Starting phenix.real_space_refine on Sat Aug 3 20:39:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsr_41599/08_2024/8tsr_41599.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsr_41599/08_2024/8tsr_41599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsr_41599/08_2024/8tsr_41599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsr_41599/08_2024/8tsr_41599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsr_41599/08_2024/8tsr_41599.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsr_41599/08_2024/8tsr_41599.cif" } resolution = 3.9 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= 0.002 sd= 0.038 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 54 5.16 5 C 5630 2.51 5 N 1548 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A GLU 552": "OE1" <-> "OE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B GLU 552": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8888 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4444 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 13, 'TRANS': 559} Chain: "B" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4444 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 13, 'TRANS': 559} Time building chain proxies: 5.21, per 1000 atoms: 0.59 Number of scatterers: 8888 At special positions: 0 Unit cell: (67.095, 139.515, 135.255, 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 54 16.00 O 1656 8.00 N 1548 7.00 C 5630 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.7 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 71.2% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 23 through 47 removed outlier: 3.855A pdb=" N LEU A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.812A pdb=" N LEU A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 66 removed outlier: 4.016A pdb=" N LEU A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 109 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 113 through 119 Processing helix chain 'A' and resid 120 through 164 removed outlier: 3.515A pdb=" N LEU A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 201 removed outlier: 4.378A pdb=" N ILE A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Proline residue: A 176 - end of helix removed outlier: 4.443A pdb=" N GLY A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.590A pdb=" N ALA A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 222 through 272 removed outlier: 4.434A pdb=" N ASP A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 294 through 323 removed outlier: 3.747A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.099A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.731A pdb=" N ALA A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.687A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 471 Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 512 through 526 Processing helix chain 'A' and resid 538 through 544 removed outlier: 3.698A pdb=" N ILE A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'B' and resid 8 through 21 Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 23 through 47 removed outlier: 3.854A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.671A pdb=" N LEU B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 66 through 109 Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 120 through 164 removed outlier: 3.977A pdb=" N ASP B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 200 removed outlier: 4.445A pdb=" N ILE B 170 " --> pdb=" O GLN B 166 " (cutoff:3.500A) Proline residue: B 176 - end of helix Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.681A pdb=" N ALA B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 222 through 272 removed outlier: 4.529A pdb=" N ASP B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 275 through 279 removed outlier: 4.024A pdb=" N SER B 278 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 279 " --> pdb=" O MET B 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 275 through 279' Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 294 through 323 removed outlier: 3.742A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.118A pdb=" N THR B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.858A pdb=" N ALA B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.813A pdb=" N LYS B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 512 through 526 Processing helix chain 'B' and resid 538 through 544 removed outlier: 3.844A pdb=" N ILE B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 570 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366 removed outlier: 6.637A pdb=" N ARG A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N THR A 348 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILE A 362 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N PHE A 344 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU A 401 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN A 346 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU A 399 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 423 removed outlier: 6.376A pdb=" N LEU A 502 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE A 535 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU A 504 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 372 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR A 371 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL A 549 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL A 551 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 375 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU A 558 " --> pdb=" O VAL A 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 366 removed outlier: 6.738A pdb=" N ARG B 360 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR B 348 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE B 362 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N PHE B 344 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU B 401 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASN B 346 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU B 399 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 419 through 423 removed outlier: 6.295A pdb=" N LEU B 502 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE B 535 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU B 504 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 372 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR B 371 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL B 549 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B 551 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL B 375 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 548 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG B 559 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 550 " --> pdb=" O VAL B 557 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 431 through 432 595 hydrogen bonds defined for protein. 1755 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: 2.79 Time building geometry restraints manager: 4.20 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: 2296 1.33 - 1.45: 1521 1.45 - 1.57: 5097 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 9018 Sorted by residual: bond pdb=" N VAL B 555 " pdb=" CA VAL B 555 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.27e+00 bond pdb=" N ILE B 556 " pdb=" CA ILE B 556 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.83e+00 bond pdb=" N ILE A 556 " pdb=" CA ILE A 556 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.30e-02 5.92e+03 8.54e+00 bond pdb=" N VAL B 549 " pdb=" CA VAL B 549 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.49e+00 bond pdb=" N VAL A 422 " pdb=" CA VAL A 422 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.35e+00 ... (remaining 9013 not shown) Histogram of bond angle deviations from ideal: 96.02 - 103.70: 95 103.70 - 111.38: 3981 111.38 - 119.05: 3474 119.05 - 126.73: 4566 126.73 - 134.41: 72 Bond angle restraints: 12188 Sorted by residual: angle pdb=" CA ILE A 556 " pdb=" C ILE A 556 " pdb=" O ILE A 556 " ideal model delta sigma weight residual 121.58 118.23 3.35 1.00e+00 1.00e+00 1.12e+01 angle pdb=" CB MET A 291 " pdb=" CG MET A 291 " pdb=" SD MET A 291 " ideal model delta sigma weight residual 112.70 122.66 -9.96 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CB MET B 291 " pdb=" CG MET B 291 " pdb=" SD MET B 291 " ideal model delta sigma weight residual 112.70 122.63 -9.93 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA GLU A 552 " pdb=" C GLU A 552 " pdb=" O GLU A 552 " ideal model delta sigma weight residual 121.89 118.02 3.87 1.17e+00 7.31e-01 1.09e+01 angle pdb=" CA VAL A 113 " pdb=" C VAL A 113 " pdb=" O VAL A 113 " ideal model delta sigma weight residual 121.05 117.71 3.34 1.04e+00 9.25e-01 1.03e+01 ... (remaining 12183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4739 17.56 - 35.12: 613 35.12 - 52.68: 106 52.68 - 70.24: 29 70.24 - 87.80: 5 Dihedral angle restraints: 5492 sinusoidal: 2178 harmonic: 3314 Sorted by residual: dihedral pdb=" CA ARG A 360 " pdb=" C ARG A 360 " pdb=" N ASN A 361 " pdb=" CA ASN A 361 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASP B 471 " pdb=" CB ASP B 471 " pdb=" CG ASP B 471 " pdb=" OD1 ASP B 471 " ideal model delta sinusoidal sigma weight residual -30.00 -86.35 56.35 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP A 471 " pdb=" CB ASP A 471 " pdb=" CG ASP A 471 " pdb=" OD1 ASP A 471 " ideal model delta sinusoidal sigma weight residual -30.00 -85.50 55.50 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 5489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1071 0.048 - 0.096: 296 0.096 - 0.144: 60 0.144 - 0.192: 21 0.192 - 0.240: 4 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CA ILE A 556 " pdb=" N ILE A 556 " pdb=" C ILE A 556 " pdb=" CB ILE A 556 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE B 20 " pdb=" N ILE B 20 " pdb=" C