Starting phenix.real_space_refine on Wed Feb 14 01:32:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq4_32699/02_2024/7wq4_32699_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq4_32699/02_2024/7wq4_32699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq4_32699/02_2024/7wq4_32699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq4_32699/02_2024/7wq4_32699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq4_32699/02_2024/7wq4_32699_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq4_32699/02_2024/7wq4_32699_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 53 5.16 5 C 5277 2.51 5 N 1451 2.21 5 O 1509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 184": "NH1" <-> "NH2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8290 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2225 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 12, 'TRANS': 269} Chain breaks: 1 Chain: "L" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 95 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "A" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1927 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} 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: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.90, per 1000 atoms: 0.59 Number of scatterers: 8290 At special positions: 0 Unit cell: (88.218, 97.344, 123.708, 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 53 16.00 O 1509 8.00 N 1451 7.00 C 5277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 175 " distance=2.03 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 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: 3.04 Conformation dependent library (CDL) restraints added in 1.5 seconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 37.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'R' and resid 27 through 51 removed outlier: 3.611A pdb=" N VAL R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 87 Proline residue: R 80 - end of helix Processing helix chain 'R' and resid 96 through 99 No H-bonds generated for 'chain 'R' and resid 96 through 99' Processing helix chain 'R' and resid 101 through 128 removed outlier: 3.720A pdb=" N PHE R 106 " --> pdb=" O HIS R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 163 Proline residue: R 159 - end of helix removed outlier: 4.804A pdb=" N SER R 162 " --> pdb=" O GLY R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 195 Processing helix chain 'R' and resid 197 through 214 Processing helix chain 'R' and resid 225 through 248 Processing helix chain 'R' and resid 250 through 261 Processing helix chain 'R' and resid 268 through 292 removed outlier: 3.696A pdb=" N ASN R 284 " --> pdb=" O VAL R 280 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 297 through 306 removed outlier: 3.760A pdb=" N LYS R 301 " --> pdb=" O LYS R 297 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLY R 302 " --> pdb=" O HIS R 298 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE R 303 " --> pdb=" O PHE R 299 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG R 304 " --> pdb=" O ARG R 300 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR R 305 " --> pdb=" O LYS R 301 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE R 306 " --> pdb=" O GLY R 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 297 through 306' Processing helix chain 'L' and resid 4 through 11 removed outlier: 3.554A pdb=" N GLY L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 30 removed outlier: 3.583A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.407A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 115 through 129 removed outlier: 4.077A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 184 through 202 removed outlier: 3.549A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 242 removed outlier: 4.292A pdb=" N ILE A 227 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.602A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' 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 'G' and resid 12 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'R' and resid 165 through 169 Processing sheet with id= B, first strand: chain 'A' and resid 211 through 