Starting phenix.real_space_refine on Tue Sep 24 01:21:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rp5_24612/09_2024/7rp5_24612.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rp5_24612/09_2024/7rp5_24612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rp5_24612/09_2024/7rp5_24612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rp5_24612/09_2024/7rp5_24612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rp5_24612/09_2024/7rp5_24612.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rp5_24612/09_2024/7rp5_24612.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.034 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 40 5.16 5 C 4333 2.51 5 N 1085 2.21 5 O 1120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6578 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3303 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 423} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3275 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 420} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 5.41, per 1000 atoms: 0.82 Number of scatterers: 6578 At special positions: 0 Unit cell: (72.312, 86.984, 115.28, 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 40 16.00 O 1120 8.00 N 1085 7.00 C 4333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 1.0 seconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 76.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.708A pdb=" N ASP A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 71 removed outlier: 3.545A pdb=" N LEU A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 87 through 99 removed outlier: 3.727A pdb=" N LEU A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 133 through 141 removed outlier: 4.044A pdb=" N LEU A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 164 removed outlier: 3.937A pdb=" N THR A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.549A pdb=" N ARG A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.924A pdb=" N ILE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 removed outlier: 3.802A pdb=" N PHE A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 269 removed outlier: 3.701A pdb=" N TYR A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.174A pdb=" N ASP A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 removed outlier: 3.711A pdb=" N TRP A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 326 removed outlier: 3.556A pdb=" N ALA A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 removed outlier: 3.960A pdb=" N THR A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 379 removed outlier: 3.606A pdb=" N VAL A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 388 through 402 removed outlier: 4.003A pdb=" N ALA A 392 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 removed outlier: 3.899A pdb=" N ILE A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 439 removed outlier: 3.775A pdb=" N THR A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 461 removed outlier: 4.058A pdb=" N LEU A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLN A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 removed outlier: 4.101A pdb=" N GLU B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 49 removed outlier: 4.108A pdb=" N LEU B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLY B 47 " --> pdb=" O GLY B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 59 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 68 through 72 removed outlier: 3.818A pdb=" N THR B 71 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 72 " --> pdb=" O VAL B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 68 through 72' Processing helix chain 'B' and resid 74 through 99 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 127 through 140 removed outlier: 3.900A pdb=" N PHE B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 166 removed outlier: 4.057A