Starting phenix.real_space_refine on Fri Nov 15 05:18:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6c_37320/11_2024/8w6c_37320.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6c_37320/11_2024/8w6c_37320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6c_37320/11_2024/8w6c_37320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6c_37320/11_2024/8w6c_37320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6c_37320/11_2024/8w6c_37320.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6c_37320/11_2024/8w6c_37320.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 58 5.16 5 Na 4 4.78 5 C 5594 2.51 5 N 1290 2.21 5 O 1412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8360 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4081 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 33, 'TRANS': 496} Chain breaks: 1 Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 133 Unusual residues: {' NA': 2, '3PH': 1, 'CIT': 1, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {' NA': 2, '3PH': 1, 'CIT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B Time building chain proxies: 7.72, per 1000 atoms: 0.92 Number of scatterers: 8360 At special positions: 0 Unit cell: (96.743, 107.613, 90.221, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 2 15.00 Na 4 11.00 O 1412 8.00 N 1290 7.00 C 5594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 76.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.007A pdb=" N GLN A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 24 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 33 through 51 removed outlier: 3.588A pdb=" N ALA A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.970A pdb=" N ILE A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.580A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.673A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 3.848A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 140 through 163 Proline residue: A 150 - end of helix removed outlier: 3.708A pdb=" N GLN A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 233 removed outlier: 3.853A pdb=" N GLN A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 254 removed outlier: 3.970A pdb=" N LEU A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 290 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 304 through 321 Processing helix chain 'A' and resid 326 through 345 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 418 through 438 removed outlier: 3.591A pdb=" N VAL A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 453 Proline residue: A 450 - end of helix removed outlier: 4.117A pdb=" N SER A 453 " --> pdb=" O PRO A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 453' Processing helix chain 'A' and resid 455 through 471 removed outlier: 3.723A pdb=" N ALA A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 494 Proline residue: A 485 - end of helix removed outlier: 3.515A pdb=" N SER A 489 " --> pdb=" O PRO A 485 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 509 removed outlier: 3.569A pdb=" N CYS A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.595A pdb=" N ALA A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 525 " --> pdb=" O PRO A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 557 removed outlier: 4.688A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.579A pdb=" N GLN A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 4.007A pdb=" N GLN B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 7 " --> pdb=" O THR B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 24 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 25 through 31 Processing helix chain 'B' and resid 33 through 51 removed outlier: 3.589A pdb=" N ALA B 41 " --> pdb=" O TYR B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.971A pdb=" N ILE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.580A pdb=" N VAL B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.672A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.848A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 137 Processing helix chain 'B' and resid 140 through 163 Proline residue: B 150 - end of helix removed outlier: 3.708A pdb=" N GLN B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 233 removed outlier: 3.854A pdb=" N GLN B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 230 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 254 removed outlier: 3.968A pdb=" N LEU B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 290 