Starting phenix.real_space_refine on Wed Sep 17 14:53:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2f_63584/09_2025/9m2f_63584.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2f_63584/09_2025/9m2f_63584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m2f_63584/09_2025/9m2f_63584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2f_63584/09_2025/9m2f_63584.map" model { file = "/net/cci-nas-00/data/ceres_data/9m2f_63584/09_2025/9m2f_63584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2f_63584/09_2025/9m2f_63584.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.012 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 68 5.16 5 C 5683 2.51 5 N 1533 2.21 5 O 1651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8935 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 51 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1811 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2259 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 3, 'HIS:plan': 2, 'TRP:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 74 Chain: "S" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1759 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 2.29, per 1000 atoms: 0.26 Number of scatterers: 8935 At special positions: 0 Unit cell: (95.63, 115.34, 127.02, 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 68 16.00 O 1651 8.00 N 1533 7.00 C 5683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 353.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 35.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.666A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.914A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.880A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.810A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.075A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 71 Processing helix chain 'R' and resid 76 through 95 removed outlier: 4.607A pdb=" N ILE R 82 " --> pdb=" O THR R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 106 removed outlier: 4.527A pdb=" N ILE R 106 " --> pdb=" O VAL R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 147 removed outlier: 4.556A pdb=" N MET R 118 " --> pdb=" O ALA R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 174 removed outlier: 4.096A pdb=" N TRP R 166 " --> pdb=" O ILE R 162 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 226 Processing helix chain 'R' and resid 226 through 243 Processing helix chain 'R' and resid 266 through 295 removed outlier: 3.530A pdb=" N TRP R 283 " --> pdb=" O PHE R 279 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 301 through 330 removed outlier: 4.567A pdb=" N THR R 307 " --> pdb=" O LEU R 303 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE R 311 " --> pdb=" O THR R 307 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 4.029A pdb=" N ASN R 321 " --> pdb=" O LEU R 317 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER R 322 " --> pdb=" O ALA R 318 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) Proline residue: R 326 - end of helix Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.974A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.897A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.565A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.609A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.784A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.660A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.847A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 5.842A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.696A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.588A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.801A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.018A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.018A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.102A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 160 434 hydrogen bonds defined for protein. 