Starting phenix.real_space_refine on Sat Apr 6 19:25:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/04_2024/8j20_35940_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/04_2024/8j20_35940.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/04_2024/8j20_35940_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/04_2024/8j20_35940_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/04_2024/8j20_35940_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/04_2024/8j20_35940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/04_2024/8j20_35940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/04_2024/8j20_35940_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/04_2024/8j20_35940_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.020 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 S 58 5.16 5 Cl 2 4.86 5 C 5634 2.51 5 N 1497 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8832 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1775 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Chain: "C" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1791 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Chain: "D" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2188 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 1 Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'9T4': 1, 'LEA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.04, per 1000 atoms: 0.57 Number of scatterers: 8832 At special positions: 0 Unit cell: (111.28, 110.24, 122.72, 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) Cl 2 17.00 S 58 16.00 O 1641 8.00 N 1497 7.00 C 5634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 267 " distance=2.04 Simple disulfide: pdb=" SG CYS D 88 " - pdb=" SG CYS D 169 " 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: 3.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 13 sheets defined 33.9% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 16 through 35 Processing helix chain 'A' and resid 41 through 47 removed outlier: 4.712A pdb=" N ASN A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'C' and resid 4 through 6 No H-bonds generated for 'chain 'C' and resid 4 through 6' Processing helix chain 'C' and resid 8 through 31 Processing helix chain 'C' and resid 46 through 53 Processing helix chain 'C' and resid 208 through 211 No H-bonds generated for 'chain 'C' and resid 208 through 211' Processing helix chain 'C' and resid 242 through 254 removed outlier: 3.728A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 249 " --> pdb=" O GLU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 removed outlier: 3.596A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 309 removed outlier: 4.029A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 350 Processing helix chain 'D' and resid 14 through 45 removed outlier: 3.707A pdb=" N VAL D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Proline residue: D 30 - end of helix removed outlier: 3.958A pdb=" N VAL D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 72 removed outlier: 3.623A pdb=" N ASP D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Proline residue: D 69 - end of helix Processing helix chain 'D' and resid 85 through 118 Proline residue: D 89 - end of helix removed outlier: 3.522A pdb=" N TYR D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 102 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 104 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 117 " --> pdb=" O ARG D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 129 through 154 removed outlier: 3.736A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 210 removed outlier: 4.213A pdb=" N ILE D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) Proline residue: D 183 - end of helix removed outlier: 3.880A pdb=" N VAL D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Proline residue: D 196 - end of helix Processing helix chain 'D' and resid 217 through 251 removed outlier: 4.236A pdb=" N LEU D 226 " --> pdb=" O ARG D 222 " (cutoff:3.500A) Proline residue: D 240 - end of helix removed outlier: 3.766A pdb=" N TYR D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 279 removed outlier: 3.954A pdb=" N LEU