pdb=" N LEU B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 190 removed outlier: 3.533A pdb=" N LEU B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 203 removed outlier: 4.322A pdb=" N ILE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.882A pdb=" N PHE B 208 " --> pdb=" O ARG B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 231 Processing helix chain 'B' and resid 251 through 266 removed outlier: 4.099A pdb=" N TYR B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 281 removed outlier: 5.523A pdb=" N VAL B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 309 removed outlier: 4.208A pdb=" N LEU B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 326 removed outlier: 3.890A pdb=" N GLY B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 347 Processing helix chain 'B' and resid 356 through 379 removed outlier: 3.811A pdb=" N VAL B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 402 removed outlier: 4.305A pdb=" N MET B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 421 through 439 removed outlier: 3.684A pdb=" N MET B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 426 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN B 437 " --> pdb=" O THR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 460 removed outlier: 4.351A pdb=" N LEU B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1236 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: 1.64 Time building geometry restraints manager: 1.93 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: 2056 1.34 - 1.46: 1186 1.46 - 1.57: 3406 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6722 Sorted by residual: bond pdb=" CA ARG B 147 " pdb=" CB ARG B 147 " ideal model delta sigma weight residual 1.524 1.550 -0.026 1.27e-02 6.20e+03 4.11e+00 bond pdb=" N ASN A 270 " pdb=" CA ASN A 270 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.45e+00 bond pdb=" C ILE A 109 " pdb=" N PRO A 110 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.25e-02 6.40e+03 2.84e+00 bond pdb=" C LEU A 423 " pdb=" N PRO A 424 " ideal model delta sigma weight residual 1.336 1.354 -0.019 1.23e-02 6.61e+03 2.28e+00 bond pdb=" CG1 ILE A 200 " pdb=" CD1 ILE A 200 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.12e+00 ... (remaining 6717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 8913 2.80 - 5.60: 176 5.60 - 8.40: 36 8.40 - 11.20: 8 11.20 - 13.99: 2 Bond angle restraints: 9135 Sorted by residual: angle pdb=" N GLU B 148 " pdb=" CA GLU B 148 " pdb=" C GLU B 148 " ideal model delta sigma weight residual 114.75 106.91 7.84 1.26e+00 6.30e-01 3.87e+01 angle pdb=" N ASN B 270 " pdb=" CA ASN B 270 " pdb=" C ASN B 270 " ideal model delta sigma weight residual 114.75 107.14 7.61 1.26e+00 6.30e-01 3.65e+01 angle pdb=" CA ARG B 147 " pdb=" CB ARG B 147 " pdb=" CG ARG B 147 " ideal model delta sigma weight residual 114.10 122.43 -8.33 2.00e+00 2.50e-01 1.73e+01 angle pdb=" CA LEU B 60 " pdb=" CB LEU B 60 " pdb=" CG LEU B 60 " ideal model delta sigma weight residual 116.30 130.29 -13.99 3.50e+00 8.16e-02 1.60e+01 angle pdb=" C PHE A 166 " pdb=" N ARG A 167 " pdb=" CA ARG A 167 " ideal model delta sigma weight residual 122.82 128.39 -5.57 1.42e+00 4.96e-01 1.54e+01 ... (remaining 9130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 3435 17.87 - 35.74: 368 35.74 - 53.62: 73 53.62 - 71.49: 5 71.49 - 89.36: 2 Dihedral angle restraints: 3883 sinusoidal: 1446 harmonic: 2437 Sorted by residual: dihedral pdb=" CA ARG B 147 " pdb=" C ARG B 147 " pdb=" N GLU B 148 " pdb=" CA GLU B 148 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ASN A 270 " pdb=" C ASN A 270 " pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta harmonic sigma weight residual 180.00 155.33 24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY B 47 " pdb=" C GLY B 47 " pdb=" N LEU B 48 " pdb=" CA LEU B 48 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 