215 removed outlier: 7.195A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN A 80 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU A 36 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS A 82 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU A 38 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 84 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N GLY A 40 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL A 86 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.688A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.993A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.939A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.110A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.068A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.608A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.508A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.764A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1050 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: 2.34 Time building geometry restraints manager: 3.33 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: 2702 1.34 - 1.46: 1972 1.46 - 1.58: 3709 1.58 - 1.70: 10 1.70 - 1.81: 74 Bond restraints: 8467 Sorted by residual: bond pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " ideal model delta sigma weight residual 1.332 1.651 -0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 1.332 1.650 -0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" C15 CLR R 402 " pdb=" C16 CLR R 402 " ideal model delta sigma weight residual 1.541 1.708 -0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" C15 CLR R 401 " pdb=" C16 CLR R 401 " ideal model delta sigma weight residual 1.541 1.705 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" C8 CLR R 402 " pdb=" C9 CLR R 402 " ideal model delta sigma weight residual 1.535 1.671 -0.136 2.00e-02 2.50e+03 4.62e+01 ... (remaining 8462 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.22: 234 107.22 - 113.91: 4782 113.91 - 120.60: 3392 120.60 - 127.28: 2988 127.28 - 133.97: 93 Bond angle restraints: 11489 Sorted by residual: angle pdb=" N VAL R 295 " pdb=" CA VAL R 295 " pdb=" C VAL R 295 " ideal model delta sigma weight residual 113.71 106.66 7.05 9.50e-01 1.11e+00 5.51e+01 angle pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " pdb=" C7 CLR R 401 " ideal model delta sigma weight residual 125.11 111.58 13.53 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " pdb=" C7 CLR R 402 " ideal model delta sigma weight residual 125.11 111.81 13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" CA ALA R 170 " pdb=" C ALA R 170 " pdb=" O ALA R 170 " ideal model delta sigma weight residual 122.03 117.50 4.53 1.17e+00 7.31e-01 1.50e+01 angle pdb=" C10 CLR R 401 " pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 122.94 111.81 11.13 3.00e+00 1.11e-01 1.38e+01 ... (remaining 11484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.16: 4849 12.16 - 24.32: 191 24.32 - 36.47: 60 36.47 - 48.63: 26 48.63 - 60.79: 9 Dihedral angle restraints: 5135 sinusoidal: 2094 harmonic: 3041 Sorted by residual: dihedral pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" CB PHE B 234 " pdb=" CG PHE B 234 " ideal model delta sinusoidal sigma weight residual -180.00 -120.16 -59.84 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG R 184 " pdb=" CA ARG R 184 " pdb=" CB ARG R 184 " pdb=" CG ARG R 184 " ideal model delta sinusoidal sigma weight residual -60.00 -117.77 57.77 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CG ARG R 184 " pdb=" CD ARG R 184 " pdb=" NE ARG R 184 " pdb=" CZ ARG R 184 " ideal model delta sinusoidal sigma weight residual 180.00 139.10 40.90 2 1.50e+01 4.44e-03 9.14e+00 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1271 0.110 - 0.221: 27 0.221 - 0.331: 4 0.331 - 0.442: 2 0.442 - 0.552: 2 Chirality restraints: 1306 Sorted by residual: chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.38 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" C13 CLR R 401 " pdb=" C12 CLR R 401 " pdb=" C14 CLR R 401 " pdb=" C17 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.39 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" C9 CLR