D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Proline residue: D 273 - end of helix removed outlier: 3.584A pdb=" N PHE D 278 " --> pdb=" O LEU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 287 Processing helix chain 'E' and resid 8 through 23 Processing helix chain 'E' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.649A pdb=" N HIS A 102 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP A 94 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS A 100 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 122 through 126 removed outlier: 3.548A pdb=" N ARG A 148 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASN A 136 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 146 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.204A pdb=" N CYS A 160 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL A 169 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 189 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP A 181 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLN A 187 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 209 through 213 removed outlier: 3.651A pdb=" N PHE A 210 " --> pdb=" O TRP A 222 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 231 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP A 223 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS A 229 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 240 through 243 removed outlier: 6.314A pdb=" N GLY A 255 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 243 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 253 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 256 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 273 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP A 265 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLU A 271 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 295 through 299 removed outlier: 3.535A pdb=" N GLY A 317 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP A 309 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG A 315 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 347 through 350 Processing sheet with id= H, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.587A pdb=" N THR B 116 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.867A pdb=" N SER B 158 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 131 through 137 removed outlier: 5.232A pdb=" N ARG B 76 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TRP B 85 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 193 through 198 Processing sheet with id= L, first strand: chain 'B' and resid 281 through 283 removed outlier: 3.541A pdb=" N GLY B 263 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 227 " --> pdb=" O TRP B 214 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU B 216 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU B 225 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 196 through 200 removed outlier: 6.481A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA C 220 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N LEU C 39 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 222 " --> pdb=" O LEU C 39 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1035 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: 2.35 Time building geometry restraints manager: 3.78 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: 1425 1.31 - 1.44: 2509 1.44 - 1.56: 5002 1.56 - 1.69: 2 1.69 - 1.82: 84 Bond restraints: 9022 Sorted by residual: bond pdb=" C26 9T4 D 401 " pdb=" C28 9T4 D 401 " ideal model delta sigma weight residual 1.385 1.529 -0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C27 9T4 D 401 " pdb=" C28 9T4 D 401 " ideal model delta sigma weight residual 1.385 1.529 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C24 9T4 D 401 " pdb=" C27 9T4 D 401 " ideal model delta sigma weight residual 1.384 1.528 -0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" C23 9T4 D 401 " pdb=" C24 9T4 D 401 " ideal model delta sigma weight residual 1.385 1.529 -0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" C23 9T4 D 401 " pdb=" C25 9T4 D 401 " ideal model delta sigma weight residual 1.385 1.524 -0.139 