ILE B 20 " pdb=" CB ILE B 20 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL A 422 " pdb=" N VAL A 422 " pdb=" C VAL A 422 " pdb=" CB VAL A 422 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.53e-01 ... (remaining 1449 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 499 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO B 500 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO B 500 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 500 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 499 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO A 500 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 21 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.83e+00 pdb=" N PRO A 22 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " -0.034 5.00e-02 4.00e+02 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1257 2.76 - 3.29: 9334 3.29 - 3.83: 15139 3.83 - 4.36: 16444 4.36 - 4.90: 27982 Nonbonded interactions: 70156 Sorted by model distance: nonbonded pdb=" OD2 ASP B 117 " pdb=" OH TYR B 393 " model vdw 2.219 3.040 nonbonded pdb=" OG SER A 249 " pdb=" OG SER B 86 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP A 117 " pdb=" OH TYR A 393 " model vdw 2.233 3.040 nonbonded pdb=" OE2 GLU B 506 " pdb=" OG1 THR B 541 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR B 350 " pdb=" OD2 ASP B 396 " model vdw 2.276 3.040 ... (remaining 70151 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' 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: 1.420 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.950 Find NCS groups from input model: 0.230 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 0.070 9018 Z= 0.293 Angle : 0.832 9.963 12188 Z= 0.483 Chirality : 0.049 0.240 1452 Planarity : 0.007 0.110 1542 Dihedral : 16.020 87.802 3348 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.51 % Allowed : 23.26 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1142 helix: 1.57 (0.19), residues: 722 sheet: 1.12 (0.65), residues: 66 loop : -1.84 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 17 HIS 0.015 0.002 HIS A 576 PHE 0.023 0.002 PHE A 56 TYR 0.007 0.001 TYR B 445 ARG 0.006 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ASP cc_start: 0.7222 (t0) cc_final: 0.6977 (t0) outliers start: 5 outliers final: 3 residues processed: 170 average time/residue: 0.2193 time to fit residues: 52.1662 Evaluate side-chains 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9018 Z= 0.244 Angle : 0.678 11.285 12188 Z= 0.335 Chirality : 0.043 0.144 1452 Planarity : 0.005 0.072 1542 Dihedral : 4.442 45.562 1253 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.41 % Allowed : 20.39 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.11 (0.25), residues: 1142 helix: 1.54 (0.19), residues: 768 sheet: 1.33 (0.66), residues: 66 loop : -1.48 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 17 HIS 0.007 0.002 HIS A 576 PHE 0.020 0.002 PHE A 230 TYR 0.012 0.001 TYR A 572 ARG 0.006 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7664 (mmt) cc_final: 0.7125 (mmt) REVERT: B 14 ARG cc_start: 0.8008 (mtt90) cc_final: 0.7792 (mtt-85) REVERT: B 17 TRP cc_start: 0.8041 (t-100) cc_final: 0.7632 (t-100) REVERT: B 54 ASP cc_start: 0.7438 (t0) cc_final: 0.6996 (t0) outliers start: 43 outliers final: 27 residues processed: 193 average time/residue: 0.1887 time to fit residues: 51.5053 Evaluate side-chains 170 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.0000 chunk 112 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 35 optimal weight: 0.0050 chunk 83 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 418 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9018 Z= 0.183 Angle : 0.634 7.793 12188 Z= 0.314 Chirality : 0.042 0.255 1452 Planarity : 0.005 0.081 1542 Dihedral : 4.141 44.719 1250 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.79 % Allowed : 22.85 % Favored : 73.36 % 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: 1.54 (0.25), residues: 1142 helix: 1.91 (0.19), residues: 756 sheet: 1.41 (0.66), residues: 66 loop : -1.27 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 17 HIS 0.005 0.001 HIS B 562 PHE 0.020 0.001 PHE A 56 TYR 0.013 0.001 TYR A 410 ARG 0.009 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 146 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7820 (mmt) cc_final: 0.7311 (mmt) REVERT: B 54 ASP cc_start: 0.7340 (t0) cc_final: 0.6875 (t0) outliers start: 37 outliers final: 23 residues processed: 172 average time/residue: 0.1887 time to fit residues: 46.2152 Evaluate side-chains 159 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9018 Z= 0.451 Angle : 0.819 10.683 12188 Z= 0.419 Chirality : 0.048 0.198 1452 Planarity : 0.006 0.071 1542 Dihedral : 4.551 43.847 1250 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.66 % Allowed : 23.36 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1142 helix: 1.17 (0.18), residues: 752 