1218 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: 1.45 Time building geometry restraints manager: 1.07 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: 2891 1.34 - 1.46: 2176 1.46 - 1.58: 3951 1.58 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 9119 Sorted by residual: bond pdb=" CB PRO S 148 " pdb=" CG PRO S 148 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.57e+00 bond pdb=" CB ASN B 237 " pdb=" CG ASN B 237 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.39e+00 bond pdb=" CG PRO B 39 " pdb=" CD PRO B 39 " ideal model delta sigma weight residual 1.503 1.543 -0.040 3.40e-02 8.65e+02 1.38e+00 bond pdb=" CG1 ILE R 162 " pdb=" CD1 ILE R 162 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.38e+00 bond pdb=" CB GLN B 13 " pdb=" CG GLN B 13 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 ... (remaining 9114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 12167 2.33 - 4.66: 156 4.66 - 6.99: 30 6.99 - 9.33: 6 9.33 - 11.66: 1 Bond angle restraints: 12360 Sorted by residual: angle pdb=" N VAL A 201 " pdb=" CA VAL A 201 " pdb=" C VAL A 201 " ideal model delta sigma weight residual 112.17 108.69 3.48 9.50e-01 1.11e+00 1.34e+01 angle pdb=" C TYR R 225 " pdb=" N LEU R 226 " pdb=" CA LEU R 226 " ideal model delta sigma weight residual 122.46 115.93 6.53 1.80e+00 3.09e-01 1.32e+01 angle pdb=" CA GLU A 28 " pdb=" CB GLU A 28 " pdb=" CG GLU A 28 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA LEU R 90 " pdb=" CB LEU R 90 " pdb=" CG LEU R 90 " ideal model delta sigma weight residual 116.30 127.96 -11.66 3.50e+00 8.16e-02 1.11e+01 angle pdb=" CA GLY B 115 " pdb=" C GLY B 115 " pdb=" N GLY B 116 " ideal model delta sigma weight residual 114.58 117.25 -2.67 8.60e-01 1.35e+00 9.61e+00 ... (remaining 12355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4597 17.86 - 35.72: 637 35.72 - 53.58: 143 53.58 - 71.44: 24 71.44 - 89.30: 10 Dihedral angle restraints: 5411 sinusoidal: 2055 harmonic: 3356 Sorted by residual: dihedral pdb=" CB CYS R 116 " pdb=" SG CYS R 116 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual 93.00 152.61 -59.61 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CA SER R 40 " pdb=" C SER R 40 " pdb=" N PRO R 41 " pdb=" CA PRO R 41 " ideal model delta harmonic sigma weight residual -180.00 -158.67 -21.33 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1058 0.046 - 0.093: 294 0.093 - 0.139: 61 0.139 - 0.186: 1 0.186 - 0.232: 2 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CG LEU R 90 " pdb=" CB LEU R 90 " pdb=" CD1 LEU R 90 " pdb=" CD2 LEU R 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 1413 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " -0.038 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO S 236 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 235 " 0.017 2.00e-02 2.50e+03 1.39e-02 3.85e+00 pdb=" CG TYR S 235 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR S 235 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR S 235 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR S 235 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 235 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR S 235 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR S 235 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 316 " -0.013 2.00e-02 2.50e+03 1.06e-02 2.81e+00 pdb=" CG TRP R 316 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP R 316 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 316 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 316 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 316 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 316 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 316 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 316 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 316 " -0.004 2.00e-02 2.50e+03 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 133 2.64 - 3.20: 8129 3.20 - 3.77: 14170 3.77 - 4.33: 19038 4.33 - 4.90: 31796 Nonbonded interactions: 73266 Sorted by model distance: nonbonded pdb=" OG SER A 6 " pdb=" OD1 ASP A 9 " model vdw 2.072 3.040 nonbonded pdb=" O VAL A 342 " pdb=" ND2 ASN A 346 " model vdw 2.126 3.120 nonbonded pdb=" O PHE R 319 " pdb=" OG SER R 322 " model vdw 2.183 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.198 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.226 3.040 ... (remaining 73261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.200 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.830 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 9121 Z= 0.178 Angle : 0.687 11.658 12362 Z= 0.365 Chirality : 0.042 0.232 1416 Planarity : 0.004 0.057 1562 Dihedral : 17.255 89.301 3238 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.31 % Allowed : 31.10 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.26), residues: 