2.00e-02 2.50e+03 4.82e+01 ... (remaining 9017 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.82: 202 106.82 - 113.89: 5055 113.89 - 120.95: 4229 120.95 - 128.01: 2663 128.01 - 135.07: 77 Bond angle restraints: 12226 Sorted by residual: angle pdb=" C TYR B 273 " pdb=" N PRO B 274 " pdb=" CA PRO B 274 " ideal model delta sigma weight residual 119.84 132.52 -12.68 1.25e+00 6.40e-01 1.03e+02 angle pdb=" N TYR B 273 " pdb=" CA TYR B 273 " pdb=" C TYR B 273 " ideal model delta sigma weight residual 109.81 129.78 -19.97 2.21e+00 2.05e-01 8.17e+01 angle pdb=" C PRO B 274 " pdb=" CA PRO B 274 " pdb=" CB PRO B 274 " ideal model delta sigma weight residual 111.56 124.57 -13.01 1.65e+00 3.67e-01 6.22e+01 angle pdb=" C GLU B 272 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " ideal model delta sigma weight residual 121.80 135.07 -13.27 2.44e+00 1.68e-01 2.96e+01 angle pdb=" CA PRO B 274 " pdb=" N PRO B 274 " pdb=" CD PRO B 274 " ideal model delta sigma weight residual 112.00 104.86 7.14 1.40e+00 5.10e-01 2.60e+01 ... (remaining 12221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.59: 4753 23.59 - 47.18: 502 47.18 - 70.77: 62 70.77 - 94.37: 10 94.37 - 117.96: 1 Dihedral angle restraints: 5328 sinusoidal: 2078 harmonic: 3250 Sorted by residual: dihedral pdb=" CA TYR B 273 " pdb=" C TYR B 273 " pdb=" N PRO B 274 " pdb=" CA PRO B 274 " ideal model delta harmonic sigma weight residual 180.00 62.04 117.96 0 5.00e+00 4.00e-02 5.57e+02 dihedral pdb=" C TYR B 273 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " pdb=" CB TYR B 273 " ideal model delta harmonic sigma weight residual -122.60 -150.58 27.98 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" N TYR B 273 " pdb=" C TYR B 273 " pdb=" CA TYR B 273 " pdb=" CB TYR B 273 " ideal model delta harmonic sigma weight residual 122.80 150.30 -27.50 0 2.50e+00 1.60e-01 1.21e+02 ... (remaining 5325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.257: 1380 0.257 - 0.514: 0 0.514 - 0.771: 1 0.771 - 1.028: 0 1.028 - 1.286: 1 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA TYR B 273 " pdb=" N TYR B 273 " pdb=" C TYR B 273 " pdb=" CB TYR B 273 " both_signs ideal model delta sigma weight residual False 2.51 1.22 1.29 2.00e-01 2.50e+01 4.13e+01 chirality pdb=" CA PRO B 274 " pdb=" N PRO B 274 " pdb=" C PRO B 274 " pdb=" CB PRO B 274 " both_signs ideal model delta sigma weight residual False 2.72 2.07 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CG LEU A 201 " pdb=" CB LEU A 201 " pdb=" CD1 LEU A 201 " pdb=" CD2 LEU A 201 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 1379 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 273 " -0.066 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO B 274 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 274 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 274 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 272 " 0.058 5.00e-02 4.00e+02 8.75e-02 1.23e+01 pdb=" N PRO D 273 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 239 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO D 240 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 240 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 240 " -0.026 5.00e-02 4.00e+02 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 685 2.74 - 3.28: 8634 3.28 - 3.82: 14957 3.82 - 4.36: 17078 4.36 - 4.90: 29909 Nonbonded interactions: 71263 Sorted by model distance: nonbonded pdb=" OH TYR B 211 " pdb=" OG SER C 6 " model vdw 2.197 2.440 nonbonded pdb=" OG SER A 342 " pdb=" OD1 ASP A 344 " model vdw 2.206 2.440 nonbonded pdb=" OG SER A 172 " pdb=" OD1 ASP A 174 " model vdw 2.236 2.440 nonbonded pdb=" O SER A 78 " pdb=" OG SER A 78 " model vdw 2.265 2.440 nonbonded pdb=" O LEU D 197 " pdb=" OG SER D 201 " model vdw 2.269 2.440 ... (remaining 71258 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=0.01 max=1.00 mean=0.99 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: 0.810 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: 3.870 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.870 Find NCS groups from input model: 0.230 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 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 : 