3880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 722 0.050 - 0.100: 286 0.100 - 0.149: 62 0.149 - 0.199: 6 0.199 - 0.249: 6 Chirality restraints: 1082 Sorted by residual: chirality pdb=" CA THR B 31 " pdb=" N THR B 31 " pdb=" C THR B 31 " pdb=" CB THR B 31 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB ILE A 109 " pdb=" CA ILE A 109 " pdb=" CG1 ILE A 109 " pdb=" CG2 ILE A 109 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CG LEU A 145 " pdb=" CB LEU A 145 " pdb=" CD1 LEU A 145 " pdb=" CD2 LEU A 145 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1079 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 147 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C ARG B 147 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG B 147 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU B 148 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 149 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO A 150 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 149 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO B 150 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " -0.031 5.00e-02 4.00e+02 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2265 2.86 - 3.37: 6278 3.37 - 3.88: 10998 3.88 - 4.39: 12097 4.39 - 4.90: 21118 Nonbonded interactions: 52756 Sorted by model distance: nonbonded pdb=" OH TYR B 94 " pdb=" OG SER B 350 " model vdw 2.346 3.040 nonbonded pdb=" OD2 ASP B 54 " pdb=" NH2 ARG B 147 " model vdw 2.361 3.120 nonbonded pdb=" OE1 GLU A 111 " pdb=" NH1 ARG A 120 " model vdw 2.386 3.120 nonbonded pdb=" O ALA B 58 " pdb=" ND2 ASN B 62 " model vdw 2.394 3.120 nonbonded pdb=" O THR A 312 " pdb=" NE ARG A 340 " model vdw 2.400 3.120 ... (remaining 52751 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 460)) selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.470 Find NCS groups from input model: 0.400 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.005 0.063 6722 Z= 0.313 Angle : 1.009 13.994 9135 Z= 0.524 Chirality : 0.055 0.249 1082 Planarity : 0.007 0.067 1145 Dihedral : 14.743 89.359 2345 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.46 % Allowed : 10.77 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.74 (0.20), residues: 879 helix: -2.76 (0.14), residues: 645 sheet: None (None), residues: 0 loop : -3.67 (0.29), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 125 HIS 0.004 0.001 HIS A 284 PHE 0.014 0.002 PHE A 348 TYR 0.016 0.002 TYR A 94 ARG 0.002 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8225 (mmtt) cc_final: 0.6778 (tptp) REVERT: A 126 ARG cc_start: 0.7443 (mtm-85) cc_final: 0.7173 (ptp-170) REVERT: A 171 ASP cc_start: 0.7933 (t0) cc_final: 0.7676 (t0) REVERT: A 245 SER cc_start: 0.9066 (t) cc_final: 0.8655 (p) REVERT: A 246 ASP cc_start: 0.8251 (p0) cc_final: 0.8002 (p0) REVERT: A 291 TRP cc_start: 0.8347 (t60) cc_final: 0.7902 (t60) REVERT: A 342 ILE cc_start: 0.9090 (tt) cc_final: 0.8722 (tp) REVERT: B 38 MET cc_start: 0.7855 (mmt) cc_final: 0.7548 (mmt) REVERT: B 85 CYS cc_start: 0.7598 (p) cc_final: 0.6972 (t) REVERT: B 164 ASP cc_start: 0.7632 (t0) cc_final: 0.6716 (t0) REVERT: B 205 ARG cc_start: 0.7425 (ttp-110) cc_final: 0.7176 (ttp80) REVERT: B 224 MET cc_start: 0.8570 (tpp) cc_final: 0.7978 (mmt) REVERT: B 373 MET cc_start: 0.7622 (mmm) cc_final: 0.7408 (mtp) outliers start: 3 outliers final: 1 residues processed: 161 average time/residue: 0.1917 time to fit residues: 40.3844 Evaluate side-chains 118 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 6722 Z= 0.421 Angle : 0.780 8.709 9135 Z= 0.382 Chirality : 0.045 0.167 1082 Planarity : 0.006 0.047 1145 Dihedral : 5.964 47.119 934 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.79 % Allowed : 17.45 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.26), residues: 879 helix: -0.99 (0.19), residues: 655 sheet: None (None), residues: 0 loop : -3.44 (0.32), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 125 HIS 0.003 0.001 HIS B 284 PHE 0.017 0.002 PHE B 328 TYR 0.014 0.002 TYR B 100 ARG 0.005 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.728 Fit side-chains REVERT: A 29 ASP cc_start: 0.8303 (m-30) cc_final: 0.8023 (m-30) REVERT: A 55 LYS cc_start: 0.8281 (mmtt) cc_final: 0.6948 (tptp) REVERT: A 91 MET cc_start: 0.6822 (mtm) cc_final: 0.6301 (tmm) REVERT: A 164 ASP cc_start: 0.8075 (t0) cc_final: 0.7613 (t0) REVERT: A 171 ASP cc_start: 0.8119 (t0) cc_final: 0.7890 (t0) REVERT: A 271 LYS cc_start: 0.8240 (tttt) cc_final: 0.7649 (ttmt) REVERT: A 290 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7787 (mttm) REVERT: A 360 MET cc_start: 0.7795 (mtt) cc_final: 0.7498 (mtt) REVERT: A 456 GLN cc_start: 0.7608 (tt0) cc_final: 0.7370 (tt0) REVERT: B 38 MET cc_start: 0.8161 (mmt) cc_final: 0.7927 (mmt) REVERT: B 164 ASP cc_start: 0.8058 (t0) cc_final: 0.7442 (t0) REVERT: B 205 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: B 305 LEU cc_start: 0.8601 (tp) cc_final: 0.8351 (tp) REVERT: B 373 MET cc_start: 0.7752 (mmm) cc_final: 0.7534 (mtp) outliers start: 25 outliers final: 16 residues processed: 142 average time/residue: 0.1528 time to fit residues: 30.2156 Evaluate side-chains 125 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 319 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 0.0670 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN B 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6722 Z= 0.183 Angle : 0.643 9.126 9135 Z= 0.310 Chirality : 0.041 0.160 1082 Planarity : 0.004 0.043 1145 Dihedral : 5.358 46.027 934 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.43 % Allowed : 22.15 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.29), residues: 879 helix: -0.04 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -2.99 (0.35), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 125 HIS 0.001 0.000 HIS A 284 PHE 0.019 0.001 PHE A 166 TYR 0.008 0.001 TYR B 229 ARG 0.002 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.727 Fit side-chains REVERT: A 29 ASP cc_start: 0.8373 (m-30) cc_final: 0.8148 (m-30) REVERT: A 55 LYS cc_start: 0.8217 (mmtt) cc_final: 0.6951 (tptp) REVERT: A 91 MET cc_start: 0.6646 (mtm) cc_final: 0.6224 (tmm) REVERT: A 164 ASP cc_start: 0.8004 (t0) cc_final: 0.7640 (t0) REVERT: A 171 ASP cc_start: 0.8014 (t0) cc_final: 0.7640 (t0) REVERT: A 271 LYS cc_start: 0.8115 (tttt) cc_final: 0.7540 (ttmt) REVERT: A 290 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7726 (mttm) REVERT: A 342 ILE cc_start: 0.9194 (tt) cc_final: 0.8890 (tt) REVERT: A 360 MET cc_start: 0.7712 (mtt) cc_final: 0.7365 (mtt) REVERT: A 401 SER cc_start: 0.9461 (t) cc_final: 0.9224 (t) REVERT: B 38 MET cc_start: 0.8019 (mmt) cc_final: 0.7653 (mmt) REVERT: B 77 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7791 (tt) REVERT: B 164 ASP cc_start: 0.8048 (t0) cc_final: 0.7414 (t0) REVERT: B 205 ARG cc_start: 0.7588 (ttp-110) cc_final: 0.7215 (ttp80) REVERT: B 373 MET cc_start: 0.7859 (mmm) cc_final: 0.7540 (mtp) outliers start: 16 outliers final: 12 residues processed: 131 average time/residue: 0.1535 time to fit residues: 28.1339 Evaluate side-chains 122 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 357 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6722 Z= 0.208 Angle : 0.644 9.476 9135 Z= 0.308 Chirality : 0.041 0.154 1082 Planarity : 0.004 0.042 1145 Dihedral : 5.113 43.991 934 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.55 % Allowed : 21.85 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.29), residues: 879 helix: 0.40 (0.22), residues: 639 sheet: None (None), residues: 0 loop : -2.68 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 125 HIS 0.001 0.000 HIS A 284 PHE 0.010 0.001 PHE B 317 TYR 0.007 0.001 TYR B 229 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 