1139 helix: 1.34 (0.29), residues: 365 sheet: -0.06 (0.30), residues: 277 loop : -1.54 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 13 TYR 0.034 0.002 TYR S 235 PHE 0.008 0.001 PHE R 81 TRP 0.028 0.002 TRP R 316 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9119) covalent geometry : angle 0.68686 (12360) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.57413 ( 2) hydrogen bonds : bond 0.08589 ( 428) hydrogen bonds : angle 5.65241 ( 1218) Misc. bond : bond 0.10102 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 209 GLU cc_start: 0.7966 (tp30) cc_final: 0.7681 (tp30) REVERT: R 212 MET cc_start: 0.4159 (mmt) cc_final: 0.3709 (mmt) REVERT: R 274 MET cc_start: 0.6693 (tpp) cc_final: 0.6330 (tmt) REVERT: R 334 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6781 (mm-30) outliers start: 3 outliers final: 3 residues processed: 195 average time/residue: 0.5797 time to fit residues: 120.7095 Evaluate side-chains 179 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 296 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.141584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091946 restraints weight = 14826.138| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.89 r_work: 0.3143 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9121 Z= 0.166 Angle : 0.633 9.297 12362 Z= 0.325 Chirality : 0.044 0.236 1416 Planarity : 0.004 0.058 1562 Dihedral : 5.808 128.761 1250 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.29 % Allowed : 30.89 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.26), residues: 1139 helix: 1.51 (0.29), residues: 364 sheet: -0.17 (0.30), residues: 276 loop : -1.49 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 13 TYR 0.032 0.001 TYR S 235 PHE 0.010 0.001 PHE B 253 TRP 0.017 0.001 TRP R 316 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9119) covalent geometry : angle 0.63349 (12360) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.29296 ( 2) hydrogen bonds : bond 0.03892 ( 428) hydrogen bonds : angle 5.03305 ( 1218) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8825 (tp30) cc_final: 0.8157 (tp30) REVERT: B 13 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8556 (pt0) REVERT: B 17 GLN cc_start: 0.8340 (tt0) cc_final: 0.7874 (tm-30) REVERT: G 22 GLU cc_start: 0.8138 (tp30) cc_final: 0.7888 (tp30) REVERT: A 32 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7448 (mmt180) REVERT: R 85 LEU cc_start: 0.8578 (tm) cc_final: 0.8251 (mp) REVERT: R 118 MET cc_start: 0.4471 (OUTLIER) cc_final: 0.3980 (ptp) REVERT: R 132 PHE cc_start: 0.8289 (m-80) cc_final: 0.8073 (m-80) REVERT: R 212 MET cc_start: 0.4691 (mmt) cc_final: 0.4108 (mmt) REVERT: R 271 MET cc_start: 0.5365 (mmm) cc_final: 0.4790 (mmm) REVERT: R 274 MET cc_start: 0.6067 (tpp) cc_final: 0.5750 (tmt) REVERT: R 334 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7004 (mm-30) REVERT: S 235 TYR cc_start: 0.6655 (OUTLIER) cc_final: 0.6161 (t80) outliers start: 41 outliers final: 17 residues processed: 218 average time/residue: 0.5242 time to fit residues: 122.3229 Evaluate side-chains 193 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 82 ILE Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 216 TYR Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 333 ASN Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.141381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.091759 restraints weight = 14780.257| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.88 r_work: 0.3175 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9121 Z= 0.152 Angle : 0.619 9.365 12362 Z= 0.316 Chirality : 0.043 0.231 1416 Planarity : 0.004 0.055 1562 Dihedral : 4.452 29.280 1247 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.38 % Rotamer: Outliers : 6.07 % Allowed : 29.74 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.26), residues: 1139 helix: 1.51 (0.29), residues: 364 sheet: -0.05 (0.30), residues: 274 loop : -1.46 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 160 TYR 0.034 0.001 TYR S 235 PHE 0.009 0.001 PHE B 253 TRP 0.018 0.001 TRP R 287 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9119) covalent geometry : angle 0.61913 (12360) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.38722 ( 2) hydrogen bonds : bond 0.03691 ( 428) hydrogen bonds : angle 4.89986 ( 1218) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 