Starting phenix.real_space_refine on Fri Jul 19 09:39:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qey_18379/07_2024/8qey_18379.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qey_18379/07_2024/8qey_18379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qey_18379/07_2024/8qey_18379.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qey_18379/07_2024/8qey_18379.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qey_18379/07_2024/8qey_18379.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qey_18379/07_2024/8qey_18379.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 31 5.16 5 C 4754 2.51 5 N 1185 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 369": "OD1" <-> "OD2" Residue "B GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7306 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3462 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain: "B" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 85 Unusual residues: {'AJP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.18, per 1000 atoms: 0.71 Number of scatterers: 7306 At special positions: 0 Unit cell: (94.734, 83.931, 131.298, 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 31 16.00 O 1336 8.00 N 1185 7.00 C 4754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS B 109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 601 " - " ASN B 264 " " NAG C 1 " - " ASN B 323 " " NAG D 1 " - " ASN B 280 " " NAG E 1 " - " ASN B 405 " Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.5 seconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1674 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 58.3% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.616A pdb=" N ALA A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 69 removed outlier: 4.019A pdb=" N ILE A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Proline residue: A 62 - end of helix Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.638A pdb=" N GLY A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 removed outlier: 4.332A pdb=" N VAL A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.434A pdb=" N ALA A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 Processing helix chain 'A' and resid 157 through 177 removed outlier: 3.570A pdb=" N SER A 161 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 210 removed outlier: 4.048A pdb=" N PHE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.713A pdb=" N GLN A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.652A pdb=" N THR A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.670A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.817A pdb=" N LEU A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.868A pdb=" N LEU A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 348 Proline residue: A 319 - end of helix removed outlier: 3.535A pdb=" N GLU A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 381 removed outlier: 3.637A pdb=" N LEU A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 370 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 413 Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 445 through 458 removed outlier: 3.806A pdb=" N CYS A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 469 removed outlier: 4.156A pdb=" N ILE A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 482 through 487 removed outlier: 4.287A pdb=" N TRP A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 73 Processing helix chain 'B' and resid 74 through 105 Processing helix chain 'B' and resid 128 through 134 Processing helix chain 'B' and resid 139 through 145 removed outlier: 4.105A pdb=" N LYS B 144 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 185 through 199 Processing helix chain 'B' and resid 221 through 240 removed outlier: 4.169A pdb=" N VAL B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 270 Processing helix chain 'B' and resid 283 through 291 Processing helix chain 'B' and resid 310 through 326 Processing helix chain 'B' and resid 348 through 357 removed outlier: 4.472A pdb=" N LEU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.565A pdb=" N ASP B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 432 removed outlier: 3.598A pdb=" N SER B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 432 " --> pdb=" O GLN B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing sheet with id=AA1, first strand: chain 'B' and resid 123 through 125 removed outlier: 6.662A pdb=" N TRP B 332 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N SER B 366 " --> pdb=" O TRP B 332 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 164 through 165 removed outlier: 4.218A pdb=" N LYS B 165 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 175 " --> pdb=" O LYS B 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 205 through 206 removed outlier: 7.050A pdb=" N LEU B 205 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE B 244 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLY B 278 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 