R 402 " pdb=" C10 CLR R 402 " pdb=" C11 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.45 -2.86 0.42 2.00e-01 2.50e+01 4.35e+00 ... (remaining 1303 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 101 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C VAL R 101 " 0.021 2.00e-02 2.50e+03 pdb=" O VAL R 101 " -0.008 2.00e-02 2.50e+03 pdb=" N HIS R 102 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO B 236 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 158 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO R 159 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 159 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 159 " -0.015 5.00e-02 4.00e+02 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 2 2.10 - 2.80: 2098 2.80 - 3.50: 11036 3.50 - 4.20: 19341 4.20 - 4.90: 34428 Nonbonded interactions: 66905 Sorted by model distance: nonbonded pdb=" OD1 ASN N 35 " pdb=" CB ASP N 50 " model vdw 1.399 3.440 nonbonded pdb=" CG2 VAL R 174 " pdb=" NE2 HIS R 176 " model vdw 2.067 3.540 nonbonded pdb=" O TYR R 129 " pdb=" OG SER R 133 " model vdw 2.247 2.440 nonbonded pdb=" O THR R 191 " pdb=" OG SER R 195 " model vdw 2.250 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.289 2.440 ... (remaining 66900 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: 0.650 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: 0.000 Extract box with map and model: 2.920 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.640 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 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 : 0.007 0.319 8467 Z= 0.511 Angle : 0.615 13.533 11489 Z= 0.339 Chirality : 0.052 0.552 1306 Planarity : 0.003 0.027 1450 Dihedral : 8.519 60.788 3162 Min Nonbonded Distance : 1.399 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.45 % Allowed : 3.38 % Favored : 96.17 % 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: -1.07 (0.24), residues: 1032 helix: 0.15 (0.26), residues: 373 sheet: -0.58 (0.31), residues: 237 loop : -1.48 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS A 209 PHE 0.010 0.001 PHE R 103 TYR 0.005 0.001 TYR N 60 ARG 0.001 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 251 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: R 184 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.4897 (mtp-110) REVERT: A 15 ARG cc_start: 0.6050 (ttt90) cc_final: 0.5842 (ttm-80) REVERT: A 17 LYS cc_start: 0.6310 (mttt) cc_final: 0.5857 (pttp) REVERT: A 69 ILE cc_start: 0.8297 (mt) cc_final: 0.8074 (mm) REVERT: A 75 GLN cc_start: 0.7309 (tt0) cc_final: 0.6941 (tm130) REVERT: A 191 TYR cc_start: 0.7616 (m-10) cc_final: 0.7346 (m-10) REVERT: A 208 ARG cc_start: 0.6356 (mtm-85) cc_final: 0.5995 (tpt90) REVERT: B 44 GLN cc_start: 0.7850 (mt0) cc_final: 0.7582 (mt0) REVERT: B 188 MET cc_start: 0.8239 (mmm) cc_final: 0.8029 (mmm) REVERT: B 197 ARG cc_start: 0.6792 (mtm180) cc_final: 0.6497 (mtp85) REVERT: B 234 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: B 254 ASP cc_start: 0.7784 (p0) cc_final: 0.7549 (p0) REVERT: N 65 LYS cc_start: 0.7321 (mttt) cc_final: 0.6892 (tmtt) REVERT: N 80 TYR cc_start: 0.6848 (m-80) cc_final: 0.6631 (m-80) outliers start: 4 outliers final: 0 residues processed: 255 average time/residue: 1.1915 time to fit residues: 321.7845 Evaluate side-chains 167 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.0570 chunk 77 optimal weight: 0.2980 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 overall best weight: 1.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 55 GLN R 82 GLN R 253 HIS A 52 GLN A 82 HIS A 119 GLN A 244 ASN B 35 ASN B 91 HIS B 176 GLN B 220 GLN B 259 GLN N 77 ASN G 11 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8467 Z= 0.230 Angle : 0.559 8.030 11489 Z= 0.291 Chirality : 0.043 0.155 1306 Planarity : 0.004 0.029 1450 Dihedral : 5.241 52.817 1286 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.72 % Allowed : 14.19 % Favored : 82.09 % 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: -0.17 (0.26), residues: 1032 helix: 0.97 (0.27), residues: 395 sheet: -0.21 (0.32), residues: 224 loop : -1.06 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 332 HIS 0.010 0.002 