185 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8886 (tp30) cc_final: 0.8104 (tp30) REVERT: B 13 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8574 (pt0) REVERT: G 62 ARG cc_start: 0.7729 (ptp-170) cc_final: 0.7324 (ptp-170) REVERT: L 6 GLN cc_start: 0.8502 (tp40) cc_final: 0.7355 (pp30) REVERT: R 55 LEU cc_start: 0.8946 (pp) cc_final: 0.8735 (mm) REVERT: R 80 MET cc_start: 0.7675 (ptt) cc_final: 0.7423 (mpp) REVERT: R 212 MET cc_start: 0.4275 (mmt) cc_final: 0.3821 (mmt) REVERT: R 271 MET cc_start: 0.5563 (mmm) cc_final: 0.4989 (mmm) REVERT: R 274 MET cc_start: 0.6108 (tpp) cc_final: 0.5782 (tmt) REVERT: R 334 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6961 (mm-30) REVERT: S 160 ARG cc_start: 0.8519 (mtp85) cc_final: 0.8061 (ttp-110) REVERT: S 235 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.6254 (t80) outliers start: 58 outliers final: 27 residues processed: 225 average time/residue: 0.4938 time to fit residues: 119.5553 Evaluate side-chains 201 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 216 TYR Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 322 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.139732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.090019 restraints weight = 15006.943| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.89 r_work: 0.3147 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9121 Z= 0.189 Angle : 0.643 8.980 12362 Z= 0.327 Chirality : 0.044 0.242 1416 Planarity : 0.004 0.056 1562 Dihedral : 4.504 29.471 1247 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.41 % Favored : 93.50 % Rotamer: Outliers : 6.07 % Allowed : 30.89 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.26), residues: 1139 helix: 1.58 (0.29), residues: 367 sheet: -0.07 (0.30), residues: 279 loop : -1.48 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 160 TYR 0.036 0.002 TYR S 235 PHE 0.012 0.001 PHE B 253 TRP 0.026 0.002 TRP R 287 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9119) covalent geometry : angle 0.64326 (12360) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.21238 ( 2) hydrogen bonds : bond 0.03798 ( 428) hydrogen bonds : angle 4.89228 ( 1218) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8905 (tp30) cc_final: 0.8472 (tp30) REVERT: B 130 GLU cc_start: 0.8944 (mp0) cc_final: 0.8739 (mp0) REVERT: B 237 ASN cc_start: 0.8819 (t0) cc_final: 0.8576 (t0) REVERT: A 271 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7472 (pttm) REVERT: R 80 MET cc_start: 0.7673 (ptt) cc_final: 0.7413 (mpp) REVERT: R 117 LYS cc_start: 0.5542 (OUTLIER) cc_final: 0.4896 (tppt) REVERT: R 176 SER cc_start: 0.4620 (OUTLIER) cc_final: 0.4364 (m) REVERT: R 212 MET cc_start: 0.4066 (mmt) cc_final: 0.3391 (mmt) REVERT: R 216 TYR cc_start: 0.3326 (OUTLIER) cc_final: 0.2590 (t80) REVERT: R 271 MET cc_start: 0.5693 (mmm) cc_final: 0.5177 (mmm) REVERT: R 274 MET cc_start: 0.6027 (tpp) cc_final: 0.5724 (tmt) REVERT: R 334 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6963 (mm-30) REVERT: S 138 ILE cc_start: 0.8115 (mm) cc_final: 0.7864 (mm) REVERT: S 160 ARG cc_start: 0.8516 (mtp85) cc_final: 0.8066 (ttp-110) REVERT: S 222 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8076 (pm20) REVERT: S 235 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.6261 (t80) outliers start: 58 outliers final: 27 residues processed: 219 average time/residue: 0.5390 time to fit residues: 126.3851 Evaluate side-chains 207 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 216 TYR Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 322 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.141027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.091619 restraints weight = 14936.908| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.89 r_work: 0.3174 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9121 Z= 0.139 Angle : 0.646 10.623 12362 Z= 0.322 Chirality : 0.043 0.213 1416 Planarity : 0.004 0.054 1562 Dihedral : 4.453 28.934 1247 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 5.55 % Allowed : 32.25 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.26), residues: 1139 helix: 1.54 (0.29), residues: 366 sheet: -0.04 (0.30), residues: 273 loop : -1.46 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 13 TYR 0.034 0.001 TYR S 235 PHE 0.013 0.001 PHE L 8 TRP 0.030 0.002 TRP R 287 