246 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA B 277 " --> pdb=" O THR B 300 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 441 through 442 removed outlier: 3.593A pdb=" N HIS B 441 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG B 524 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU B 494 " --> pdb=" O ARG B 524 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA B 492 " --> pdb=" O LEU B 508 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1339 1.33 - 1.45: 1942 1.45 - 1.57: 4168 1.57 - 1.69: 2 1.69 - 1.82: 49 Bond restraints: 7500 Sorted by residual: bond pdb=" CB PRO B 526 " pdb=" CG PRO B 526 " ideal model delta sigma weight residual 1.492 1.608 -0.116 5.00e-02 4.00e+02 5.35e+00 bond pdb=" C65 AJP A 601 " pdb=" O64 AJP A 601 " ideal model delta sigma weight residual 1.373 1.407 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.553 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" CB PRO A 149 " pdb=" CG PRO A 149 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.75e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 7495 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.19: 210 106.19 - 113.26: 4176 113.26 - 120.34: 2824 120.34 - 127.42: 2919 127.42 - 134.50: 99 Bond angle restraints: 10228 Sorted by residual: angle pdb=" CA PRO B 526 " pdb=" N PRO B 526 " pdb=" CD PRO B 526 " ideal model delta sigma weight residual 112.00 102.58 9.42 1.40e+00 5.10e-01 4.53e+01 angle pdb=" CA PRO A 149 " pdb=" N PRO A 149 " pdb=" CD PRO A 149 " ideal model delta sigma weight residual 112.00 103.38 8.62 1.40e+00 5.10e-01 3.79e+01 angle pdb=" CA LEU A 310 " pdb=" CB LEU A 310 " pdb=" CG LEU A 310 " ideal model delta sigma weight residual 116.30 134.50 -18.20 3.50e+00 8.16e-02 2.70e+01 angle pdb=" C ILE A 129 " pdb=" N MET A 130 " pdb=" CA MET A 130 " ideal model delta sigma weight residual 122.58 113.49 9.09 2.07e+00 2.33e-01 1.93e+01 angle pdb=" CA TYR A 337 " pdb=" CB TYR A 337 " pdb=" CG TYR A 337 " ideal model delta sigma weight residual 113.90 120.98 -7.08 1.80e+00 3.09e-01 1.55e+01 ... (remaining 10223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.22: 4035 22.22 - 44.43: 472 44.43 - 66.65: 89 66.65 - 88.86: 28 88.86 - 111.08: 12 Dihedral angle restraints: 4636 sinusoidal: 2021 harmonic: 2615 Sorted by residual: dihedral pdb=" CA LEU A 350 " pdb=" C LEU A 350 " pdb=" N PRO A 351 " pdb=" CA PRO A 351 " ideal model delta harmonic sigma weight residual -180.00 -142.44 -37.56 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS B 109 " pdb=" CB CYS B 109 " ideal model delta sinusoidal sigma weight residual -86.00 -149.89 63.89 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CA ILE A 100 " pdb=" C ILE A 100 " pdb=" N PRO A 101 " pdb=" CA PRO A 101 " ideal model delta harmonic sigma weight residual 180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 4633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1018 0.065 - 0.130: 166 0.130 - 0.196: 22 0.196 - 0.261: 5 0.261 - 0.326: 2 Chirality restraints: 1213 Sorted by residual: chirality pdb=" CG LEU B 233 " pdb=" CB LEU B 233 " pdb=" CD1 LEU B 233 " pdb=" CD2 LEU B 233 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C08 AJP A 601 " pdb=" C07 AJP A 601 " pdb=" C10 AJP A 601 " pdb=" O09 AJP A 601 " both_signs ideal model delta sigma weight residual False 2.56 2.82 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1210 not shown) Planarity restraints: 1254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 525 " 0.104 5.00e-02 4.00e+02 1.50e-01 3.60e+01 pdb=" N PRO B 526 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO B 526 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 526 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 148 " 0.077 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO A 149 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 399 " 0.020 2.00e-02 2.50e+03 2.08e-02 8.68e+00 pdb=" CG TYR A 399 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 399 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 399 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 399 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 399 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 399 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 399 " 0.001 2.00e-02 2.50e+03 ... (remaining 1251 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1790 2.79 - 3.31: 7031 3.31 - 3.84: 12106 3.84 - 4.37: 12654 4.37 - 4.90: 21712 Nonbonded interactions: 55293 Sorted by model distance: nonbonded pdb=" OH TYR B 367 " pdb=" O PRO B 386 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR B 149 " pdb=" OE2 GLU B 370 " model vdw 2.289 2.440 nonbonded pdb=" O LYS B 315 " pdb=" OG1 THR B 319 " model vdw 2.289 2.440 nonbonded pdb=" O GLY A 57 " pdb=" OG SER A 61 " model vdw 2.289 2.440 nonbonded pdb=" O VAL A 279 " pdb=" OG1 THR A 283 " model vdw 2.291 2.440 ... (remaining 55288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } 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: 1.290 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.780 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 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 0.116 7500 Z= 0.308 Angle : 0.959 18.202 10228 Z= 0.452 Chirality : 0.052 0.326 1213 Planarity : 0.007 0.150 1250 Dihedral : 19.802 111.079 2959 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.91 % Allowed : 41.20 % Favored : 57.