HIS A 209 PHE 0.018 0.002 PHE B 199 TYR 0.012 0.002 TYR G 40 ARG 0.004 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 0.947 Fit side-chains REVERT: R 88 LEU cc_start: 0.6426 (mt) cc_final: 0.6123 (mt) REVERT: R 122 ASP cc_start: 0.7793 (t70) cc_final: 0.7482 (t70) REVERT: R 166 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7068 (tt0) REVERT: R 298 HIS cc_start: 0.6719 (t70) cc_final: 0.5993 (m-70) REVERT: A 8 GLU cc_start: 0.6266 (mm-30) cc_final: 0.6060 (mm-30) REVERT: A 15 ARG cc_start: 0.6298 (ttt90) cc_final: 0.5999 (ttm-80) REVERT: A 71 GLU cc_start: 0.7521 (tt0) cc_final: 0.6840 (tt0) REVERT: A 73 LYS cc_start: 0.8626 (mttp) cc_final: 0.8003 (mttp) REVERT: A 98 GLN cc_start: 0.8788 (mt0) cc_final: 0.8488 (mt0) REVERT: A 208 ARG cc_start: 0.6774 (mtm-85) cc_final: 0.6069 (tpt90) REVERT: B 57 LYS cc_start: 0.8604 (pttm) cc_final: 0.8228 (pttt) REVERT: B 134 ARG cc_start: 0.6657 (ptm-80) cc_final: 0.5942 (tpm170) REVERT: B 186 ASP cc_start: 0.7843 (m-30) cc_final: 0.7541 (m-30) REVERT: B 188 MET cc_start: 0.8429 (mmm) cc_final: 0.7894 (mmm) REVERT: B 197 ARG cc_start: 0.6973 (mtm180) cc_final: 0.6522 (mtp85) REVERT: B 212 ASP cc_start: 0.7397 (t0) cc_final: 0.7148 (t0) REVERT: B 234 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: B 260 GLU cc_start: 0.7336 (tt0) cc_final: 0.7022 (tt0) REVERT: B 263 THR cc_start: 0.8173 (t) cc_final: 0.7749 (m) REVERT: G 21 MET cc_start: 0.5884 (ttp) cc_final: 0.5646 (ttp) outliers start: 33 outliers final: 14 residues processed: 191 average time/residue: 1.1787 time to fit residues: 239.1778 Evaluate side-chains 148 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 GLN ** R 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 168 GLN A 75 GLN B 155 ASN G 24 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8467 Z= 0.296 Angle : 0.581 9.253 11489 Z= 0.306 Chirality : 0.044 0.164 1306 Planarity : 0.004 0.033 1450 Dihedral : 5.194 55.641 1282 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.95 % Allowed : 15.43 % Favored : 79.62 % 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: 0.20 (0.26), residues: 1032 helix: 1.15 (0.27), residues: 397 sheet: 0.02 (0.32), residues: 230 loop : -0.75 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 332 HIS 0.011 0.002 HIS A 209 PHE 0.016 0.002 PHE B 151 TYR 0.011 0.002 TYR R 86 ARG 0.006 0.001 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 133 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: R 122 ASP cc_start: 0.7859 (t70) cc_final: 0.7400 (t70) REVERT: R 136 LEU cc_start: 0.7534 (tt) cc_final: 0.7195 (tp) REVERT: R 166 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: R 298 HIS cc_start: 0.6757 (t70) cc_final: 0.6230 (m-70) REVERT: A 15 ARG cc_start: 0.6346 (ttt90) cc_final: 0.5907 (ttm-80) REVERT: A 73 LYS cc_start: 0.8608 (mttp) cc_final: 0.8001 (mttt) REVERT: A 208 ARG cc_start: 0.6978 (mtm-85) cc_final: 0.6258 (mmm-85) REVERT: B 29 THR cc_start: 0.7419 (OUTLIER) cc_final: 0.6869 (p) REVERT: B 57 LYS cc_start: 0.8561 (pttm) cc_final: 0.8108 (pttt) REVERT: B 59 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7912 (t80) REVERT: B 188 MET cc_start: 0.8091 (mmm) cc_final: 0.7619 (mmm) REVERT: B 197 ARG cc_start: 0.7184 (mtm180) cc_final: 0.6738 (mtp85) REVERT: B 220 GLN cc_start: 0.7748 (tt0) cc_final: 0.7446 (tt0) REVERT: B 260 GLU cc_start: 0.7656 (tt0) cc_final: 0.7302 (tt0) REVERT: B 263 THR cc_start: 0.8338 (t) cc_final: 0.7880 (m) REVERT: G 37 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7234 (mp) REVERT: G 42 GLU cc_start: 0.7071 (pp20) cc_final: 0.6488 (mm-30) outliers start: 44 outliers final: 17 residues processed: 165 average time/residue: 1.2780 time to fit residues: 224.0097 Evaluate side-chains 148 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 0.0470 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8467 Z= 0.162 Angle : 0.487 7.154 11489 Z= 0.257 Chirality : 0.041 0.164 1306 Planarity : 0.003 0.028 1450 Dihedral : 4.591 56.051 1280 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.83 % Allowed : 18.58 % Favored : 77.59 % 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: 0.58 (0.26), residues: 1032 helix: 1.51 (0.27), residues: 398 