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9119) covalent geometry : angle 0.64573 (12360) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.47401 ( 2) hydrogen bonds : bond 0.03590 ( 428) hydrogen bonds : angle 4.83507 ( 1218) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8920 (tp30) cc_final: 0.8108 (tp30) REVERT: B 13 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8521 (pp30) REVERT: B 17 GLN cc_start: 0.8418 (tt0) cc_final: 0.7925 (tm-30) REVERT: B 130 GLU cc_start: 0.8953 (mp0) cc_final: 0.8734 (mp0) REVERT: B 237 ASN cc_start: 0.8745 (t0) cc_final: 0.8511 (t0) REVERT: B 264 TYR cc_start: 0.9022 (m-80) cc_final: 0.8542 (m-80) REVERT: A 271 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7487 (pttm) REVERT: A 302 TYR cc_start: 0.8196 (t80) cc_final: 0.7928 (t80) REVERT: R 80 MET cc_start: 0.7646 (ptt) cc_final: 0.6751 (ptp) REVERT: R 117 LYS cc_start: 0.5546 (OUTLIER) cc_final: 0.4945 (tppt) REVERT: R 140 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8600 (tm-30) REVERT: R 176 SER cc_start: 0.4554 (OUTLIER) cc_final: 0.4280 (m) REVERT: R 212 MET cc_start: 0.3851 (mmt) cc_final: 0.3169 (mmt) REVERT: R 216 TYR cc_start: 0.3158 (OUTLIER) cc_final: 0.2288 (t80) REVERT: R 271 MET cc_start: 0.5696 (mmm) cc_final: 0.5179 (mmm) REVERT: R 274 MET cc_start: 0.6085 (tpp) cc_final: 0.5768 (tmt) REVERT: S 65 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.8917 (ttpt) REVERT: S 138 ILE cc_start: 0.8070 (mm) cc_final: 0.7838 (mm) REVERT: S 160 ARG cc_start: 0.8540 (mtp85) cc_final: 0.8113 (ttp-110) REVERT: S 235 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.6241 (t80) outliers start: 53 outliers final: 30 residues processed: 226 average time/residue: 0.5391 time to fit residues: 130.7487 Evaluate side-chains 213 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 216 TYR Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 322 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 109 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.143062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093141 restraints weight = 14800.606| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.99 r_work: 0.3176 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9121 Z= 0.120 Angle : 0.627 9.472 12362 Z= 0.315 Chirality : 0.043 0.205 1416 Planarity : 0.004 0.058 1562 Dihedral : 4.354 30.131 1247 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.88 % Favored : 94.03 % Rotamer: Outliers : 5.45 % Allowed : 32.36 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.26), residues: 1139 helix: 1.55 (0.28), residues: 365 sheet: 0.20 (0.30), residues: 280 loop : -1.50 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 13 TYR 0.031 0.001 TYR S 235 PHE 0.008 0.001 PHE B 151 TRP 0.029 0.002 TRP R 287 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9119) covalent geometry : angle 0.62715 (12360) SS BOND : bond 0.00198 ( 1) SS BOND : angle 0.54828 ( 2) hydrogen bonds : bond 0.03440 ( 428) hydrogen bonds : angle 4.78609 ( 1218) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8921 (tp30) cc_final: 0.8140 (tp30) REVERT: B 13 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8471 (pp30) REVERT: B 17 GLN cc_start: 0.8391 (tt0) cc_final: 0.7895 (tm-30) REVERT: B 130 GLU cc_start: 0.8926 (mp0) cc_final: 0.8661 (mp0) REVERT: B 155 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8562 (t0) REVERT: B 264 TYR cc_start: 0.8940 (m-80) cc_final: 0.8436 (m-80) REVERT: A 32 ARG cc_start: 0.7644 (mtt-85) cc_final: 0.7375 (mtt-85) REVERT: A 312 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8786 (mmmt) REVERT: R 55 LEU cc_start: 0.8966 (pp) cc_final: 0.8721 (mm) REVERT: R 80 MET cc_start: 0.7561 (ptt) cc_final: 0.6773 (ptp) REVERT: R 112 ASP cc_start: 0.4868 (OUTLIER) cc_final: 0.4512 (m-30) REVERT: R 117 LYS cc_start: 0.5573 (OUTLIER) cc_final: 0.4960 (tppt) REVERT: R 140 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8614 (tm-30) REVERT: R 212 MET cc_start: 0.3827 (mmt) cc_final: 0.2876 (mmt) REVERT: R 216 TYR cc_start: 0.3111 (OUTLIER) cc_final: 0.2141 (t80) REVERT: R 271 MET cc_start: 0.5722 (mmm) cc_final: 0.5233 (mmm) REVERT: R 274 MET cc_start: 0.5896 (tpp) cc_final: 0.5622 (tmt) REVERT: S 65 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.8865 (ttpt) REVERT: S 93 MET cc_start: 0.8745 (tpt) cc_final: 0.8337 (tpt) REVERT: S 138 ILE cc_start: 0.7960 (mm) cc_final: 0.7747 (mm) REVERT: S 160 