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.09 (0.27), residues: 914 helix: 0.30 (0.23), residues: 483 sheet: -0.51 (0.67), residues: 59 loop : -2.15 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 316 HIS 0.008 0.001 HIS A 213 PHE 0.045 0.002 PHE A 440 TYR 0.052 0.002 TYR A 399 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7980 (tp30) cc_final: 0.7032 (tm-30) REVERT: A 140 MET cc_start: 0.8817 (ttm) cc_final: 0.8589 (ttp) REVERT: A 215 GLU cc_start: 0.7309 (mp0) cc_final: 0.6593 (pm20) REVERT: A 221 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7492 (p0) outliers start: 7 outliers final: 2 residues processed: 162 average time/residue: 0.1445 time to fit residues: 33.6624 Evaluate side-chains 154 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain B residue 357 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 0.0370 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7500 Z= 0.171 Angle : 0.638 9.876 10228 Z= 0.301 Chirality : 0.040 0.220 1213 Planarity : 0.005 0.084 1250 Dihedral : 11.414 95.336 1371 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 5.35 % Allowed : 35.46 % Favored : 59.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.28), residues: 914 helix: 1.07 (0.24), residues: 478 sheet: -0.55 (0.65), residues: 55 loop : -1.74 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.003 0.001 HIS B 441 PHE 0.013 0.001 PHE A 393 TYR 0.035 0.002 TYR A 399 ARG 0.005 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 162 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 166 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7150 (mmm) REVERT: A 215 GLU cc_start: 0.7372 (mp0) cc_final: 0.6710 (pm20) REVERT: A 296 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8338 (tt) REVERT: A 356 MET cc_start: 0.6363 (mpp) cc_final: 0.5958 (mpp) REVERT: A 360 ARG cc_start: 0.2116 (OUTLIER) cc_final: 0.1511 (ttp-170) outliers start: 41 outliers final: 21 residues processed: 190 average time/residue: 0.1338 time to fit residues: 37.5739 Evaluate side-chains 180 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 0.2980 chunk 81 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7500 Z= 0.193 Angle : 0.645 9.797 10228 Z= 0.302 Chirality : 0.041 0.276 1213 Planarity : 0.004 0.068 1250 Dihedral : 10.027 84.493 1369 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 7.82 % Allowed : 34.55 % Favored : 57.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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 (0.28), residues: 914 helix: 1.39 (0.24), residues: 485 sheet: -0.14 (0.66), residues: 60 loop : -1.77 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 316 HIS 0.002 0.001 HIS B 437 PHE 0.014 0.001 PHE A 463 TYR 0.030 0.002 TYR A 399 ARG 0.001 0.000 ARG B 423 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 169 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7431 (mp0) cc_final: 0.6896 (pm20) REVERT: A 221 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7422 (p0) REVERT: A 356 MET cc_start: 0.6485 (mpp) cc_final: 0.6122 (mpp) REVERT: A 395 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.8929 (p0) REVERT: B 175 ASP cc_start: 0.8935 (t0) cc_final: 0.8691 (t0) REVERT: B 237 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7802 (mm) REVERT: B 336 GLN cc_start: 0.8585 (tp40) cc_final: 0.8282 (tp40) outliers start: 60 outliers final: 36 residues processed: 207 average time/residue: 0.1332 time to fit residues: 40.9826 Evaluate side-chains 196 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.9980 chunk 42 optimal weight: 0.0010 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 0.0060 chunk 49 optimal weight: 3.9990 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7500 Z= 0.171 Angle : 0.646 9.661 10228 Z= 0.298 Chirality : 0.041 0.232 1213 Planarity : 0.004 0.058 1250 Dihedral : 9.438 75.937 1369 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 6.39 % Allowed : 36.38 % Favored : 57.