1.227 Fit side-chains REVERT: A 29 ASP cc_start: 0.8343 (m-30) cc_final: 0.8060 (m-30) REVERT: A 55 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7012 (tptp) REVERT: A 91 MET cc_start: 0.6693 (mtm) cc_final: 0.6231 (tmm) REVERT: A 164 ASP cc_start: 0.7987 (t0) cc_final: 0.7551 (t0) REVERT: A 171 ASP cc_start: 0.7995 (t0) cc_final: 0.7644 (t0) REVERT: A 271 LYS cc_start: 0.8005 (tttt) cc_final: 0.7600 (ttmt) REVERT: A 290 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7739 (mttm) REVERT: A 342 ILE cc_start: 0.9198 (tt) cc_final: 0.8899 (tt) REVERT: A 360 MET cc_start: 0.7744 (mtt) cc_final: 0.7456 (mtt) REVERT: B 38 MET cc_start: 0.8015 (mmt) cc_final: 0.7609 (mmt) REVERT: B 77 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7857 (tt) REVERT: B 164 ASP cc_start: 0.8079 (t0) cc_final: 0.7489 (t0) REVERT: B 205 ARG cc_start: 0.7607 (ttp-110) cc_final: 0.7229 (ttp80) REVERT: B 274 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7910 (mm) REVERT: B 305 LEU cc_start: 0.8442 (tp) cc_final: 0.8136 (tp) REVERT: B 373 MET cc_start: 0.7829 (mmm) cc_final: 0.7555 (mtp) outliers start: 30 outliers final: 18 residues processed: 139 average time/residue: 0.1602 time to fit residues: 31.5365 Evaluate side-chains 130 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 63 optimal weight: 0.0570 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 0.0570 chunk 58 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6722 Z= 0.163 Angle : 0.621 9.716 9135 Z= 0.295 Chirality : 0.040 0.154 1082 Planarity : 0.004 0.042 1145 Dihedral : 4.730 35.412 934 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.64 % Allowed : 23.22 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.30), residues: 879 helix: 0.67 (0.22), residues: 642 sheet: None (None), residues: 0 loop : -2.62 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 125 HIS 0.001 0.000 HIS A 284 PHE 0.008 0.001 PHE B 307 TYR 0.008 0.001 TYR B 210 ARG 0.002 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 0.724 Fit side-chains REVERT: A 29 ASP cc_start: 0.8334 (m-30) cc_final: 0.8081 (m-30) REVERT: A 55 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7024 (tptp) REVERT: A 91 MET cc_start: 0.6692 (mtm) cc_final: 0.6249 (tmm) REVERT: A 136 LEU cc_start: 0.9071 (tt) cc_final: 0.8858 (tp) REVERT: A 143 MET cc_start: 0.7287 (tpp) cc_final: 0.7061 (tpp) REVERT: A 164 ASP cc_start: 0.8054 (t0) cc_final: 0.7456 (t0) REVERT: A 171 ASP cc_start: 0.7832 (t0) cc_final: 0.7514 (t0) REVERT: A 271 LYS cc_start: 0.7931 (tttt) cc_final: 0.7591 (ttmt) REVERT: A 290 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7713 (mttm) REVERT: A 342 ILE cc_start: 0.9142 (tt) cc_final: 0.8850 (tt) REVERT: A 360 MET cc_start: 0.7645 (mtt) cc_final: 0.7344 (mtt) REVERT: B 38 MET cc_start: 0.7895 (mmt) cc_final: 0.7498 (mmt) REVERT: B 77 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7823 (tt) REVERT: B 164 ASP cc_start: 0.8100 (t0) cc_final: 0.7522 (t0) REVERT: B 205 ARG cc_start: 0.7566 (ttp-110) cc_final: 0.7204 (ttp80) REVERT: B 274 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7751 (mm) REVERT: B 294 MET cc_start: 0.7983 (tmm) cc_final: 0.7776 (tmm) REVERT: B 305 LEU cc_start: 0.8424 (tp) cc_final: 0.8096 (tp) outliers start: 24 outliers final: 18 residues processed: 137 average time/residue: 0.1529 time to fit residues: 29.0930 Evaluate side-chains 130 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 0.0870 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6722 Z= 0.172 Angle : 0.627 9.345 9135 Z= 0.296 Chirality : 0.040 0.160 1082 Planarity : 0.003 0.042 1145 Dihedral : 4.625 33.465 934 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.10 % Allowed : 24.28 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.30), residues: 879 helix: 0.81 (0.22), residues: 642 sheet: None (None), residues: 0 loop : -2.52 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.001 