Starting phenix.real_space_refine on Fri Jul 19 20:20:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsr_41599/07_2024/8tsr_41599.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsr_41599/07_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_41599/07_2024/8tsr_41599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsr_41599/07_2024/8tsr_41599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsr_41599/07_2024/8tsr_41599.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsr_41599/07_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-5388/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: 5.03, per 1000 atoms: 0.57 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: 3.62 Conformation dependent library (CDL) restraints added in 1.6 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: 0.99 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: 2.86 Time building geometry restraints manager: 3.96 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 2.440 nonbonded pdb=" OG SER A 249 " pdb=" OG SER B 86 " model vdw 2.225 2.440 nonbonded pdb=" OD2 ASP A 117 " pdb=" OH TYR A 393 " model vdw 2.233 2.440 nonbonded pdb=" OE2 GLU B 506 " pdb=" OG1 THR B 541 " model vdw 2.274 2.440 nonbonded pdb=" OG1 THR B 350 " pdb=" OD2 ASP B 396 " model vdw 2.276 2.440 ... (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 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: 1.060 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.550 Find NCS groups from input model: 0.280 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.220 ------------------------------------------------------------------------------- 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 : 1.149 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: 0.2042 time to fit residues: 48.3304 Evaluate side-chains 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.0470 chunk 46 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 405 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9018 Z= 0.300 Angle : 0.710 11.293 12188 Z= 0.352 Chirality : 0.044 0.140 1452 Planarity : 0.005 0.072 1542 Dihedral : 4.555 45.003 1253 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.82 % Allowed : 21.21 % Favored : 73.98 % 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: 1.00 (0.25), residues: 1142 helix: 1.48 (0.19), residues: 758 sheet: 1.45 (0.66), residues: 66 loop : -1.54 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 17 HIS 0.008 0.002 HIS A 576 PHE 0.023 0.002 PHE A 230 TYR 0.011 0.001 TYR B 572 ARG 0.006 0.001 ARG A 517 *********************** 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 199 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 152 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7809 (mmt) cc_final: 0.7399 (mmt) REVERT: B 14 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7786 (mtt-85) REVERT: B 17 TRP cc_start: 0.8084 (t-100) cc_final: 0.7729 (t-100) REVERT: B 54 ASP cc_start: 0.7514 (t0) cc_final: 0.7076 (t0) outliers start: 47 outliers final: 32 residues processed: 188 average time/residue: 0.1928 time to fit residues: 51.5730 Evaluate side-chains 171 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 128 ILE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 245 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 63 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 276 MET 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: 8.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9018 Z= 0.194 Angle : 0.630 7.772 12188 Z= 0.310 Chirality : 0.042 0.231 1452 Planarity : 0.004 0.059 1542 Dihedral : 4.161 44.770 1250 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.69 % Allowed : 24.28 % Favored : 72.03 % 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: 1.41 (0.25), residues: 1142 helix: 1.75 (0.19), residues: 764 sheet: 1.57 (0.65), residues: 66 loop : -1.31 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 17 HIS 0.008 0.001 HIS B 576 PHE 0.021 0.002 PHE A 56 TYR 0.011 0.001 TYR A 572 ARG 0.004 0.000 ARG A 333 *********************** 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 178 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7853 (mmt) cc_final: 0.7648 (mmt) REVERT: B 54 ASP cc_start: 0.7398 (t0) cc_final: 0.6951 (t0) REVERT: B 242 MET cc_start: 0.7822 (mmt) cc_final: 0.7587 (mmp) outliers start: 36 outliers final: 24 residues processed: 167 average time/residue: 0.1857 time to fit residues: 45.6820 Evaluate side-chains 158 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 186 SER 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 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 85 SER Chi-restraints excluded: chain B residue 159 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 371 THR 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 525 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2366 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= 0.354 Angle : 0.743 9.089 12188 Z= 0.373 Chirality : 0.045 0.188 1452 Planarity : 0.005 0.050 1542 Dihedral : 4.347 43.384 1250 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.94 % Allowed : 25.31 % Favored : 68.75 % 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: 0.98 (0.25), residues: 1142 helix: 1.37 (0.19), residues: 762 sheet: 1.51 (0.67), residues: 66 loop : -1.31 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 91 HIS 0.011 0.002 HIS A 576 PHE 0.031 0.002 PHE A 56 TYR 0.016 0.002 TYR B 410 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 205 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 147 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7834 (t80) cc_final: 0.7625 (t80) REVERT: A 153 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8014 (tt) REVERT: A 200 MET cc_start: 0.6819 (mmm) cc_final: 0.6557 (mtp) REVERT: A 242 MET cc_start: 0.7900 (mmt) cc_final: 0.7670 (mmt) REVERT: B 54 ASP cc_start: 0.7586 (t0) cc_final: 0.7097 (t0) REVERT: B 153 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7925 (tt) outliers start: 58 outliers final: 42 residues processed: 188 