ARG cc_start: 0.8500 (mtp85) cc_final: 0.8002 (ttp-110) REVERT: S 235 TYR cc_start: 0.6403 (OUTLIER) cc_final: 0.6047 (t80) outliers start: 52 outliers final: 32 residues processed: 238 average time/residue: 0.5288 time to fit residues: 135.1203 Evaluate side-chains 218 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 216 TYR Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 315 HIS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN R 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.137568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087822 restraints weight = 14941.550| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.86 r_work: 0.3106 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 9121 Z= 0.281 Angle : 0.718 10.442 12362 Z= 0.366 Chirality : 0.047 0.276 1416 Planarity : 0.004 0.056 1562 Dihedral : 4.610 29.535 1245 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.85 % Favored : 93.06 % Rotamer: Outliers : 5.24 % Allowed : 33.09 % Favored : 61.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.25), residues: 1139 helix: 1.46 (0.28), residues: 368 sheet: -0.14 (0.30), residues: 278 loop : -1.53 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 13 TYR 0.042 0.002 TYR S 235 PHE 0.017 0.002 PHE B 253 TRP 0.035 0.002 TRP R 287 HIS 0.004 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00658 ( 9119) covalent geometry : angle 0.71785 (12360) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.20391 ( 2) hydrogen bonds : bond 0.04074 ( 428) hydrogen bonds : angle 4.98609 ( 1218) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8925 (tp30) cc_final: 0.8120 (tp30) REVERT: B 13 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8496 (pp30) REVERT: B 30 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7759 (tm) REVERT: B 130 GLU cc_start: 0.9003 (mp0) cc_final: 0.8738 (mp0) REVERT: B 172 GLU cc_start: 0.8831 (tp30) cc_final: 0.8571 (tp30) REVERT: A 261 ASP cc_start: 0.7855 (t70) cc_final: 0.7367 (t70) REVERT: A 271 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7493 (pttm) REVERT: A 302 TYR cc_start: 0.8209 (t80) cc_final: 0.7877 (t80) REVERT: R 80 MET cc_start: 0.7607 (ptt) cc_final: 0.7400 (mpt) REVERT: R 85 LEU cc_start: 0.8443 (tm) cc_final: 0.8192 (mp) REVERT: R 117 LYS cc_start: 0.5553 (OUTLIER) cc_final: 0.4917 (tppt) REVERT: R 207 TRP cc_start: 0.6652 (t-100) cc_final: 0.6376 (t-100) REVERT: R 212 MET cc_start: 0.3188 (mmt) cc_final: 0.2665 (mmt) REVERT: R 216 TYR cc_start: 0.3512 (OUTLIER) cc_final: 0.2406 (t80) REVERT: R 225 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.4705 (t80) REVERT: R 229 LEU cc_start: 0.6552 (mm) cc_final: 0.6317 (mm) REVERT: R 271 MET cc_start: 0.5675 (mmm) cc_final: 0.5172 (mmm) REVERT: R 274 MET cc_start: 0.6078 (tpp) cc_final: 0.5786 (tmt) REVERT: S 138 ILE cc_start: 0.8184 (mm) cc_final: 0.7934 (mm) REVERT: S 220 GLU cc_start: 0.8622 (pm20) cc_final: 0.8165 (pm20) REVERT: S 235 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6364 (t80) outliers start: 50 outliers final: 30 residues processed: 212 average time/residue: 0.5672 time to fit residues: 128.4788 Evaluate side-chains 206 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 216 TYR Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 315 HIS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 44 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 0.0270 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 ASN S 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.141234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.091976 restraints weight = 14807.104| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.86 r_work: 0.3174 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9121 Z= 0.136 Angle : 0.699 17.677 12362 Z= 0.345 Chirality : 0.044 0.219 1416 Planarity : 0.004 0.053 1562 Dihedral : 4.494 31.721 1245 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.06 % Favored : 93.85 % Rotamer: Outliers : 3.77 % Allowed : 35.71 % Favored : 60.