sheet: 1.45 (0.68), residues: 66 loop : -1.34 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 91 HIS 0.011 0.002 HIS A 576 PHE 0.023 0.003 PHE A 230 TYR 0.014 0.002 TYR A 572 ARG 0.008 0.001 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 144 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7916 (t80) cc_final: 0.7712 (t80) REVERT: A 153 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.7934 (tt) REVERT: A 242 MET cc_start: 0.7822 (mmt) cc_final: 0.7476 (mmt) REVERT: A 435 ASN cc_start: 0.8296 (m-40) cc_final: 0.7712 (t0) REVERT: B 54 ASP cc_start: 0.7633 (t0) cc_final: 0.7142 (t0) REVERT: B 75 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6769 (tmm) REVERT: B 153 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7854 (tt) outliers start: 65 outliers final: 41 residues processed: 184 average time/residue: 0.1663 time to fit residues: 45.0632 Evaluate side-chains 175 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 131 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 20.0000 chunk 62 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN A 576 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 418 GLN ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9018 Z= 0.193 Angle : 0.651 11.703 12188 Z= 0.315 Chirality : 0.042 0.174 1452 Planarity : 0.004 0.059 1542 Dihedral : 4.216 45.879 1250 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.51 % Allowed : 26.43 % Favored : 69.06 % 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: 1.39 (0.25), residues: 1142 helix: 1.70 (0.19), residues: 752 sheet: 1.74 (0.70), residues: 66 loop : -1.14 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.003 0.001 HIS B 562 PHE 0.016 0.001 PHE A 189 TYR 0.010 0.001 TYR A 572 ARG 0.006 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7219 (t0) cc_final: 0.6911 (t0) REVERT: A 242 MET cc_start: 0.8030 (mmt) cc_final: 0.7721 (mmt) REVERT: A 418 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8663 (mm-40) REVERT: B 54 ASP cc_start: 0.7410 (t0) cc_final: 0.6954 (t0) REVERT: B 418 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8675 (mm-40) outliers start: 44 outliers final: 25 residues processed: 172 average time/residue: 0.1826 time to fit residues: 45.5623 Evaluate side-chains 153 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 571 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.0370 chunk 57 optimal weight: 8.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN B 576 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9018 Z= 0.204 Angle : 0.670 11.057 12188 Z= 0.320 Chirality : 0.042 0.170 1452 Planarity : 0.004 0.053 1542 Dihedral : 4.162 45.323 1250 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.61 % Allowed : 26.33 % Favored : 69.06 % 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: 1.57 (0.25), residues: 1142 helix: 1.82 (0.19), residues: 756 sheet: 1.70 (0.71), residues: 66 loop : -1.03 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 91 HIS 0.003 0.001 HIS A 107 PHE 0.015 0.001 PHE A 189 TYR 0.015 0.001 TYR B 439 ARG 0.006 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 130 time to evaluate : 1.147 Fit side-chains REVERT: A 54 ASP cc_start: 0.7284 (t0) cc_final: 0.6952 (t0) REVERT: A 127 ARG cc_start: 0.7462 (ttm170) cc_final: 0.7229 (ttm170) REVERT: A 242 MET cc_start: 0.8071 (mmt) cc_final: 0.7742 (mmt) REVERT: A 244 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6226 (mtt) REVERT: B 54 ASP cc_start: 0.7457 (t0) cc_final: 0.6953 (t0) outliers start: 45 outliers final: 35 residues processed: 160 average time/residue: 0.1666 time to fit residues: 39.6019 Evaluate side-chains 163 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN A 427 HIS B 418 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9018 Z= 0.200 Angle : 0.682 10.744 12188 Z= 0.324 Chirality : 0.042 0.167 1452 Planarity : 0.004 0.049 1542 Dihedral : 4.144 45.265 1250 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.61 % Allowed : 26.54 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1142 helix: 1.83 (0.19), residues: 756 sheet: 1.50 (0.70), residues: 66 loop : -0.98 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 91 HIS 0.006 0.001 HIS B 576 PHE 0.015 0.001 PHE A 189 TYR 0.013 0.001 TYR A 439 ARG 0.005 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 136 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7302 (t0) cc_final: 0.6902 (t0) REVERT: A 242 MET cc_start: 0.8045 (mmt) cc_final: 0.7754 (mmt) REVERT: A 513 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.7215 (p) REVERT: B 54 ASP cc_start: 0.7434 (t0) cc_final: 0.6931 (t0) outliers start: 45 outliers final: 39 residues processed: 167 average time/residue: 0.1695 time to fit residues: 41.4849 Evaluate side-chains 170 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 571 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 99 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9018 Z= 0.178 Angle : 0.663 10.962 12188 Z= 0.313 Chirality : 0.042 0.184 1452 Planarity : 0.004 0.045 1542 Dihedral : 4.053 45.474 1250 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.30 % Allowed : 27.15 % Favored : 68.55 % 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: 1.74 (0.26), residues: 1142 helix: 1.97 (0.19), residues: 746 sheet: 1.38 (0.70), residues: 66 loop : -0.82 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 91 HIS 0.003 0.001 HIS A 107 PHE 0.021 0.001 PHE A 115 TYR 0.011 0.001 TYR B 439 ARG 0.004 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 140 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7176 (t0) cc_final: 0.6772 (t0) REVERT: A 242 MET cc_start: 0.7991 (mmt) cc_final: 0.7704 (mmt) REVERT: A 513 THR cc_start: 0.7420 (OUTLIER) cc_final: 0.7173 (p) REVERT: A 556 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7502 (tt) REVERT: B 54 ASP cc_start: 0.7451 (t0) cc_final: 0.6959 (t0) REVERT: B 513 THR cc_start: 0.7475 (OUTLIER) cc_final: 0.7204 (p) outliers start: 42 outliers final: 35 residues processed: 168 average time/residue: 0.1636 time to fit residues: 40.6499 Evaluate side-chains 170 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 571 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 0.0770 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9018 Z= 0.192 Angle : 0.702 12.363 12188 Z= 0.328 Chirality : 0.042 0.179 1452 Planarity : 0.004 0.042 1542 Dihedral : 4.117 45.263 1250 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.51 % Allowed : 27.56 % Favored : 67.93 % 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: 1.73 (0.26), residues: 1142 helix: 1.99 (0.19), residues: 746 sheet: 1.16 (0.67), residues: 66 loop : -0.82 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 91 HIS 0.003 0.001 HIS A 107 PHE 0.019 0.001 PHE A 115 TYR 0.021 0.001 TYR A 439 ARG 0.004 0.000 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7255 (t0) cc_final: 0.6803 (t0) REVERT: A 210 MET cc_start: 0.6898 (tmm) cc_final: 0.6411 (tmm) REVERT: A 242 MET cc_start: 0.7939 (mmt) cc_final: 0.7594 (mmt) REVERT: A 513 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7175 (p) REVERT: B 54 ASP cc_start: 0.7466 (t0) cc_final: 0.6935 (t0) REVERT: B 513 THR cc_start: 0.7515 (OUTLIER) cc_final: 0.7257 (p) outliers start: 44 outliers final: 37 residues processed: 165 average time/residue: 0.1567 time to fit residues: 38.7602 Evaluate side-chains 169 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 571 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9018 Z= 0.357 Angle : 0.821 12.594 12188 Z= 0.399 Chirality : 0.046 0.157 1452 Planarity : 0.005 0.044 1542 Dihedral : 4.380 44.612 1250 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.71 % Allowed : 27.56 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1142 helix: 1.50 (0.19), residues: 742 sheet: 0.65 (0.65), residues: 66 loop : -0.93 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 91 HIS 0.007 0.001 HIS A 576 PHE 0.021 0.002 PHE A 230 TYR 0.025 0.002 TYR A 439 ARG 0.005 0.001 ARG A 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 132 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7446 (t0) cc_final: 0.7000 (t0) REVERT: A 200 MET cc_start: 0.6638 (mmm) cc_final: 0.6333 (tpt) REVERT: A 210 MET cc_start: 0.7223 (tmm) cc_final: 0.6727 (tmm) REVERT: A 242 MET cc_start: 0.7826 (mmt) cc_final: 0.7508 (mmt) REVERT: A 517 ARG cc_start: 0.6823 (mtm110) cc_final: 0.6579 (mtm180) REVERT: B 54 ASP cc_start: 0.7599 (t0) cc_final: 0.7018 (t0) REVERT: B 513 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7274 (p) outliers start: 46 outliers final: 39 residues processed: 166 average time/residue: 0.1623 time to fit residues: 39.9174 Evaluate side-chains 169 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 chunk 65 optimal weight: 0.4980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 427 HIS ** 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 = 0.4296 r_free = 0.4296 target = 0.191422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142119 restraints weight = 12274.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140868 restraints weight = 14372.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.145310 restraints weight = 10984.774| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9018 Z= 0.195 Angle : 0.730 12.679 12188 Z= 0.343 Chirality : 0.043 0.178 1452 Planarity : 0.004 0.042 1542 Dihedral : 4.244 46.177 1250 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.38 % Allowed : 29.71 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1142 helix: 1.90 (0.19), residues: 746 sheet: 0.65 (0.65), residues: 66 loop : -0.73 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 91 HIS 0.003 0.001 HIS A 576 PHE 0.019 0.001 PHE A 115 TYR 0.018 0.001 TYR A 439 ARG 0.005 0.000 ARG A 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1929.38 seconds wall clock time: 35 minutes 29.45 seconds (2129.45 seconds total)