0.004 0.144 9022 Z= 0.277 Angle : 0.685 19.972 12226 Z= 0.350 Chirality : 0.056 1.286 1382 Planarity : 0.005 0.097 1544 Dihedral : 17.919 117.958 3227 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.43 % Favored : 95.03 % Rotamer: Outliers : 0.62 % Allowed : 35.69 % Favored : 63.68 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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: 0.12 (0.26), residues: 1107 helix: 1.66 (0.28), residues: 355 sheet: 0.71 (0.33), residues: 243 loop : -1.45 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 15 HIS 0.006 0.001 HIS B 205 PHE 0.017 0.001 PHE A 210 TYR 0.011 0.001 TYR D 202 ARG 0.007 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 197 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7726 (mm110) REVERT: A 163 LEU cc_start: 0.7931 (mm) cc_final: 0.7715 (mt) outliers start: 6 outliers final: 3 residues processed: 199 average time/residue: 0.2498 time to fit residues: 65.1256 Evaluate side-chains 195 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 220 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.1980 chunk 46 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9022 Z= 0.209 Angle : 0.607 14.381 12226 Z= 0.302 Chirality : 0.044 0.348 1382 Planarity : 0.004 0.063 1544 Dihedral : 5.731 82.679 1243 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.88 % Favored : 94.67 % Rotamer: Outliers : 4.58 % Allowed : 31.74 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.09 (0.26), residues: 1107 helix: 1.58 (0.28), residues: 374 sheet: 0.55 (0.33), residues: 252 loop : -1.50 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 15 HIS 0.010 0.001 HIS D 14 PHE 0.021 0.001 PHE D 95 TYR 0.013 0.001 TYR D 151 ARG 0.005 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 219 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.6903 (mmp80) cc_final: 0.6674 (mmp80) REVERT: A 72 MET cc_start: 0.6988 (mmt) cc_final: 0.6781 (mmt) REVERT: A 140 ARG cc_start: 0.7163 (mtp85) cc_final: 0.6926 (mmp80) REVERT: A 163 LEU cc_start: 0.8011 (mm) cc_final: 0.7674 (mp) REVERT: A 222 TRP cc_start: 0.8320 (m100) cc_final: 0.7896 (m100) REVERT: A 269 ASP cc_start: 0.7569 (t0) cc_final: 0.7258 (t0) REVERT: A 297 LEU cc_start: 0.8412 (mp) cc_final: 0.8204 (mp) REVERT: A 326 VAL cc_start: 0.8007 (t) cc_final: 0.7754 (p) REVERT: B 70 PHE cc_start: 0.8452 (m-80) cc_final: 0.8248 (m-10) REVERT: B 268 MET cc_start: 0.8118 (ttm) cc_final: 0.7819 (ttm) REVERT: B 269 GLN cc_start: 0.8508 (pp30) cc_final: 0.8237 (pp30) REVERT: B 271 LEU cc_start: 0.7636 (mt) cc_final: 0.7277 (mt) REVERT: C 200 ASP cc_start: 0.7849 (t0) cc_final: 0.7598 (t0) REVERT: C 283 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7940 (mp) REVERT: C 316 THR cc_start: 0.7641 (p) cc_final: 0.7368 (t) REVERT: D 29 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7340 (mt) REVERT: D 231 LEU cc_start: 0.7729 (tt) cc_final: 0.7513 (tt) outliers start: 44 outliers final: 24 residues processed: 241 average time/residue: 0.2653 time to fit residues: 84.7050 Evaluate side-chains 240 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 214 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 226 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 89 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 231 GLN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9022 Z= 0.237 Angle : 0.611 14.165 12226 Z= 0.304 Chirality : 0.044 0.282 1382 Planarity : 0.004 0.052 1544 Dihedral : 5.639 84.307 1239 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.15 % Favored : 94.40 % Rotamer: Outliers : 5.93 % Allowed : 31.22 % Favored : 62.85 % 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: -0.01 (0.26), residues: 1107 helix: 1.47 (0.27), residues: 380 sheet: 0.30 (0.32), residues: 264 loop : -1.48 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 180 HIS 0.004 0.001 HIS A 102 PHE 0.017 0.002 PHE A 210 TYR 0.016 0.002 TYR B 88 ARG 0.004 0.000 ARG D 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 223 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 112 MET cc_start: 0.7407 (ptp) cc_final: 0.7191 (ptp) REVERT: A 135 TYR cc_start: 0.8871 (m-80) cc_final: 0.8350 (m-80) REVERT: A 158 SER cc_start: 