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 304 through 321 Processing helix chain 'B' and resid 326 through 345 Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 369 through 381 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 418 through 438 removed outlier: 3.590A pdb=" N VAL B 422 " --> pdb=" O PRO B 418 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 447 through 453 Proline residue: B 450 - end of helix removed outlier: 4.117A pdb=" N SER B 453 " --> pdb=" O PRO B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 447 through 453' Processing helix chain 'B' and resid 455 through 471 removed outlier: 3.723A pdb=" N ALA B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 461 " --> pdb=" O PRO B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 494 Proline residue: B 485 - end of helix removed outlier: 3.516A pdb=" N SER B 489 " --> pdb=" O PRO B 485 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 494 " --> pdb=" O MET B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 509 removed outlier: 3.570A pdb=" N CYS B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 509 " --> pdb=" O CYS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 removed outlier: 3.596A pdb=" N ALA B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 525 " --> pdb=" O PRO B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 557 removed outlier: 4.688A pdb=" N LEU B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.579A pdb=" N GLN B 573 " --> pdb=" O SER B 570 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1455 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: 2.37 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1267 1.32 - 1.44: 2253 1.44 - 1.56: 4966 1.56 - 1.69: 2 1.69 - 1.81: 96 Bond restraints: 8584 Sorted by residual: bond pdb=" O11 3PH A 806 " pdb=" P 3PH A 806 " ideal model delta sigma weight residual 1.703 1.606 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" O11 3PH B1101 " pdb=" P 3PH B1101 " ideal model delta sigma weight residual 1.703 1.608 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C1 3PH A 806 " pdb=" O11 3PH A 806 " ideal model delta sigma weight residual 1.385 1.453 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1 3PH B1101 " pdb=" O11 3PH B1101 " ideal model delta sigma weight residual 1.385 1.452 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C PHE A 359 " pdb=" N PRO A 360 " ideal model delta sigma weight residual 1.329 1.365 -0.036 1.22e-02 6.72e+03 8.51e+00 ... (remaining 8579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 11263 2.30 - 4.59: 363 4.59 - 6.89: 72 6.89 - 9.18: 20 9.18 - 11.48: 6 Bond angle restraints: 11724 Sorted by residual: angle pdb=" C GLU A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta sigma weight residual 121.80 131.71 -9.91 2.44e+00 1.68e-01 1.65e+01 angle pdb=" C GLU B 396 " pdb=" N ASN B 397 " pdb=" CA ASN B 397 " ideal model delta sigma weight residual 121.80 131.63 -9.83 2.44e+00 1.68e-01 1.62e+01 angle pdb=" C LEU A 61 " pdb=" N PHE A 62 " pdb=" CA PHE A 62 " ideal model delta sigma weight residual 120.06 124.85 -4.79 1.19e+00 7.06e-01 1.62e+01 angle pdb=" C LEU B 61 " pdb=" N PHE B 62 " pdb=" CA PHE B 62 " ideal model delta sigma weight residual 120.06 124.84 -4.78 1.19e+00 7.06e-01 1.61e+01 angle pdb=" C GLU A 302 " pdb=" N LYS A 303 " pdb=" CA LYS A 303 " ideal model delta sigma weight residual 125.66 131.99 -6.33 1.85e+00 2.92e-01 1.17e+01 ... (remaining 11719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.64: 4989 30.64 - 61.28: 133 61.28 - 91.93: 14 91.93 - 122.57: 0 122.57 - 153.21: 2 Dihedral angle restraints: 5138 sinusoidal: 2076 harmonic: 3062 Sorted by residual: dihedral pdb=" C21 3PH A 806 " pdb=" C2 3PH A 806 " pdb=" O21 3PH A 806 " pdb=" C3 3PH A 806 " ideal model delta sinusoidal sigma weight residual 147.58 -59.21 -153.21 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C21 3PH B1101 " pdb=" C2 3PH B1101 " pdb=" O21 3PH B1101 " pdb=" C3 3PH B1101 " ideal model delta sinusoidal sigma weight residual 147.58 -64.65 -147.77 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CA LYS B 400 " pdb=" C LYS B 400 " pdb=" N LEU B 401 " pdb=" CA LEU B 401 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 865 0.044 - 0.088: 382 0.088 - 0.132: 110 0.132 - 0.176: 27 0.176 - 0.220: 10 Chirality restraints: 1394 Sorted by residual: chirality pdb=" CB VAL A 73 " pdb=" CA VAL A 73 " pdb=" CG1 VAL A 73 " pdb=" CG2 VAL A 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB VAL B 73 " pdb=" CA VAL B 73 " pdb=" CG1 VAL B 73 " pdb=" CG2 VAL B 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA VAL A 454 " pdb=" N VAL A 454 " pdb=" C VAL A 454 " pdb=" CB VAL A 454 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1391 not shown) Planarity restraints: 1414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 25 " -0.052 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO A 26 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 25 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.44e+00 pdb=" N PRO B 26 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 519 " -0.050 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO A 520 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " -0.042 5.00e-02 4.00e+02 ... (remaining 1411 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 273 2.71 - 3.26: 7857 3.26 - 3.81: 13065 3.81 - 4.35: 17801 4.35 - 4.90: 29368 Nonbonded interactions: 68364 Sorted by model distance: nonbonded pdb=" O1 CIT B1104 " pdb=" O7 CIT B1104 " model vdw 2.163 3.040 nonbonded pdb=" O3 CIT A 804 " pdb=" O7 CIT A 804 " model vdw 2.164 3.040 nonbonded pdb=" OG SER B 140 " pdb=" O6 CIT B1104 " model vdw 2.280 3.040 nonbonded pdb=" OG SER A 140 " pdb=" O6 CIT A 804 " model vdw 2.281 3.040 nonbonded pdb=" O GLN B 158 " pdb=" OG SER B 162 " model vdw 2.302 3.040 ... (remaining 68359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 578 or resid 802 or resid 804)) selection = (chain 'B' and (resid 1 through 578 or resid 1102 or resid 1104)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.620 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 : 0.007 0.097 8584 Z= 0.429 Angle : 1.049 11.479 11724 Z= 0.560 Chirality : 0.055 0.220 1394 Planarity : 0.009 0.077 1414 Dihedral : 14.780 153.210 3150 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.13 % Allowed : 4.76 % Favored : 94.10 % 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: -3.18 (0.21), residues: 1052 helix: -1.80 (0.15), residues: 756 sheet: None (None), residues: 0 loop : -2.47 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 410 HIS 0.006 0.001 HIS B 497 PHE 0.022 0.002 PHE A 359 TYR 0.008 0.002 TYR A 500 ARG 0.003 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8573 (mtp) cc_final: 0.8329 (mtm) REVERT: A 129 MET cc_start: 0.9117 (mtp) cc_final: 0.8600 (mtp) REVERT: A 286 GLN cc_start: 0.8403 (tt0) cc_final: 0.8157 (tt0) REVERT: A 295 ARG cc_start: 0.7066 (mtp-110) cc_final: 0.6582 (mpt180) REVERT: A 320 ARG cc_start: 0.7362 (ttm110) cc_final: 0.7087 (ttp-170) REVERT: A 433 LYS cc_start: 0.8507 (tptt) cc_final: 0.8198 (tptm) REVERT: A 514 MET cc_start: 0.8702 (mtm) cc_final: 0.8409 (mtm) REVERT: B 69 MET cc_start: 0.8619 (mtp) cc_final: 0.8368 (mtm) REVERT: B 129 MET cc_start: 0.9128 (mtp) cc_final: 0.8595 (mtp) REVERT: B 295 ARG cc_start: 0.7077 (mtp-110) cc_final: 0.6642 (mpt180) REVERT: B 433 LYS cc_start: 0.8500 (tptt) cc_final: 0.8181 (tptp) REVERT: B 514 MET cc_start: 0.8705 (mtm) cc_final: 0.8407 (mtm) outliers start: 10 outliers final: 2 residues processed: 143 average time/residue: 1.2306 time to fit residues: 187.6939 Evaluate side-chains 112 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 240 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 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 6 GLN A 257 ASN A 297 ASN A 308 GLN A 356 ASN A 414 ASN A 556 ASN B 6 GLN B 257 ASN B 286 GLN B 297 ASN B 308 GLN B 356 ASN B 414 ASN B 556 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8584 Z= 0.197 Angle : 0.666 7.864 11724 Z= 0.321 Chirality : 0.042 0.153 1394 Planarity : 0.007 0.059 1414 Dihedral : 10.545 153.360 1334 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.49 % Allowed : 8.96 % Favored : 88.55 % 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: -0.70 (0.26), residues: 1052 helix: 0.27 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -2.32 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 410 HIS 0.002 0.001 HIS A 106 PHE 0.013 0.001 PHE B 351 TYR 0.007 0.001 TYR B 500 ARG 0.001 0.000 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8830 (mtp) cc_final: 0.8571 (mtm) REVERT: A 88 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8312 (mm) REVERT: A 129 MET cc_start: 0.9021 (mtp) cc_final: 0.8471 (mtp) REVERT: A 286 GLN cc_start: 0.8377 (tt0) cc_final: 0.8064 (tt0) REVERT: A 295 ARG cc_start: 0.7162 (mtp-110) cc_final: 0.6762 (mpt180) REVERT: A 433 LYS cc_start: 0.8525 (tptt) cc_final: 0.8200 (tptp) REVERT: A 514 MET cc_start: 