 LYS cc_start: 0.8911 (mmtm) cc_final: 0.8601 (mmtt) REVERT: B 219 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7286 (mmp80) REVERT: B 254 ASP cc_start: 0.8043 (t70) cc_final: 0.7637 (t0) REVERT: C 20 LYS cc_start: 0.8289 (ptpt) cc_final: 0.7638 (ptpp) REVERT: N 5 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7707 (mt0) REVERT: N 70 ILE cc_start: 0.8822 (tt) cc_final: 0.8576 (tt) REVERT: N 73 ASP cc_start: 0.7673 (t0) cc_final: 0.7303 (t0) REVERT: N 76 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8236 (mmmm) REVERT: R 55 VAL cc_start: 0.8209 (m) cc_final: 0.8000 (t) REVERT: R 92 MET cc_start: 0.8483 (mmm) cc_final: 0.8241 (mmm) REVERT: R 127 HIS cc_start: 0.7350 (OUTLIER) cc_final: 0.6624 (m170) REVERT: R 172 LEU cc_start: 0.8496 (mt) cc_final: 0.8129 (mp) REVERT: R 183 VAL cc_start: 0.8683 (t) cc_final: 0.8459 (p) REVERT: R 301 ARG cc_start: 0.7086 (mtm110) cc_final: 0.6842 (mtm-85) outliers start: 36 outliers final: 30 residues processed: 179 average time/residue: 0.2642 time to fit residues: 60.9240 Evaluate side-chains 184 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 299 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 0.0010 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8503 Z= 0.137 Angle : 0.461 6.248 11533 Z= 0.238 Chirality : 0.040 0.178 1300 Planarity : 0.003 0.040 1457 Dihedral : 6.162 78.268 1298 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.16 % Allowed : 15.22 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1031 helix: 2.38 (0.26), residues: 395 sheet: 0.51 (0.32), residues: 219 loop : 0.20 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.002 0.001 HIS R 274 PHE 0.025 0.001 PHE R 119 TYR 0.022 0.001 TYR N 60 ARG 0.007 0.000 ARG A 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7586 (mtm180) cc_final: 0.6920 (mtm-85) REVERT: A 23 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7215 (t0) REVERT: A 35 GLN cc_start: 0.7563 (tp40) cc_final: 0.6962 (tt0) REVERT: A 211 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8130 (mttp) REVERT: A 213 GLN cc_start: 0.8235 (tt0) cc_final: 0.7923 (tt0) REVERT: A 307 LYS cc_start: 0.8888 (mttt) cc_final: 0.8541 (mtmm) REVERT: A 335 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8033 (m) REVERT: A 358 TYR cc_start: 0.9039 (m-80) cc_final: 0.8713 (m-80) REVERT: B 17 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7950 (tm-30) REVERT: B 219 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7293 (mmp80) REVERT: B 254 ASP cc_start: 0.7937 (t70) cc_final: 0.7517 (t0) REVERT: N 5 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7674 (mt0) REVERT: N 70 ILE cc_start: 0.8786 (tt) cc_final: 0.8475 (tt) REVERT: N 73 ASP cc_start: 0.7664 (t0) cc_final: 0.7296 (t0) REVERT: N 76 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8241 (mmmm) REVERT: R 92 MET cc_start: 0.8432 (mmm) cc_final: 0.8186 (mmm) REVERT: R 127 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6704 (m170) REVERT: R 183 VAL cc_start: 0.8669 (t) cc_final: 0.8434 (p) REVERT: R 273 PHE cc_start: 0.8556 (t80) cc_final: 0.8288 (t80) outliers start: 28 outliers final: 24 residues processed: 178 average time/residue: 0.2611 time to fit residues: 59.6480 Evaluate side-chains 180 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 127 HIS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 299 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.163494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.122145 restraints weight = 9735.332| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.32 r_work: 0.3188 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8503 Z= 0.189 Angle : 0.484 6.318 11533 Z= 0.250 Chirality : 0.041 0.175 1300 Planarity : 0.003 0.049 1457 Dihedral : 6.216 79.628 1298 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.61 % Allowed : 14.54 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1031 helix: 2.36 (0.26), residues: 394 sheet: 0.55 (0.32), residues: 219 loop : 0.23 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS R 274 PHE 0.028 0.001 PHE R 119 TYR 0.023 0.001 TYR N 60 ARG 0.009 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2291.24 seconds wall clock time: 42 minutes 9.54 seconds (2529.54 seconds total)