sheet: 0.25 (0.31), residues: 235 loop : -0.61 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.010 0.001 PHE A 74 TYR 0.009 0.001 TYR R 160 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 0.892 Fit side-chains REVERT: R 122 ASP cc_start: 0.7751 (t70) cc_final: 0.7271 (t70) REVERT: R 136 LEU cc_start: 0.7472 (tt) cc_final: 0.7165 (tp) REVERT: R 166 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6879 (tt0) REVERT: R 298 HIS cc_start: 0.6705 (t70) cc_final: 0.6150 (m-70) REVERT: A 15 ARG cc_start: 0.6363 (ttt90) cc_final: 0.6149 (ttt-90) REVERT: A 17 LYS cc_start: 0.6865 (mttt) cc_final: 0.6615 (mtmt) REVERT: A 28 GLN cc_start: 0.7310 (mm-40) cc_final: 0.7108 (mm-40) REVERT: A 208 ARG cc_start: 0.6911 (mtm-85) cc_final: 0.6265 (mmm-85) REVERT: B 57 LYS cc_start: 0.8525 (pttm) cc_final: 0.8103 (pttt) REVERT: B 134 ARG cc_start: 0.6524 (ptm-80) cc_final: 0.5743 (tpp-160) REVERT: B 188 MET cc_start: 0.8082 (mmm) cc_final: 0.7588 (mmm) REVERT: B 197 ARG cc_start: 0.7178 (mtm180) cc_final: 0.6823 (mtp85) REVERT: B 214 ARG cc_start: 0.7636 (mmt180) cc_final: 0.7324 (mpp-170) REVERT: B 220 GLN cc_start: 0.7565 (tt0) cc_final: 0.7128 (tt0) REVERT: B 234 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: B 258 ASP cc_start: 0.6759 (t0) cc_final: 0.6455 (t70) REVERT: B 260 GLU cc_start: 0.7545 (tt0) cc_final: 0.7253 (tt0) REVERT: B 263 THR cc_start: 0.8299 (t) cc_final: 0.7917 (m) REVERT: B 329 THR cc_start: 0.8656 (m) cc_final: 0.8431 (t) REVERT: G 37 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7147 (mp) REVERT: G 42 GLU cc_start: 0.7017 (pp20) cc_final: 0.6522 (mm-30) outliers start: 34 outliers final: 19 residues processed: 164 average time/residue: 1.2606 time to fit residues: 219.1484 Evaluate side-chains 148 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 84 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 GLN ** R 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 32 GLN B 35 ASN B 340 ASN G 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8467 Z= 0.175 Angle : 0.489 6.265 11489 Z= 0.259 Chirality : 0.041 0.132 1306 Planarity : 0.003 0.027 1450 Dihedral : 4.628 58.243 1280 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.94 % Allowed : 20.38 % Favored : 75.68 % 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: 0.72 (0.26), residues: 1032 helix: 1.63 (0.27), residues: 397 sheet: 0.36 (0.31), residues: 236 loop : -0.58 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.007 0.001 HIS A 209 PHE 0.011 0.001 PHE B 199 TYR 0.013 0.001 TYR R 129 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: R 122 ASP cc_start: 0.7736 (t70) cc_final: 0.7206 (t70) REVERT: R 136 LEU cc_start: 0.7453 (tt) cc_final: 0.7167 (tp) REVERT: R 166 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: R 298 HIS cc_start: 0.6967 (t70) cc_final: 0.6111 (m-70) REVERT: A 15 ARG cc_start: 0.6366 (ttt90) cc_final: 0.6145 (ttt-90) REVERT: A 17 LYS cc_start: 0.6805 (mttt) cc_final: 0.6599 (mttt) REVERT: A 28 GLN cc_start: 0.7283 (mm-40) cc_final: 0.7069 (mm-40) REVERT: A 51 LYS cc_start: 0.7197 (pptt) cc_final: 0.6943 (mmmt) REVERT: A 82 HIS cc_start: 0.7980 (m170) cc_final: 0.7661 (m170) REVERT: A 208 ARG cc_start: 0.6951 (mtm-85) cc_final: 0.6256 (mmm-85) REVERT: B 29 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.6858 (p) REVERT: B 57 LYS cc_start: 0.8512 (pttm) cc_final: 0.8110 (pttt) REVERT: B 59 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7711 (t80) REVERT: B 134 ARG cc_start: 0.6705 (ptm-80) cc_final: 0.6017 (tpp-160) REVERT: B 155 ASN cc_start: 0.6978 (p0) cc_final: 0.6521 (t0) REVERT: B 197 ARG cc_start: 0.7235 (mtm180) cc_final: 0.6841 (mtp85) REVERT: B 214 ARG cc_start: 0.7540 (mmt180) cc_final: 0.7258 (mpp-170) REVERT: B 234 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: B 260 GLU cc_start: 0.7640 (tt0) cc_final: 0.7276 (tt0) REVERT: B 263 THR cc_start: 0.8345 (t) cc_final: 0.7874 (m) REVERT: B 329 THR cc_start: 0.8670 (m) cc_final: 0.8423 (t) REVERT: G 37 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7172 (mp) REVERT: G 42 GLU cc_start: 0.7016 (pp20) cc_final: 0.6546 (mm-30) outliers start: 35 outliers final: 21 residues processed: 158 average time/residue: 1.3211 time to fit residues: 220.9348 Evaluate side-chains 158 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 0.0020 chunk 56 optimal weight: 4.