0.7119 (OUTLIER) cc_final: 0.6179 (p) REVERT: A 269 ASP cc_start: 0.7638 (t0) cc_final: 0.7248 (t0) REVERT: B 75 VAL cc_start: 0.8883 (t) cc_final: 0.8609 (m) REVERT: B 268 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7951 (ttm) REVERT: C 17 LYS cc_start: 0.8347 (mttm) cc_final: 0.8115 (mmtm) REVERT: C 200 ASP cc_start: 0.7921 (t0) cc_final: 0.7618 (t0) REVERT: C 316 THR cc_start: 0.7724 (p) cc_final: 0.7410 (t) REVERT: D 29 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7129 (mt) outliers start: 57 outliers final: 33 residues processed: 258 average time/residue: 0.2390 time to fit residues: 83.2810 Evaluate side-chains 249 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 213 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.0870 chunk 52 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9022 Z= 0.185 Angle : 0.604 14.922 12226 Z= 0.295 Chirality : 0.043 0.241 1382 Planarity : 0.004 0.054 1544 Dihedral : 5.537 83.833 1239 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.24 % Favored : 94.31 % Rotamer: Outliers : 5.41 % Allowed : 32.36 % Favored : 62.23 % 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: -0.05 (0.26), residues: 1107 helix: 1.41 (0.27), residues: 383 sheet: 0.33 (0.33), residues: 255 loop : -1.49 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 180 HIS 0.003 0.001 HIS B 73 PHE 0.023 0.001 PHE D 95 TYR 0.012 0.001 TYR B 88 ARG 0.008 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 214 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 112 MET cc_start: 0.7403 (ptp) cc_final: 0.7145 (ptp) REVERT: A 135 TYR cc_start: 0.8862 (m-80) cc_final: 0.8417 (m-80) REVERT: A 158 SER cc_start: 0.7020 (OUTLIER) cc_final: 0.6187 (t) REVERT: A 163 LEU cc_start: 0.8053 (mm) cc_final: 0.7820 (mt) REVERT: A 203 LEU cc_start: 0.7818 (tp) cc_final: 0.7577 (tp) REVERT: A 245 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8258 (t80) REVERT: A 269 ASP cc_start: 0.7647 (t0) cc_final: 0.7125 (t0) REVERT: B 75 VAL cc_start: 0.8880 (t) cc_final: 0.8592 (m) REVERT: B 268 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7939 (ttp) REVERT: C 17 LYS cc_start: 0.8335 (mttm) cc_final: 0.8077 (mmtm) REVERT: C 189 PHE cc_start: 0.7574 (p90) cc_final: 0.7122 (p90) REVERT: C 200 ASP cc_start: 0.7927 (t0) cc_final: 0.7622 (t0) REVERT: C 283 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8148 (mp) REVERT: C 316 THR cc_start: 0.7671 (p) cc_final: 0.7377 (t) REVERT: D 29 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7321 (mt) REVERT: D 71 ARG cc_start: 0.6848 (ttp80) cc_final: 0.6332 (ttp-110) outliers start: 52 outliers final: 32 residues processed: 241 average time/residue: 0.2215 time to fit residues: 72.2754 Evaluate side-chains 248 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 0.0170 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN C 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9022 Z= 0.191 Angle : 0.590 15.131 12226 Z= 0.293 Chirality : 0.043 0.271 1382 Planarity : 0.005 0.090 1544 Dihedral : 5.495 83.993 1239 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.33 % Favored : 94.22 % Rotamer: Outliers : 6.45 % Allowed : 31.63 % Favored : 61.91 % 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: -0.10 (0.26), residues: 1107 helix: 1.41 (0.27), residues: 383 sheet: 0.16 (0.32), residues: 254 loop : -1.46 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 180 HIS 0.004 0.001 HIS A 65 PHE 0.019 0.001 PHE D 95 TYR 0.012 0.001 TYR B 88 ARG 0.008 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 215 time to evaluate : 0.940 Fit side-chains REVERT: A 112 MET cc_start: 0.7344 (ptp) cc_final: 0.7109 (ptp) REVERT: A 135 TYR cc_start: 0.8882 (m-80) cc_final: 0.8419 (m-80) REVERT: A 163 LEU cc_start: 0.8045 (mm) cc_final: 0.7819 (mt) REVERT: A 203 LEU cc_start: 0.7986 (tp) cc_final: 0.7741 (tp) REVERT: A 230 ARG cc_start: 0.7525 (mtm180) cc_final: 0.7201 (mtm180) REVERT: A 245 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8251 (t80) REVERT: A 269 ASP cc_start: 0.7701 (t0) cc_final: 0.7175 (t0) REVERT: B 75 VAL cc_start: 0.8890 (t) cc_final: 0.8598 (m) REVERT: B 268 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7946 (ttp) REVERT: C 17 