0.000 HIS B 70 PHE 0.010 0.001 PHE B 307 TYR 0.007 0.001 TYR B 419 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.740 Fit side-chains REVERT: A 29 ASP cc_start: 0.8407 (m-30) cc_final: 0.8151 (m-30) REVERT: A 55 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7015 (tptp) REVERT: A 91 MET cc_start: 0.6697 (mtm) cc_final: 0.6253 (tmm) REVERT: A 164 ASP cc_start: 0.8132 (t0) cc_final: 0.7578 (t0) REVERT: A 171 ASP cc_start: 0.7785 (t0) cc_final: 0.7491 (t0) REVERT: A 271 LYS cc_start: 0.7840 (tttt) cc_final: 0.7431 (ttmt) REVERT: A 290 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7735 (mttm) REVERT: A 342 ILE cc_start: 0.9141 (tt) cc_final: 0.8884 (tt) REVERT: A 360 MET cc_start: 0.7627 (mtt) cc_final: 0.7353 (mtt) REVERT: B 38 MET cc_start: 0.7912 (mmt) cc_final: 0.7519 (mmt) REVERT: B 77 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7844 (tt) REVERT: B 84 LEU cc_start: 0.8865 (mt) cc_final: 0.8660 (mt) REVERT: B 164 ASP cc_start: 0.8113 (t0) cc_final: 0.7546 (t0) REVERT: B 205 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.7212 (ttp80) REVERT: B 274 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7743 (mm) REVERT: B 301 LEU cc_start: 0.7873 (tt) cc_final: 0.6823 (mt) REVERT: B 305 LEU cc_start: 0.8493 (tp) cc_final: 0.8120 (tp) outliers start: 27 outliers final: 18 residues processed: 128 average time/residue: 0.1466 time to fit residues: 26.8101 Evaluate side-chains 125 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 382 TYR Chi-restraints excluded: chain B residue 383 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 0.0570 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6722 Z= 0.178 Angle : 0.628 10.322 9135 Z= 0.295 Chirality : 0.040 0.161 1082 Planarity : 0.003 0.042 1145 Dihedral : 4.569 31.696 934 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.70 % Allowed : 24.43 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.30), residues: 879 helix: 0.91 (0.22), residues: 643 sheet: None (None), residues: 0 loop : -2.48 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 125 HIS 0.001 0.000 HIS B 284 PHE 0.009 0.001 PHE B 307 TYR 0.006 0.001 TYR B 229 ARG 0.002 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 0.683 Fit side-chains REVERT: A 29 ASP cc_start: 0.8415 (m-30) cc_final: 0.8179 (m-30) REVERT: A 55 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7009 (tptp) REVERT: A 91 MET cc_start: 0.6718 (mtm) cc_final: 0.6266 (tmm) REVERT: A 164 ASP cc_start: 0.8130 (t0) cc_final: 0.7620 (t0) REVERT: A 171 ASP cc_start: 0.7746 (t0) cc_final: 0.7502 (t0) REVERT: A 271 LYS cc_start: 0.7796 (tttt) cc_final: 0.7440 (ttmt) REVERT: A 290 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7741 (mttm) REVERT: A 294 MET cc_start: 0.8661 (tmm) cc_final: 0.8429 (tmm) REVERT: A 342 ILE cc_start: 0.9169 (tt) cc_final: 0.8907 (tt) REVERT: A 360 MET cc_start: 0.7639 (mtt) cc_final: 0.7358 (mtt) REVERT: A 382 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8265 (m-10) REVERT: B 38 MET cc_start: 0.7929 (mmt) cc_final: 0.7527 (mmt) REVERT: B 77 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7845 (tt) REVERT: B 84 LEU cc_start: 0.8804 (mt) cc_final: 0.8572 (mt) REVERT: B 164 ASP cc_start: 0.8176 (t0) cc_final: 0.7637 (t0) REVERT: B 205 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.7219 (ttp80) REVERT: B 274 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7773 (mm) REVERT: B 301 LEU cc_start: 0.7869 (tt) cc_final: 0.6827 (mt) REVERT: B 305 LEU cc_start: 0.8460 (tp) cc_final: 0.8105 (tp) outliers start: 31 outliers final: 20 residues processed: 128 average time/residue: 0.1440 time to fit residues: 26.5430 Evaluate side-chains 129 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 382 TYR Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain B residue 435 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 0.0010 