average time/residue: 0.1748 time to fit residues: 48.2747 Evaluate side-chains 179 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 135 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 124 LEU Chi-restraints excluded: chain A residue 128 ILE 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 203 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 ASP 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 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 96 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2466 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= 0.203 Angle : 0.650 9.521 12188 Z= 0.311 Chirality : 0.041 0.166 1452 Planarity : 0.004 0.045 1542 Dihedral : 4.118 44.785 1250 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.12 % Allowed : 27.56 % Favored : 67.32 % 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: 1.51 (0.25), residues: 1142 helix: 1.84 (0.19), residues: 750 sheet: 1.67 (0.68), residues: 66 loop : -1.18 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 17 HIS 0.009 0.001 HIS B 576 PHE 0.022 0.002 PHE B 13 TYR 0.011 0.001 TYR A 445 ARG 0.008 0.001 ARG A 517 *********************** 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 193 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 143 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.8094 (mmt) cc_final: 0.7854 (mmt) REVERT: A 301 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7869 (tt) REVERT: B 54 ASP cc_start: 0.7418 (t0) cc_final: 0.6955 (t0) REVERT: B 242 MET cc_start: 0.7935 (mmt) cc_final: 0.7712 (mmt) outliers start: 50 outliers final: 33 residues processed: 179 average time/residue: 0.1857 time to fit residues: 47.3839 Evaluate side-chains 166 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 121 THR Chi-restraints excluded: chain A residue 186 SER 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 301 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 317 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR 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 525 GLU 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: 0.8980 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 57 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9018 Z= 0.209 Angle : 0.666 9.345 12188 Z= 0.317 Chirality : 0.042 0.157 1452 Planarity : 0.004 0.042 1542 Dihedral : 4.115 44.720 1250 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.82 % Allowed : 28.07 % Favored : 67.11 % 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: 1.61 (0.25), residues: 1142 helix: 1.87 (0.19), residues: 756 sheet: 1.75 (0.69), residues: 66 loop : -1.04 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 91 HIS 0.007 0.001 HIS A 576 PHE 0.016 0.001 PHE A 189 TYR 0.015 0.001 TYR B 439 ARG 0.005 0.000 ARG B 333 *********************** 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 180 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 133 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7709 (ttm) cc_final: 0.7467 (ttm) REVERT: A 242 MET cc_start: 0.8002 (mmt) cc_final: 0.7795 (mmt) REVERT: A 301 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 418 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8356 (mm-40) REVERT: A 556 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7617 (tt) REVERT: B 54 ASP cc_start: 0.7551 (t0) cc_final: 0.7057 (t0) REVERT: B 242 MET cc_start: 0.8006 (mmt) cc_final: 0.7741 (mmt) outliers start: 47 outliers final: 36 residues processed: 167 average time/residue: 0.1654 time to fit residues: 40.4668 Evaluate side-chains 172 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 121 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 301 LEU 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 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 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 244 MET Chi-restraints excluded: chain B residue 255 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 61 optimal weight: 0.0870 chunk 109 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 HIS B 209 GLN B 436 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2830 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= 0.176 Angle : 0.652 10.840 12188 Z= 0.307 Chirality : 0.041 0.159 1452 Planarity : 0.004 0.042 1542 Dihedral : 4.066 44.995 1250 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.41 % Allowed : 28.28 % Favored : 67.32 % 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: 1.83 (0.26), residues: 1142 helix: 2.10 (0.19), residues: 742 sheet: 1.69 (0.69), residues: 66 loop : -0.99 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 91 HIS 0.003 0.001 HIS A 576 PHE 0.017 0.001 PHE B 13 TYR 0.009 0.001 TYR A 572 ARG 0.006 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 183 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 140 time to evaluate : 1.822 Fit side-chains revert: symmetry clash REVERT: A 127 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.6906 (ttm170) REVERT: A 200 MET cc_start: 0.6500 (mtp) cc_final: 0.6166 (tpt) REVERT: A 242 MET cc_start: 0.8016 (mmt) cc_final: 0.7814 (mmt) REVERT: A 301 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7694 (tt) REVERT: B 54 ASP cc_start: 0.7461 (t0) cc_final: 0.6960 (t0) outliers start: 43 outliers final: 31 residues processed: 171 average time/residue: 0.2013 time to fit residues: 49.5877 Evaluate side-chains 163 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 121 THR Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 301 LEU 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 534 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 298 LEU 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: 0.2980 chunk 65 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9018 Z= 0.178 Angle : 0.672 11.201 12188 Z= 0.317 Chirality : 0.042 0.164 1452 Planarity : 0.004 0.039 1542 Dihedral : 4.085 45.341 1250 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.30 % Allowed : 27.66 % Favored : 68.03 % 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: 1.85 (0.26), residues: 1142 