LYS cc_start: 0.8317 (mttm) cc_final: 0.8070 (mmtm) REVERT: C 189 PHE cc_start: 0.7640 (p90) cc_final: 0.7159 (p90) REVERT: C 200 ASP cc_start: 0.7933 (t0) cc_final: 0.7632 (t0) REVERT: C 316 THR cc_start: 0.7676 (p) cc_final: 0.7350 (t) REVERT: D 29 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7269 (mt) REVERT: D 52 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7422 (m) REVERT: D 71 ARG cc_start: 0.6948 (ttp80) cc_final: 0.6470 (ttp-110) REVERT: D 178 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7327 (mt) outliers start: 62 outliers final: 40 residues processed: 246 average time/residue: 0.2304 time to fit residues: 75.9380 Evaluate side-chains 252 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 207 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 107 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.0470 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN C 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9022 Z= 0.154 Angle : 0.574 15.747 12226 Z= 0.283 Chirality : 0.042 0.234 1382 Planarity : 0.004 0.084 1544 Dihedral : 5.397 83.301 1239 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.06 % Favored : 94.49 % Rotamer: Outliers : 6.76 % Allowed : 31.22 % Favored : 62.02 % 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: -0.02 (0.25), residues: 1107 helix: 1.55 (0.27), residues: 377 sheet: 0.20 (0.32), residues: 249 loop : -1.43 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 140 HIS 0.003 0.001 HIS D 245 PHE 0.020 0.001 PHE D 95 TYR 0.011 0.001 TYR D 151 ARG 0.008 0.000 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 209 time to evaluate : 0.926 Fit side-chains REVERT: A 72 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6901 (mmt) REVERT: A 135 TYR cc_start: 0.8870 (m-80) cc_final: 0.8383 (m-80) REVERT: A 230 ARG cc_start: 0.7417 (mtm180) cc_final: 0.7160 (mtm180) REVERT: A 245 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8273 (t80) REVERT: A 269 ASP cc_start: 0.7703 (t0) cc_final: 0.7128 (t0) REVERT: B 75 VAL cc_start: 0.8869 (t) cc_final: 0.8598 (m) REVERT: C 17 LYS cc_start: 0.8291 (mttm) cc_final: 0.8069 (mmtm) REVERT: C 189 PHE cc_start: 0.7666 (p90) cc_final: 0.7094 (p90) REVERT: C 200 ASP cc_start: 0.7927 (t0) cc_final: 0.7662 (t0) REVERT: D 18 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6709 (p90) REVERT: D 29 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7242 (mt) REVERT: D 52 VAL cc_start: 0.7762 (OUTLIER) cc_final: 0.7408 (m) REVERT: D 71 ARG cc_start: 0.6565 (ttp80) cc_final: 0.6324 (ttp-110) outliers start: 65 outliers final: 42 residues processed: 241 average time/residue: 0.2371 time to fit residues: 76.2218 Evaluate side-chains 254 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 207 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS C 331 ASN D 284 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9022 Z= 0.242 Angle : 0.629 15.391 12226 Z= 0.310 Chirality : 0.044 0.255 1382 Planarity : 0.005 0.082 1544 Dihedral : 5.542 85.483 1237 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.69 % Favored : 93.86 % Rotamer: Outliers : 6.24 % Allowed : 32.26 % Favored : 61.50 % 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: -0.14 (0.26), residues: 1107 helix: 1.34 (0.27), residues: 387 sheet: 0.04 (0.32), residues: 262 loop : -1.44 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 180 HIS 0.004 0.001 HIS A 102 PHE 0.022 0.002 PHE D 95 TYR 0.012 0.002 TYR A 96 ARG 0.008 0.000 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 216 time to evaluate : 1.014 Fit side-chains REVERT: A 135 TYR cc_start: 0.8893 (m-80) cc_final: 0.8449 (m-80) REVERT: A 158 SER cc_start: 0.7062 (OUTLIER) cc_final: 0.6109 (t) REVERT: A 203 LEU cc_start: 0.7940 (tp) cc_final: 0.7735 (tp) REVERT: A 230 ARG cc_start: 0.7412 (mtm180) cc_final: 0.7169 (mtm180) REVERT: A 265 ASP cc_start: 0.6978 (t70) cc_final: 0.6714 (t70) REVERT: A 269 ASP cc_start: 0.7725 (t0) cc_final: 0.7164 (t0) REVERT: B 75 VAL cc_start: 0.8893 (t) cc_final: 0.8585 (m) REVERT: C 17 LYS cc_start: 0.8294 (mttm) cc_final: 0.8061 (mmtm) REVERT: C 200 ASP cc_start: 0.8008 (t0) cc_final: 0.7750 (t0) REVERT: D 18 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6762 (p90) REVERT: D 29 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7295 (mt) REVERT: D 52 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7455 (m) REVERT: D 59 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7810 (pt) REVERT: D 126 ARG cc_start: 0.7282 (mtm-85) cc_final: 0.7072 (mtm-85) REVERT: D 182 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7293 (mm) REVERT: D 278 PHE cc_start: 0.6658 (p90) cc_final: 0.6303 (p90) outliers start: 60 outliers final: 43 residues processed: 245 average time/residue: 0.2384 time to fit residues: 77.5578 Evaluate side-chains 260 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 211 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 9 optimal weight: 0.0370 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 93 optimal weight: 0.0470 chunk 99 optimal weight: 2.9990 overall best weight: 0.1556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9022 Z= 0.149 Angle : 0.591 17.182 12226 Z= 0.288 Chirality : 0.041 0.169 1382 Planarity : 0.005 0.094 1544 Dihedral : 5.345 82.883 1237 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.51 % Favored : 94.22 % Rotamer: Outliers : 6.66 % Allowed : 32.99 % Favored : 60.35 % 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: -0.03 (0.26), residues: 1107 helix: 1.51 (0.27), residues: 385 sheet: 0.18 (0.32), residues: 244 loop : -1.44 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 74 HIS 0.004 0.001 HIS D 245 PHE 0.021 0.001 PHE D 95 TYR 0.017 0.001 TYR B 273 ARG 0.016 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 213 time to evaluate : 1.025 Fit side-chains REVERT: A 72 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6832 (mmt) REVERT: A 135 TYR cc_start: 0.8855 (m-80) cc_final: 0.8416 (m-80) REVERT: A 158 SER cc_start: 0.6828 (OUTLIER) cc_final: 0.5556 (t) REVERT: A 166 ASN cc_start: 0.8256 (t0) cc_final: 0.8012 (t160) REVERT: A 269 ASP cc_start: 0.7701 (t0) cc_final: 0.7143 (t0) REVERT: B 75 VAL cc_start: 0.8817 (t) cc_final: 0.8506 (m) REVERT: B 201 LYS cc_start: 0.8253 (ttpp) cc_final: 0.8030 (ttpp) REVERT: C 189 PHE cc_start: 0.7993 (p90) cc_final: 0.7621 (p90) REVERT: C 200 ASP cc_start: 0.7987 (t0) cc_final: 0.7717 (t0) REVERT: C 317 LYS cc_start: 0.7183 (mtmm) cc_final: 0.6860 (ttpt) REVERT: D 18 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6694 (p90) REVERT: D 29 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7065 (mt) REVERT: D 52 VAL cc_start: 0.7740 (p) cc_final: 0.7404 (m) REVERT: D 59 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7803 (pt) REVERT: D 72 MET cc_start: 0.5636 (OUTLIER) cc_final: 0.5253 (tpt) REVERT: D 126 ARG cc_start: 0.7306 (mtm-85) cc_final: 0.7102 (mtm-85) REVERT: D 182 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7141 (mm) REVERT: D 220 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.5781 (mpp-170) REVERT: D 231 LEU cc_start: 0.7855 (tt) cc_final: 0.7477 (tp) REVERT: D 278 PHE cc_start: 0.6583 (p90) cc_final: 0.6240 (p90) outliers start: 64 outliers final: 41 residues processed: 242 average time/residue: 0.2536 time to fit residues: 80.5431 Evaluate side-chains 257 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 208 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN D 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9022 Z= 0.292 Angle : 0.673 15.190 12226 Z= 0.331 Chirality : 0.045 0.214 1382 Planarity : 0.005 0.077 1544 Dihedral : 5.683 86.446 1237 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.14 % Favored : 93.59 % Rotamer: Outliers : 6.04 % Allowed : 33.61 % Favored : 60.35 % 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: -0.24 (0.25), residues: 1107 helix: 1.20 (0.27), residues: 391 sheet: 0.04 (0.31), residues: 262 loop : -1.50 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 180 HIS 0.005 0.001 HIS A 102 PHE 0.034 0.002 PHE B 106 TYR 0.015 0.002 TYR A 96 ARG 0.009 0.001 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 223 time to evaluate : 1.024 Fit side-chains REVERT: A 135 TYR cc_start: 0.8899 (m-80) cc_final: 0.8482 (m-80) REVERT: A 166 ASN cc_start: 0.8263 (t0) cc_final: 0.8045 (t160) REVERT: A 209 LEU cc_start: 0.8162 (mt) cc_final: 0.7892 (mt) REVERT: A 230 ARG