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 35 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8467 Z= 0.204 Angle : 0.512 6.571 11489 Z= 0.270 Chirality : 0.042 0.135 1306 Planarity : 0.003 0.027 1450 Dihedral : 4.784 57.990 1280 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.62 % Allowed : 19.71 % Favored : 75.68 % 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: 0.62 (0.26), residues: 1032 helix: 1.51 (0.27), residues: 404 sheet: 0.51 (0.32), residues: 225 loop : -0.74 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.007 0.001 HIS A 209 PHE 0.012 0.002 PHE B 151 TYR 0.014 0.001 TYR R 129 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 133 time to evaluate : 0.974 Fit side-chains REVERT: R 122 ASP cc_start: 0.7767 (t70) cc_final: 0.7196 (t70) REVERT: R 136 LEU cc_start: 0.7306 (tt) cc_final: 0.6994 (tp) REVERT: R 166 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6825 (tt0) REVERT: R 200 VAL cc_start: 0.7284 (OUTLIER) cc_final: 0.7057 (p) REVERT: R 298 HIS cc_start: 0.7002 (t70) cc_final: 0.6101 (m-70) REVERT: A 10 LYS cc_start: 0.6872 (mttt) cc_final: 0.6571 (mmtp) REVERT: A 15 ARG cc_start: 0.6386 (ttt90) cc_final: 0.6147 (ttt-90) REVERT: A 28 GLN cc_start: 0.7247 (mm-40) cc_final: 0.7038 (mm-40) REVERT: A 208 ARG cc_start: 0.7014 (mtm-85) cc_final: 0.6290 (mmm-85) REVERT: B 29 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.6821 (p) REVERT: B 32 GLN cc_start: 0.7475 (mt0) cc_final: 0.7244 (mt0) REVERT: B 57 LYS cc_start: 0.8522 (pttm) cc_final: 0.8105 (pttt) REVERT: B 59 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7713 (t80) REVERT: B 134 ARG cc_start: 0.6712 (ptm-80) cc_final: 0.6026 (tpp-160) REVERT: B 155 ASN cc_start: 0.6983 (p0) cc_final: 0.6515 (t0) REVERT: B 197 ARG cc_start: 0.7271 (mtm180) cc_final: 0.6948 (mtp85) REVERT: B 214 ARG cc_start: 0.7565 (mmt180) cc_final: 0.7284 (mpp-170) REVERT: B 234 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: B 260 GLU cc_start: 0.7632 (tt0) cc_final: 0.7253 (tt0) REVERT: B 263 THR cc_start: 0.8341 (t) cc_final: 0.7852 (m) REVERT: B 329 THR cc_start: 0.8686 (m) cc_final: 0.8433 (t) REVERT: G 37 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7195 (mp) REVERT: G 42 GLU cc_start: 0.6995 (pp20) cc_final: 0.6559 (mm-30) outliers start: 41 outliers final: 24 residues processed: 163 average time/residue: 1.2683 time to fit residues: 218.7221 Evaluate side-chains 156 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 61 optimal weight: 0.0770 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 35 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8467 Z= 0.157 Angle : 0.481 5.980 11489 Z= 0.253 Chirality : 0.041 0.132 1306 Planarity : 0.003 0.028 1450 Dihedral : 4.590 55.375 1280 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.05 % Allowed : 20.61 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1032 helix: 1.71 (0.27), residues: 397 sheet: 0.53 (0.32), residues: 230 loop : -0.59 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.011 0.001 PHE B 199 TYR 0.015 0.001 TYR R 129 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 1.018 Fit side-chains REVERT: R 122 ASP cc_start: 0.7729 (t70) cc_final: 0.7150 (t70) REVERT: R 136 LEU cc_start: 0.7290 (tt) cc_final: 0.6980 (tp) REVERT: R 166 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: R 298 HIS cc_start: 0.7013 (t70) cc_final: 0.6060 (m-70) REVERT: A 10 LYS cc_start: 0.6843 (mttt) cc_final: 0.6547 (mmtp) REVERT: A 15 ARG cc_start: 0.6389 (ttt90) cc_final: 0.6171 (ttt-90) REVERT: A 28 GLN cc_start: 0.7222 (mm-40) cc_final: 0.7019 (mm-40) REVERT: A 208 ARG cc_start: 0.6995 (mtm-85) cc_final: 0.6257 (mmm-85) REVERT: B 29 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.6855 (p) REVERT: B 32 GLN cc_start: 0.7445 (mt0) cc_final: 0.7193 (mt0) REVERT: B 57 LYS cc_start: 0.8505 (pttm) cc_final: 0.8082 (pttt) REVERT: B 59 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7524 (t80) REVERT: B 134 ARG cc_start: 0.6629 (ptm-80) cc_final: 0.5998 (tpp-160) REVERT: B 155 