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.23 (0.29), residues: 914 helix: 1.50 (0.24), residues: 485 sheet: -0.37 (0.66), residues: 56 loop : -1.64 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.002 0.001 HIS B 313 PHE 0.019 0.001 PHE A 463 TYR 0.026 0.002 TYR A 399 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 162 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7990 (tp30) cc_final: 0.6963 (tm-30) REVERT: A 215 GLU cc_start: 0.7433 (mp0) cc_final: 0.6967 (pm20) REVERT: A 221 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7416 (p0) REVERT: A 356 MET cc_start: 0.6463 (mpp) cc_final: 0.6129 (mpp) REVERT: A 360 ARG cc_start: 0.2090 (OUTLIER) cc_final: 0.1737 (ttp-170) REVERT: B 175 ASP cc_start: 0.8767 (t0) cc_final: 0.8491 (t0) REVERT: B 237 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7781 (mm) REVERT: B 315 LYS cc_start: 0.8201 (tppt) cc_final: 0.7950 (tppt) outliers start: 49 outliers final: 30 residues processed: 194 average time/residue: 0.1416 time to fit residues: 39.7711 Evaluate side-chains 193 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7500 Z= 0.179 Angle : 0.636 9.566 10228 Z= 0.297 Chirality : 0.040 0.209 1213 Planarity : 0.004 0.054 1250 Dihedral : 8.675 62.794 1367 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 7.30 % Allowed : 35.20 % Favored : 57.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.42 (0.29), residues: 914 helix: 1.71 (0.24), residues: 485 sheet: 0.05 (0.67), residues: 61 loop : -1.72 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 316 HIS 0.002 0.001 HIS B 313 PHE 0.014 0.001 PHE A 463 TYR 0.020 0.001 TYR A 399 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 167 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7971 (tp30) cc_final: 0.6948 (tm-30) REVERT: A 140 MET cc_start: 0.8725 (ttm) cc_final: 0.8498 (ttp) REVERT: A 166 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7752 (mmm) REVERT: A 215 GLU cc_start: 0.7402 (mp0) cc_final: 0.6999 (pm20) REVERT: A 221 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7493 (p0) REVERT: A 356 MET cc_start: 0.6490 (mpp) cc_final: 0.6177 (mpp) REVERT: A 360 ARG cc_start: 0.2091 (OUTLIER) cc_final: 0.1802 (ttp-170) REVERT: B 175 ASP cc_start: 0.8859 (t0) cc_final: 0.8521 (t0) REVERT: B 315 LYS cc_start: 0.8191 (tppt) cc_final: 0.7986 (tppt) outliers start: 56 outliers final: 38 residues processed: 203 average time/residue: 0.1493 time to fit residues: 44.7609 Evaluate side-chains 200 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 159 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.0000 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7500 Z= 0.242 Angle : 0.672 11.176 10228 Z= 0.318 Chirality : 0.042 0.269 1213 Planarity : 0.004 0.052 1250 Dihedral : 8.179 57.174 1367 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 8.34 % Allowed : 34.94 % Favored : 56.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.39 (0.29), residues: 914 helix: 1.66 (0.24), residues: 489 sheet: 0.17 (0.69), residues: 61 loop : -1.77 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 316 HIS 0.003 0.001 HIS B 119 PHE 0.015 0.001 PHE B 269 TYR 0.016 0.002 TYR A 396 ARG 0.002 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 165 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7435 (mp0) cc_final: 0.6948 (pm20) REVERT: A 221 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7479 (p0) REVERT: A 356 MET cc_start: 0.6674 (mpp) cc_final: 0.6383 (mpp) REVERT: A 360 ARG cc_start: 0.2186 (OUTLIER) cc_final: 0.1756 (ttp-170) REVERT: A 395 ASN cc_start: 0.9284 (OUTLIER) cc_final: 0.9017 (p0) REVERT: B 175 ASP cc_start: 0.8902 (t0) cc_final: 0.8562 (t0) outliers start: 64 outliers final: 46 residues processed: 208 average time/residue: 0.1408 time to fit residues: 42.3465 Evaluate side-chains 204 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 155 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.0270 chunk 49 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7500 Z= 0.205 Angle : 0.689 10.578 10228 Z= 0.320 Chirality : 0.042 0.256 1213 Planarity : 0.004 0.050 1250 Dihedral : 7.976 57.417 1367 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 7.17 % Allowed : 35.59 % Favored : 57.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.28), residues: 914 helix: 1.59 (0.24), residues: 489 sheet: 0.27 (0.69), residues: 61 loop : -1.78 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 316 HIS 0.004 0.001 HIS B 313 PHE 0.029 0.001 PHE A 433 TYR 0.021 0.001 TYR A 396 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 164 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7373 (mp0) cc_final: 0.7072 (pm20) REVERT: A 221 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7477 (p0) REVERT: A 270 PHE cc_start: 0.5916 (m-80) cc_final: 0.5340 (m-80) REVERT: A 356 MET cc_start: 0.6591 (mpp) cc_final: 0.6355 (mpp) REVERT: B 175 ASP cc_start: 0.8895 (t0) cc_final: 0.8597 (t0) REVERT: B 406 MET cc_start: 0.7911 (pmm) cc_final: 0.6991 (pmm) outliers start: 55 outliers final: 39 residues processed: 203 average time/residue: 0.1405 time to fit residues: 40.9561 Evaluate side-chains 196 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 156 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 0.0070 chunk 42 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 0.0980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7500 Z= 0.171 Angle : 0.682 9.963 10228 Z= 0.317 Chirality : 0.042 0.205 1213 Planarity : 0.004 0.048 1250 Dihedral : 7.735 57.540 1367 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 6.00 % Allowed : 35.85 % Favored : 58.