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 0.0270 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6722 Z= 0.174 Angle : 0.632 12.536 9135 Z= 0.295 Chirality : 0.040 0.162 1082 Planarity : 0.003 0.041 1145 Dihedral : 4.493 29.013 934 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.95 % Allowed : 25.49 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.30), residues: 879 helix: 1.01 (0.22), residues: 643 sheet: None (None), residues: 0 loop : -2.39 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 125 HIS 0.001 0.000 HIS B 284 PHE 0.012 0.001 PHE A 132 TYR 0.007 0.001 TYR B 419 ARG 0.002 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 0.747 Fit side-chains REVERT: A 25 LEU cc_start: 0.7334 (mp) cc_final: 0.6876 (pt) REVERT: A 29 ASP cc_start: 0.8412 (m-30) cc_final: 0.8182 (m-30) REVERT: A 55 LYS cc_start: 0.8215 (mmtt) cc_final: 0.6996 (tptp) REVERT: A 91 MET cc_start: 0.6720 (mtm) cc_final: 0.6263 (tmm) REVERT: A 171 ASP cc_start: 0.7715 (t0) cc_final: 0.7496 (t0) REVERT: A 271 LYS cc_start: 0.7728 (tttt) cc_final: 0.7286 (ttmt) REVERT: A 290 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7743 (mttm) REVERT: A 294 MET cc_start: 0.8637 (tmm) cc_final: 0.8390 (tmm) REVERT: A 342 ILE cc_start: 0.9183 (tt) cc_final: 0.8910 (tt) REVERT: A 360 MET cc_start: 0.7647 (mtt) cc_final: 0.7350 (mtt) REVERT: A 382 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8267 (m-10) REVERT: B 38 MET cc_start: 0.7925 (mmt) cc_final: 0.7520 (mmt) REVERT: B 77 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7847 (tt) REVERT: B 164 ASP cc_start: 0.8170 (t0) cc_final: 0.7600 (t0) REVERT: B 205 ARG cc_start: 0.7562 (ttp-110) cc_final: 0.7211 (ttp80) REVERT: B 231 ILE cc_start: 0.8585 (tt) cc_final: 0.8337 (tt) REVERT: B 274 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7693 (mm) REVERT: B 301 LEU cc_start: 0.7943 (tt) cc_final: 0.6902 (mt) REVERT: B 305 LEU cc_start: 0.8408 (tp) cc_final: 0.8064 (tp) REVERT: B 367 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8576 (tt) outliers start: 26 outliers final: 19 residues processed: 131 average time/residue: 0.1431 time to fit residues: 26.6008 Evaluate side-chains 130 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 382 TYR Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain B residue 435 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.0070 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6722 Z= 0.178 Angle : 0.649 12.267 9135 Z= 0.300 Chirality : 0.041 0.165 1082 Planarity : 0.004 0.042 1145 Dihedral : 4.280 19.186 932 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.40 % Allowed : 25.19 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.30), residues: 879 helix: 1.09 (0.22), residues: 643 sheet: None (None), residues: 0 loop : -2.35 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 253 HIS 0.001 0.000 HIS B 284 PHE 0.015 0.001 PHE A 132 TYR 0.011 0.001 TYR A 100 ARG 0.002 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 0.680 Fit side-chains REVERT: A 29 ASP cc_start: 0.8409 (m-30) cc_final: 0.8197 (m-30) REVERT: A 55 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7022 (tptp) REVERT: A 91 MET cc_start: 0.6725 (mtm) cc_final: 0.6262 (tmm) REVERT: A 171 ASP cc_start: 0.7754 (t0) cc_final: 0.7549 (t0) REVERT: A 202 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 290 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7750 (mttm) REVERT: A 294 MET cc_start: 0.8614 (tmm) cc_final: 0.8358 (tmm) REVERT: A 342 ILE cc_start: 0.9177 (tt) cc_final: 0.8934 (tt) REVERT: A 360 MET cc_start: 0.7594 (mtt) cc_final: 0.7327 (mtt) REVERT: A 382 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.8174 (m-10) REVERT: B 38 MET cc_start: 0.7932 (mmt) cc_final: 0.7529 (mmt) REVERT: B 77 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7832 (tt) REVERT: B 164 ASP cc_start: 0.8158 (t0) cc_final: 0.7597 (t0) REVERT: B 205 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.7208 (ttp80) REVERT: B 231 ILE cc_start: 0.8560 (tt) cc_final: 0.8301 (tt) REVERT: B 274 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7697 (mm) REVERT: B 301 LEU cc_start: 0.7928 (tt) cc_final: 0.6901 (mt) REVERT: B 305 LEU cc_start: 0.8366 (tp) cc_final: 0.8010 (tp) REVERT: B 367 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8578 (tt) REVERT: B 385 GLU cc_start: 0.7471 (tp30) cc_final: 0.7066 (tt0) outliers start: 29 outliers final: 19 residues processed: 131 average time/residue: 0.1436 time to fit residues: 26.9836 Evaluate side-chains 128 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 382 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6722 Z= 0.203 Angle : 0.662 12.015 9135 Z= 0.307 Chirality : 0.041 0.143 1082 Planarity : 0.004 0.041 1145 Dihedral : 4.322 19.298 932 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.79 % Allowed : 26.40 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.30), residues: 879 helix: 1.11 (0.22), residues: 646 sheet: None (None), residues: 0 loop : -2.40 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 253 HIS 0.001 0.000 HIS B 284 PHE 0.014 0.001 PHE A 132 TYR 0.012 0.001 TYR A 100 ARG 0.002 0.000 ARG A 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 0.959 Fit side-chains REVERT: A 25 LEU cc_start: 0.7336 (mp) cc_final: 0.6925 (pt) REVERT: A 55 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7004 (tptp) REVERT: A 91 MET cc_start: 0.6730 (mtm) cc_final: 0.6255 (tmm) REVERT: A 164 ASP cc_start: 0.8061 (t0) cc_final: 0.7436 (t0) REVERT: A 171 ASP cc_start: 0.7721 (t0) cc_final: 0.7515 (t0) REVERT: A 276 MET cc_start: 0.7614 (tpp) cc_final: 0.7390 (tpp) REVERT: A 290 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7753 (mttm) REVERT: A 294 MET cc_start: 0.8637 (tmm) cc_final: 0.8344 (tmm) REVERT: A 342 ILE cc_start: 0.9176 (tt) cc_final: 0.8957 (tt) REVERT: A 360 MET cc_start: 0.7607 (mtt) cc_final: 0.7354 (mtt) REVERT: A 382 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8232 (m-10) REVERT: B 38 MET cc_start: 0.8007 (mmt) cc_final: 0.7637 (mmt) REVERT: B 77 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7832 (tt) REVERT: B 164 ASP cc_start: 0.8181 (t0) cc_final: 0.7642 (t0) REVERT: B 205 ARG cc_start: 0.7581 (ttp-110) cc_final: 0.7224 (ttp80) REVERT: B 231 ILE cc_start: 0.8558 (tt) cc_final: 0.8300 (tt) REVERT: B 274 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7642 (mm) REVERT: B 301 LEU cc_start: 0.7846 (tt) cc_final: 0.6911 (mt) REVERT: B 305 LEU cc_start: 0.8365 (tp) cc_final: 0.8010 (tp) REVERT: B 385 GLU cc_start: 0.7499 (tp30) cc_final: 0.7115 (tt0) outliers start: 25 outliers final: 20 residues processed: 128 average time/residue: 0.1954 time to fit residues: 36.7334 Evaluate side-chains 130 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 382 TYR Chi-restraints excluded: chain B residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116992 restraints weight = 10856.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119968 restraints weight = 6194.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122003 restraints weight = 4197.167| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6722 Z= 0.227 Angle : 0.681 11.830 9135 Z= 0.316 Chirality : 0.041 0.158 1082 Planarity : 0.004 0.041 1145 Dihedral : 4.387 19.322 932 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.64 % Allowed : 26.40 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.30), residues: 879 helix: 1.09 (0.22), residues: 645 sheet: None (None), residues: 0 loop : -2.36 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 253 HIS 0.001 0.000 HIS B 284 PHE 0.015 0.001 PHE A 132 TYR 0.019 0.001 TYR A 100 ARG 0.002 0.000 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.16 seconds wall clock time: 27 minutes 32.48 seconds (1652.48 seconds total)