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.25), residues: 1139 helix: 1.48 (0.28), residues: 359 sheet: 0.08 (0.31), residues: 261 loop : -1.45 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 160 TYR 0.034 0.001 TYR S 235 PHE 0.010 0.001 PHE R 46 TRP 0.038 0.002 TRP R 316 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9119) covalent geometry : angle 0.69886 (12360) SS BOND : bond 0.00184 ( 1) SS BOND : angle 0.45569 ( 2) hydrogen bonds : bond 0.03611 ( 428) hydrogen bonds : angle 4.95203 ( 1218) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8936 (tp30) cc_final: 0.8141 (tp30) REVERT: B 13 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8477 (pp30) REVERT: B 130 GLU cc_start: 0.8984 (mp0) cc_final: 0.8740 (mp0) REVERT: B 264 TYR cc_start: 0.9018 (m-80) cc_final: 0.8518 (m-80) REVERT: A 32 ARG cc_start: 0.7734 (mtt-85) cc_final: 0.7503 (mtt-85) REVERT: A 271 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7369 (pttm) REVERT: R 80 MET cc_start: 0.7627 (ptt) cc_final: 0.7282 (mpp) REVERT: R 112 ASP cc_start: 0.5368 (OUTLIER) cc_final: 0.4377 (m-30) REVERT: R 117 LYS cc_start: 0.5522 (OUTLIER) cc_final: 0.4929 (tppt) REVERT: R 140 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8581 (tm-30) REVERT: R 207 TRP cc_start: 0.6712 (t-100) cc_final: 0.6477 (t-100) REVERT: R 212 MET cc_start: 0.3256 (mmt) cc_final: 0.2692 (mmt) REVERT: R 216 TYR cc_start: 0.3385 (OUTLIER) cc_final: 0.2287 (t80) REVERT: R 225 TYR cc_start: 0.6293 (OUTLIER) cc_final: 0.4681 (t80) REVERT: R 229 LEU cc_start: 0.6506 (mm) cc_final: 0.6278 (mm) REVERT: R 271 MET cc_start: 0.5724 (mmm) cc_final: 0.5237 (mmm) REVERT: R 274 MET cc_start: 0.6049 (tpp) cc_final: 0.5759 (tmt) REVERT: S 160 ARG cc_start: 0.8401 (mtp85) cc_final: 0.7886 (ttp-110) REVERT: S 235 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.6110 (t80) outliers start: 36 outliers final: 24 residues processed: 206 average time/residue: 0.5665 time to fit residues: 124.8634 Evaluate side-chains 207 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 216 TYR Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 315 HIS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 10 optimal weight: 0.0670 chunk 61 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.138737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.089373 restraints weight = 14731.903| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.84 r_work: 0.3130 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9121 Z= 0.221 Angle : 0.748 15.795 12362 Z= 0.371 Chirality : 0.047 0.250 1416 Planarity : 0.004 0.057 1562 Dihedral : 4.597 33.462 1245 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.46 % Favored : 92.45 % Rotamer: Outliers : 4.50 % Allowed : 34.76 % Favored : 60.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.25), residues: 1139 helix: 1.34 (0.28), residues: 369 sheet: -0.17 (0.30), residues: 277 loop : -1.52 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 160 TYR 0.038 0.002 TYR S 235 PHE 0.013 0.001 PHE B 253 TRP 0.044 0.002 TRP R 316 HIS 0.003 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 9119) covalent geometry : angle 0.74823 (12360) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.76470 ( 2) hydrogen bonds : bond 0.03900 ( 428) hydrogen bonds : angle 5.01200 ( 1218) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8935 (tp30) cc_final: 0.8128 (tp30) REVERT: B 13 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8471 (pp30) REVERT: B 30 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7718 (tm) REVERT: B 130 GLU cc_start: 0.8998 (mp0) cc_final: 0.8728 (mp0) REVERT: B 172 GLU cc_start: 0.8829 (tp30) cc_final: 0.8560 (tp30) REVERT: B 237 ASN cc_start: 0.8857 (t0) cc_final: 0.8631 (t0) REVERT: A 261 ASP cc_start: 0.7810 (t70) cc_final: 0.7312 (t70) REVERT: A 271 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7502 (pttm) REVERT: R 55 LEU cc_start: 0.8977 (pp) cc_final: 0.8736 (mm) REVERT: R 80 MET cc_start: 0.7636 (ptt) cc_final: 0.7388 (mpt) REVERT: R 117 LYS cc_start: 0.5526 (OUTLIER) cc_final: 0.4922 (tppt) REVERT: R 140 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8668 (tm-30) REVERT: R 207 TRP cc_start: 0.6700 (t-100) cc_final: 0.6478 (t-100) REVERT: R 212 MET cc_start: 0.3463 (mmt) cc_final: 0.2871 (mmt) REVERT: R 216 TYR cc_start: 0.3429 (OUTLIER) cc_final: 0.2405 (t80) REVERT: R 225 TYR cc_start: 0.6328 (OUTLIER) cc_final: 0.4761 (t80) REVERT: R 229 LEU cc_start: 0.6510 (mm) cc_final: 0.6297 (mm) REVERT: R 271 MET cc_start: 0.5666 (mmm) cc_final: 0.5183 (mmm) REVERT: R 274 MET cc_start: 0.6006 (tpp) cc_final: 0.5747 (tmt) REVERT: S 160 ARG cc_start: 0.8369 (mtp85) cc_final: 0.7864 (ttp-110) REVERT: S 220 GLU cc_start: 0.8625 (pm20) cc_final: 0.8166 (pm20) REVERT: S 235 