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.50 (0.29), residues: 914 helix: 1.74 (0.24), residues: 485 sheet: 0.23 (0.70), residues: 56 loop : -1.64 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 316 HIS 0.009 0.001 HIS A 213 PHE 0.022 0.001 PHE A 463 TYR 0.031 0.001 TYR A 399 ARG 0.002 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 163 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7751 (mtp) cc_final: 0.7500 (mtp) REVERT: A 215 GLU cc_start: 0.7343 (mp0) cc_final: 0.7097 (pm20) REVERT: A 221 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7449 (p0) REVERT: A 258 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.5593 (mmt) REVERT: A 294 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8751 (mm-40) REVERT: A 356 MET cc_start: 0.6646 (mpp) cc_final: 0.6444 (mpp) REVERT: B 175 ASP cc_start: 0.8889 (t0) cc_final: 0.8556 (t0) outliers start: 46 outliers final: 38 residues processed: 195 average time/residue: 0.1390 time to fit residues: 39.6242 Evaluate side-chains 199 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 159 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 0.0870 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7500 Z= 0.204 Angle : 0.685 9.517 10228 Z= 0.320 Chirality : 0.042 0.203 1213 Planarity : 0.004 0.048 1250 Dihedral : 7.675 57.262 1367 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 6.39 % Allowed : 36.38 % Favored : 57.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.49 (0.29), residues: 914 helix: 1.76 (0.24), residues: 486 sheet: 0.27 (0.68), residues: 61 loop : -1.72 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 316 HIS 0.003 0.001 HIS B 313 PHE 0.023 0.001 PHE A 393 TYR 0.028 0.002 TYR A 399 ARG 0.001 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 167 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8560 (pptt) cc_final: 0.8318 (pptt) REVERT: A 96 LEU cc_start: 0.7916 (tp) cc_final: 0.7650 (tp) REVERT: A 213 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.8074 (m170) REVERT: A 215 GLU cc_start: 0.7538 (mp0) cc_final: 0.7302 (mp0) REVERT: A 221 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7486 (p0) REVERT: A 258 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.5606 (mmt) REVERT: B 175 ASP cc_start: 0.8907 (t0) cc_final: 0.8569 (t0) REVERT: B 406 MET cc_start: 0.7981 (pmm) cc_final: 0.7107 (pmm) outliers start: 49 outliers final: 42 residues processed: 197 average time/residue: 0.1365 time to fit residues: 39.5534 Evaluate side-chains 207 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 162 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 0.0070 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7500 Z= 0.189 Angle : 0.705 9.802 10228 Z= 0.324 Chirality : 0.043 0.259 1213 Planarity : 0.004 0.048 1250 Dihedral : 7.616 57.507 1367 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.74 % Allowed : 37.81 % Favored : 56.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.49 (0.29), residues: 914 helix: 1.75 (0.25), residues: 485 sheet: 0.15 (0.69), residues: 56 loop : -1.66 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 316 HIS 0.003 0.001 HIS B 313 PHE 0.022 0.001 PHE A 393 TYR 0.030 0.002 TYR A 399 ARG 0.002 0.000 ARG B 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8494 (pptt) cc_final: 0.8269 (pptt) REVERT: A 213 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.8114 (m170) REVERT: A 221 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7456 (p0) REVERT: A 258 MET cc_start: 0.6604 (OUTLIER) cc_final: 0.5623 (mmt) REVERT: A 356 MET cc_start: 0.6608 (mpp) cc_final: 0.6299 (mpp) REVERT: B 175 ASP cc_start: 0.8914 (t0) cc_final: 0.8580 (t0) REVERT: B 406 MET cc_start: 0.7940 (pmm) cc_final: 0.7007 (pmm) outliers start: 44 outliers final: 38 residues processed: 194 average time/residue: 0.1369 time to fit residues: 39.1737 Evaluate side-chains 199 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 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 = 0.4099 r_free = 0.4099 target = 0.177538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142846 restraints weight = 13646.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145011 restraints weight = 9273.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145782 restraints weight = 8570.860| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7500 Z= 0.206 Angle : 0.703 9.333 10228 Z= 0.327 Chirality : 0.043 0.250 1213 Planarity : 0.004 0.048 1250 Dihedral : 7.572 57.316 1367 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.87 % Allowed : 37.94 % Favored : 56.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.29), residues: 914 helix: 1.76 (0.24), residues: 485 sheet: 0.27 (0.68), residues: 61 loop : -1.77 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 316 HIS 0.007 0.001 HIS A 213 PHE 0.021 0.001 PHE A 393 TYR 0.027 0.002 TYR A 399 ARG 0.001 0.000 ARG A 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1846.46 seconds wall clock time: 33 minutes 36.68 seconds (2016.68 seconds total)