cc_start: 0.7414 (mtm180) cc_final: 0.7181 (mtm180) REVERT: A 265 ASP cc_start: 0.6981 (t70) cc_final: 0.6743 (t70) REVERT: A 269 ASP cc_start: 0.7767 (t0) cc_final: 0.7175 (t0) REVERT: B 75 VAL cc_start: 0.8914 (t) cc_final: 0.8609 (m) REVERT: C 17 LYS cc_start: 0.8296 (mmtm) cc_final: 0.8096 (mmtm) REVERT: C 197 LYS cc_start: 0.7881 (mttp) cc_final: 0.7533 (mttp) REVERT: C 200 ASP cc_start: 0.8009 (t0) cc_final: 0.7753 (t0) REVERT: C 308 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6646 (mp0) REVERT: C 317 LYS cc_start: 0.7619 (mtmm) cc_final: 0.7282 (ttmt) REVERT: D 18 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6762 (p90) REVERT: D 29 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7390 (mt) REVERT: D 52 VAL cc_start: 0.7782 (p) cc_final: 0.7455 (m) REVERT: D 59 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7764 (pt) REVERT: D 126 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.7096 (mtm-85) outliers start: 58 outliers final: 41 residues processed: 251 average time/residue: 0.2389 time to fit residues: 79.6012 Evaluate side-chains 256 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 212 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.0070 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.0670 chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9022 Z= 0.179 Angle : 0.629 15.864 12226 Z= 0.306 Chirality : 0.043 0.297 1382 Planarity : 0.004 0.075 1544 Dihedral : 5.519 84.770 1237 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.51 % Favored : 94.13 % Rotamer: Outliers : 4.99 % Allowed : 34.76 % Favored : 60.25 % 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: -0.22 (0.25), residues: 1107 helix: 1.23 (0.27), residues: 391 sheet: 0.09 (0.32), residues: 250 loop : -1.50 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 180 HIS 0.004 0.001 HIS D 245 PHE 0.035 0.002 PHE D 278 TYR 0.012 0.001 TYR D 170 ARG 0.009 0.000 ARG D 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 211 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.7027 (mmp80) REVERT: A 135 TYR cc_start: 0.8865 (m-80) cc_final: 0.8504 (m-80) REVERT: A 166 ASN cc_start: 0.8258 (t0) cc_final: 0.8051 (t160) REVERT: A 269 ASP cc_start: 0.7743 (t0) cc_final: 0.7129 (t0) REVERT: A 294 ARG cc_start: 0.7766 (mmm-85) cc_final: 0.7299 (tpt-90) REVERT: C 17 LYS cc_start: 0.8331 (mmtm) cc_final: 0.8122 (mmtm) REVERT: C 200 ASP cc_start: 0.7991 (t0) cc_final: 0.7748 (t0) REVERT: C 308 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6601 (mp0) REVERT: C 317 LYS cc_start: 0.7452 (mtmm) cc_final: 0.7148 (ttmt) REVERT: D 18 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.6716 (p90) REVERT: D 29 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7367 (mt) REVERT: D 52 VAL cc_start: 0.7765 (p) cc_final: 0.7439 (m) REVERT: D 59 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7748 (pt) REVERT: D 126 ARG cc_start: 0.7291 (mtm-85) cc_final: 0.7087 (mtm-85) REVERT: D 185 ARG cc_start: 0.7277 (ttt180) cc_final: 0.6970 (ttt-90) outliers start: 48 outliers final: 37 residues processed: 236 average time/residue: 0.2416 time to fit residues: 75.8119 Evaluate side-chains 245 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 0.0770 chunk 16 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.151258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130776 restraints weight = 12983.547| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.14 r_work: 0.3495 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9022 Z= 0.243 Angle : 0.668 15.290 12226 Z= 0.324 Chirality : 0.045 0.285 1382 Planarity : 0.005 0.079 1544 Dihedral : 5.638 86.731 1237 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.14 % Favored : 93.59 % Rotamer: Outliers : 5.31 % Allowed : 34.96 % Favored : 59.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1107 helix: 1.16 (0.27), residues: 392 sheet: -0.09 (0.32), residues: 256 loop : -1.50 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 180 HIS 0.004 0.001 HIS D 245 PHE 0.032 0.002 PHE B 106 TYR 0.013 0.002 TYR A 96 ARG 0.009 0.000 ARG D 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2612.97 seconds wall clock time: 48 minutes 3.19 seconds (2883.19 seconds total)