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.6346 (t80) outliers start: 43 outliers final: 26 residues processed: 212 average time/residue: 0.5561 time to fit residues: 125.9111 Evaluate side-chains 208 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 216 TYR Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 315 HIS Chi-restraints excluded: chain R residue 322 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.0050 chunk 110 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN R 61 ASN S 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.141966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.092820 restraints weight = 14815.968| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.87 r_work: 0.3191 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9121 Z= 0.135 Angle : 0.725 14.997 12362 Z= 0.356 Chirality : 0.045 0.215 1416 Planarity : 0.004 0.054 1562 Dihedral : 4.483 34.339 1245 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.23 % Favored : 93.68 % Rotamer: Outliers : 3.25 % Allowed : 36.13 % Favored : 60.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.25), residues: 1139 helix: 1.19 (0.28), residues: 367 sheet: 0.01 (0.30), residues: 266 loop : -1.53 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 160 TYR 0.034 0.001 TYR S 235 PHE 0.010 0.001 PHE R 46 TRP 0.051 0.002 TRP R 316 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9119) covalent geometry : angle 0.72474 (12360) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.36513 ( 2) hydrogen bonds : bond 0.03630 ( 428) hydrogen bonds : angle 4.97149 ( 1218) Misc. bond : bond 0.00012 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8944 (tp30) cc_final: 0.8151 (tp30) REVERT: B 13 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8539 (pp30) REVERT: B 30 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7629 (tm) REVERT: B 130 GLU cc_start: 0.8992 (mp0) cc_final: 0.8687 (mp0) REVERT: B 262 MET cc_start: 0.8583 (ttp) cc_final: 0.8317 (ttt) REVERT: B 264 TYR cc_start: 0.8977 (m-80) cc_final: 0.8481 (m-80) REVERT: A 271 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7403 (pttm) REVERT: R 55 LEU cc_start: 0.8993 (pp) cc_final: 0.8764 (mm) REVERT: R 117 LYS cc_start: 0.5526 (OUTLIER) cc_final: 0.4990 (tppt) REVERT: R 140 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8599 (tm-30) REVERT: R 207 TRP cc_start: 0.6732 (t-100) cc_final: 0.6287 (t-100) REVERT: R 212 MET cc_start: 0.3493 (mmt) cc_final: 0.3257 (mmt) REVERT: R 216 TYR cc_start: 0.3268 (OUTLIER) cc_final: 0.2300 (t80) REVERT: R 225 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.4676 (t80) REVERT: R 271 MET cc_start: 0.5603 (mmm) cc_final: 0.5161 (mmm) REVERT: R 274 MET cc_start: 0.5855 (tpp) cc_final: 0.5575 (tmt) REVERT: S 160 ARG cc_start: 0.8390 (mtp85) cc_final: 0.7893 (ttp-110) REVERT: S 235 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.6043 (t80) outliers start: 31 outliers final: 23 residues processed: 204 average time/residue: 0.5576 time to fit residues: 121.5781 Evaluate side-chains 203 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 216 TYR Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 315 HIS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.138602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089146 restraints weight = 14843.347| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.86 r_work: 0.3130 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9121 Z= 0.233 Angle : 0.767 14.299 12362 Z= 0.383 Chirality : 0.048 0.246 1416 Planarity : 0.004 0.058 1562 Dihedral : 4.670 35.137 1245 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.11 % Favored : 92.80 % Rotamer: Outliers : 3.87 % Allowed : 35.50 % Favored : 60.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.25), residues: 1139 helix: 1.19 (0.28), residues: 363 sheet: -0.19 (0.30), residues: 273 loop : -1.57 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 160 TYR 0.039 0.002 TYR S 235 PHE 0.012 0.001 PHE B 253 TRP 0.056 0.002 TRP R 316 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 9119) covalent geometry : angle 0.76684 (12360) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.76926 ( 2) hydrogen bonds : bond 0.03936 ( 428) hydrogen bonds : angle 5.04655 ( 1218) Misc. bond : bond 0.00030 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3882.65 seconds wall clock time: 67 minutes 6.61 seconds (4026.61 seconds total)