helix: 2.08 (0.19), residues: 746 sheet: 1.49 (0.68), residues: 66 loop : -0.85 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 91 HIS 0.004 0.001 HIS B 576 PHE 0.021 0.001 PHE A 115 TYR 0.019 0.001 TYR B 439 ARG 0.005 0.000 ARG A 127 *********************** 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 179 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7244 (t0) cc_final: 0.6831 (t0) REVERT: A 127 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.7039 (ttm170) REVERT: A 242 MET cc_start: 0.8012 (mmt) cc_final: 0.7784 (mmt) REVERT: A 301 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7561 (tt) REVERT: A 418 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8800 (mm-40) REVERT: A 556 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7539 (tt) REVERT: B 54 ASP cc_start: 0.7424 (t0) cc_final: 0.6926 (t0) outliers start: 42 outliers final: 31 residues processed: 165 average time/residue: 0.1731 time to fit residues: 41.8879 Evaluate side-chains 166 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 186 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 301 LEU 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 418 GLN 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3154 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= 0.200 Angle : 0.685 12.267 12188 Z= 0.323 Chirality : 0.042 0.159 1452 Planarity : 0.004 0.040 1542 Dihedral : 4.108 45.204 1250 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.00 % Allowed : 28.48 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.75 (0.26), residues: 1142 helix: 1.99 (0.19), residues: 746 sheet: 1.37 (0.67), residues: 66 loop : -0.84 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 91 HIS 0.009 0.001 HIS B 576 PHE 0.019 0.002 PHE A 115 TYR 0.018 0.001 TYR B 439 ARG 0.004 0.000 ARG A 127 *********************** 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 168 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7264 (t0) cc_final: 0.6810 (t0) REVERT: A 242 MET cc_start: 0.7978 (mmt) cc_final: 0.7751 (mmt) REVERT: A 261 LEU cc_start: 0.8464 (tp) cc_final: 0.8176 (tt) REVERT: A 301 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7717 (tt) REVERT: A 341 ASP cc_start: 0.6000 (OUTLIER) cc_final: 0.5380 (t0) REVERT: A 556 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7539 (tt) REVERT: B 54 ASP cc_start: 0.7453 (t0) cc_final: 0.6956 (t0) REVERT: B 341 ASP cc_start: 0.6289 (OUTLIER) cc_final: 0.5762 (t0) outliers start: 39 outliers final: 34 residues processed: 155 average time/residue: 0.1739 time to fit residues: 39.7568 Evaluate side-chains 160 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 159 MET Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 341 ASP 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 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 275 VAL Chi-restraints excluded: chain B residue 285 THR 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 341 ASP 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: 4.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 71 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 576 HIS ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9018 Z= 0.287 Angle : 0.746 12.310 12188 Z= 0.361 Chirality : 0.044 0.140 1452 Planarity : 0.004 0.068 1542 Dihedral : 4.264 45.521 1250 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.20 % Allowed : 29.30 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1142 helix: 1.73 (0.19), residues: 738 sheet: 1.10 (0.68), residues: 66 loop : -0.92 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 91 HIS 0.009 0.001 HIS B 576 PHE 0.018 0.002 PHE A 230 TYR 0.023 0.002 TYR B 439 ARG 0.010 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 166 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 125 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7313 (t0) cc_final: 0.6860 (t0) REVERT: A 242 MET cc_start: 0.7940 (mmt) cc_final: 0.7735 (mmt) REVERT: A 261 LEU cc_start: 0.8525 (tp) cc_final: 0.8233 (tt) REVERT: A 341 ASP cc_start: 0.5979 (OUTLIER) cc_final: 0.5417 (t70) REVERT: A 402 MET cc_start: 0.7224 (ppp) cc_final: 0.7011 (ppp) REVERT: A 435 ASN cc_start: 0.8317 (m-40) cc_final: 0.7979 (t0) REVERT: A 556 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7735 (tt) REVERT: B 54 ASP cc_start: 0.7613 (t0) cc_final: 0.7072 (t0) REVERT: B 341 ASP cc_start: 0.6471 (t0) cc_final: 0.5975 (t0) outliers start: 41 outliers final: 35 residues processed: 154 average time/residue: 0.1548 time to fit residues: 36.0985 Evaluate side-chains 161 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 96 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 186 SER 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 341 ASP 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 534 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 285 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 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 ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.190643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143096 restraints weight = 12264.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.141274 restraints weight = 15795.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.145046 restraints weight = 12244.796| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3372 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= 0.190 Angle : 0.690 12.584 12188 Z= 0.325 Chirality : 0.042 0.157 1452 Planarity : 0.004 0.073 1542 Dihedral : 4.148 45.836 1250 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.89 % Allowed : 29.41 % Favored : 66.70 % 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: 1.61 (0.26), residues: 1142 helix: 1.87 (0.19), residues: 746 sheet: 0.88 (0.68), residues: 66 loop : -0.75 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 91 HIS 0.005 0.001 HIS B 576 PHE 0.018 0.001 PHE A 115 TYR 0.019 0.001 TYR B 439 ARG 0.007 0.000 ARG A 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1886.11 seconds wall clock time: 34 minutes 26.58 seconds (2066.58 seconds total)