ASN cc_start: 0.6979 (p0) cc_final: 0.6482 (t0) REVERT: B 197 ARG cc_start: 0.7149 (mtm180) cc_final: 0.6839 (mtp85) REVERT: B 214 ARG cc_start: 0.7582 (mmt180) cc_final: 0.7235 (mpp-170) REVERT: B 220 GLN cc_start: 0.7487 (tt0) cc_final: 0.7277 (mt0) REVERT: B 234 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: B 260 GLU cc_start: 0.7614 (tt0) cc_final: 0.7261 (tt0) REVERT: B 263 THR cc_start: 0.8348 (t) cc_final: 0.7852 (m) REVERT: B 329 THR cc_start: 0.8645 (m) cc_final: 0.8408 (t) REVERT: G 37 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7151 (mp) REVERT: G 42 GLU cc_start: 0.6966 (pp20) cc_final: 0.6552 (mm-30) outliers start: 36 outliers final: 18 residues processed: 166 average time/residue: 1.3129 time to fit residues: 230.7113 Evaluate side-chains 164 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN R 102 HIS ** R 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 35 ASN B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8467 Z= 0.321 Angle : 0.604 8.985 11489 Z= 0.317 Chirality : 0.045 0.191 1306 Planarity : 0.004 0.033 1450 Dihedral : 5.171 50.937 1280 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.83 % Allowed : 20.95 % Favored : 75.23 % 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: 0.46 (0.26), residues: 1032 helix: 1.38 (0.27), residues: 403 sheet: 0.50 (0.32), residues: 225 loop : -0.87 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 96 HIS 0.011 0.001 HIS A 209 PHE 0.015 0.002 PHE B 151 TYR 0.016 0.002 TYR R 129 ARG 0.007 0.001 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: R 136 LEU cc_start: 0.7295 (tt) cc_final: 0.6959 (tp) REVERT: R 140 ARG cc_start: 0.6416 (ttt180) cc_final: 0.6019 (ttm-80) REVERT: R 166 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6724 (tt0) REVERT: R 298 HIS cc_start: 0.7008 (t70) cc_final: 0.6047 (m-70) REVERT: A 10 LYS cc_start: 0.6884 (mttt) cc_final: 0.6666 (mmtp) REVERT: A 15 ARG cc_start: 0.6332 (ttt90) cc_final: 0.5698 (ttm-80) REVERT: A 82 HIS cc_start: 0.8076 (m170) cc_final: 0.7794 (m170) REVERT: A 208 ARG cc_start: 0.7023 (mtm-85) cc_final: 0.6272 (mmm-85) REVERT: B 29 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.6885 (t) REVERT: B 57 LYS cc_start: 0.8540 (pttm) cc_final: 0.8071 (pttt) REVERT: B 59 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7817 (t80) REVERT: B 155 ASN cc_start: 0.7035 (p0) cc_final: 0.6584 (t0) REVERT: B 172 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6679 (tt0) REVERT: B 197 ARG cc_start: 0.7162 (mtm180) cc_final: 0.6947 (mtp85) REVERT: B 214 ARG cc_start: 0.7687 (mmt180) cc_final: 0.7306 (mpp-170) REVERT: B 220 GLN cc_start: 0.7617 (tt0) cc_final: 0.7328 (mt0) REVERT: B 260 GLU cc_start: 0.7620 (tt0) cc_final: 0.7252 (tt0) REVERT: B 263 THR cc_start: 0.8389 (t) cc_final: 0.7847 (m) REVERT: B 329 THR cc_start: 0.8724 (m) cc_final: 0.8453 (t) REVERT: G 37 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7268 (mp) REVERT: G 42 GLU cc_start: 0.7105 (pp20) cc_final: 0.6639 (mm-30) outliers start: 34 outliers final: 20 residues processed: 161 average time/residue: 1.2915 time to fit residues: 219.9075 Evaluate side-chains 155 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 75 GLN B 35 ASN B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8467 Z= 0.148 Angle : 0.493 9.402 11489 Z= 0.257 Chirality : 0.041 0.132 1306 Planarity : 0.003 0.032 1450 Dihedral : 4.676 50.495 1280 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.93 % Allowed : 22.07 % Favored : 75.00 % 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: 0.72 (0.26), residues: 1032 helix: 1.66 (0.27), residues: 402 sheet: 0.52 (0.32), residues: 230 loop : -0.73 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.011 0.001 PHE B 199 TYR 0.017 0.001 TYR R 129 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: R 136 LEU cc_start: 0.7267 (tt) cc_final: 0.6959 (tp) REVERT: R 166 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6773 (tt0) REVERT: R 298 HIS cc_start: 0.7073 (t70) cc_final: 0.6080 (m-70) REVERT: A 10 LYS cc_start: 0.6849 (mttt) cc_final: 0.6497 (mmtm) REVERT: A 15 ARG cc_start: 0.6375 (ttt90) cc_final: 0.6104 (ttt-90) REVERT: A 208 ARG cc_start: 0.6929 (mtm-85) cc_final: 0.6220 (mmm-85) REVERT: B 29 THR cc_start: 0.7404 (OUTLIER) cc_final: 0.6880 (t) REVERT: B 57 LYS cc_start: 0.8517 (pttm) cc_final: 0.8097 (pttt) REVERT: B 59 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7429 (t80) REVERT: B 134 ARG cc_start: 0.6741 (ptm-80) cc_final: 0.6025 (tpp-160) REVERT: B 155 ASN cc_start: 0.6992 (p0) cc_final: 0.6546 (t0) REVERT: B 172 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6625 (tt0) REVERT: B 214 ARG cc_start: 0.7610 (mmt180) cc_final: 0.7272 (mpp-170) REVERT: B 220 GLN cc_start: 0.7492 (tt0) cc_final: 0.7226 (tt0) REVERT: B 234 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: B 260 GLU cc_start: 0.7555 (tt0) cc_final: 0.7281 (tt0) REVERT: B 263 THR cc_start: 0.8318 (t) cc_final: 0.7901 (m) REVERT: B 329 THR cc_start: 0.8642 (m) cc_final: 0.8306 (p) REVERT: N 59 SER cc_start: 0.8814 (t) cc_final: 0.8491 (m) REVERT: G 37 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7143 (mp) REVERT: G 42 GLU cc_start: 0.6941 (pp20) cc_final: 0.6552 (mm-30) outliers start: 26 outliers final: 12 residues processed: 159 average time/residue: 1.3505 time to fit residues: 227.1422 Evaluate side-chains 152 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 0.0020 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8467 Z= 0.175 Angle : 0.510 9.754 11489 Z= 0.266 Chirality : 0.041 0.131 1306 Planarity : 0.003 0.033 1450 Dihedral : 4.669 52.770 1280 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.03 % Allowed : 23.09 % Favored : 74.89 % 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: 0.78 (0.26), residues: 1032 helix: 1.71 (0.27), residues: 402 sheet: 0.55 (0.32), residues: 230 loop : -0.70 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.012 0.001 PHE B 199 TYR 0.017 0.001 TYR R 129 ARG 0.007 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: R 136 LEU cc_start: 0.7223 (tt) cc_final: 0.6913 (tp) REVERT: R 166 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6743 (tt0) REVERT: R 298 HIS cc_start: 0.7070 (t70) cc_final: 0.6075 (m-70) REVERT: A 10 LYS cc_start: 0.6844 (mttt) cc_final: 0.6635 (mmtp) REVERT: A 15 ARG cc_start: 0.6384 (ttt90) cc_final: 0.6138 (ttt-90) REVERT: A 208 ARG cc_start: 0.6885 (mtm-85) cc_final: 0.6210 (mmm-85) REVERT: B 29 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.6948 (t) REVERT: B 57 LYS cc_start: 0.8518 (pttm) cc_final: 0.8085 (pttt) REVERT: B 59 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7617 (t80) REVERT: B 134 ARG cc_start: 0.6770 (ptm-80) cc_final: 0.6041 (tpp-160) REVERT: B 155 ASN cc_start: 0.6994 (p0) cc_final: 0.6553 (t0) REVERT: B 197 ARG cc_start: 0.6784 (mtp85) cc_final: 0.6284 (mtp85) REVERT: B 214 ARG cc_start: 0.7488 (mmt180) cc_final: 0.7198 (mpp-170) REVERT: B 260 GLU cc_start: 0.7472 (tt0) cc_final: 0.7263 (tt0) REVERT: B 263 THR cc_start: 0.8331 (t) cc_final: 0.7942 (m) REVERT: B 329 THR cc_start: 0.8665 (m) cc_final: 0.8407 (t) REVERT: N 59 SER cc_start: 0.8828 (t) cc_final: 0.8502 (m) REVERT: G 37 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7184 (mp) REVERT: G 42 GLU cc_start: 0.7089 (pp20) cc_final: 0.6631 (mm-30) outliers start: 18 outliers final: 14 residues processed: 149 average time/residue: 1.4634 time to fit residues: 230.0580 Evaluate side-chains 149 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.0870 chunk 33 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122495 restraints weight = 8826.105| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.92 r_work: 0.3324 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8467 Z= 0.134 Angle : 0.476 9.767 11489 Z= 0.248 Chirality : 0.040 0.134 1306 Planarity : 0.003 0.031 1450 Dihedral : 4.410 52.869 1280 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.14 % Allowed : 22.75 % Favored : 75.11 % 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: 0.95 (0.26), residues: 1032 helix: 1.88 (0.27), residues: 402 sheet: 0.59 (0.33), residues: 229 loop : -0.62 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.011 0.001 PHE B 199 TYR 0.016 0.001 TYR R 129 ARG 0.007 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4023.68 seconds wall clock time: 71 minutes 42.05 seconds (4302.05 seconds total)