0.8749 (mtm) cc_final: 0.8416 (mtm) REVERT: B 69 MET cc_start: 0.8820 (mtp) cc_final: 0.8564 (mtm) REVERT: B 88 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8387 (mm) REVERT: B 129 MET cc_start: 0.9026 (mtp) cc_final: 0.8462 (mtp) REVERT: B 295 ARG cc_start: 0.7162 (mtp-110) cc_final: 0.6741 (mmt180) REVERT: B 433 LYS cc_start: 0.8483 (tptt) cc_final: 0.8149 (tptm) REVERT: B 514 MET cc_start: 0.8737 (mtm) cc_final: 0.8441 (mtm) outliers start: 22 outliers final: 9 residues processed: 127 average time/residue: 1.2158 time to fit residues: 164.6546 Evaluate side-chains 121 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 286 GLN B 6 GLN B 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8584 Z= 0.213 Angle : 0.648 7.682 11724 Z= 0.313 Chirality : 0.042 0.156 1394 Planarity : 0.006 0.054 1414 Dihedral : 10.488 152.758 1332 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.61 % Allowed : 10.66 % Favored : 86.73 % 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: 0.30 (0.27), residues: 1052 helix: 1.07 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -2.09 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 410 HIS 0.001 0.000 HIS A 106 PHE 0.013 0.001 PHE B 350 TYR 0.007 0.001 TYR B 500 ARG 0.001 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8823 (mtp) cc_final: 0.8563 (mtm) REVERT: A 101 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: A 129 MET cc_start: 0.9013 (mtp) cc_final: 0.8466 (mtp) REVERT: A 295 ARG cc_start: 0.7296 (mtp-110) cc_final: 0.6951 (mpt180) REVERT: A 411 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7849 (tttt) REVERT: A 433 LYS cc_start: 0.8529 (tptt) cc_final: 0.8170 (tptm) REVERT: A 514 MET cc_start: 0.8740 (mtm) cc_final: 0.8461 (mtm) REVERT: B 69 MET cc_start: 0.8821 (mtp) cc_final: 0.8572 (mtm) REVERT: B 101 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: B 129 MET cc_start: 0.9017 (mtp) cc_final: 0.8458 (mtp) REVERT: B 295 ARG cc_start: 0.7278 (mtp-110) cc_final: 0.6937 (mpt180) REVERT: B 433 LYS cc_start: 0.8569 (tptt) cc_final: 0.8205 (tptm) REVERT: B 514 MET cc_start: 0.8738 (mtm) cc_final: 0.8459 (mtm) outliers start: 23 outliers final: 15 residues processed: 125 average time/residue: 1.2454 time to fit residues: 165.6377 Evaluate side-chains 128 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 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 6 GLN B 6 GLN B 286 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8584 Z= 0.179 Angle : 0.606 7.358 11724 Z= 0.292 Chirality : 0.041 0.154 1394 Planarity : 0.006 0.052 1414 Dihedral : 10.368 152.314 1332 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.29 % Allowed : 11.90 % Favored : 84.81 % 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: 0.87 (0.28), residues: 1052 helix: 1.50 (0.20), residues: 760 sheet: None (None), residues: 0 loop : -1.95 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 410 HIS 0.002 0.000 HIS B 497 PHE 0.012 0.001 PHE B 351 TYR 0.004 0.001 TYR B 500 ARG 0.001 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8806 (mtp) cc_final: 0.8552 (mtm) REVERT: A 88 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8403 (mm) REVERT: A 94 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8763 (mm) REVERT: A 129 MET cc_start: 0.9006 (mtp) cc_final: 0.8498 (mtp) REVERT: A 295 ARG cc_start: 0.7299 (mtp-110) cc_final: 0.6961 (mpt180) REVERT: A 409 ASP cc_start: 0.8352 (p0) cc_final: 0.7933 (p0) REVERT: A 433 LYS cc_start: 0.8510 (tptt) cc_final: 0.8201 (tptp) REVERT: B 69 MET cc_start: 0.8792 (mtp) cc_final: 0.8559 (mtm) REVERT: B 88 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8434 (mm) REVERT: B 129 MET cc_start: 0.9012 (mtp) cc_final: 0.8496 (mtp) REVERT: B 295 ARG cc_start: 0.7316 (mtp-110) cc_final: 0.6925 (mpt180) REVERT: B 409 ASP cc_start: 0.8227 (p0) cc_final: 0.7935 (p0) REVERT: B 411 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7978 (mttt) REVERT: B 433 LYS cc_start: 0.8564 (tptt) cc_final: 0.8199 (tptm) outliers start: 29 outliers final: 14 residues processed: 129 average time/residue: 1.1233 time to fit residues: 155.2930 Evaluate side-chains 128 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.0870 chunk 42 optimal weight: 0.4980 chunk 87 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 0.0980 chunk 34 optimal weight: 9.9990 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 286 GLN B 6 GLN B 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8584 Z= 0.278 Angle : 0.690 8.628 11724 Z= 0.333 Chirality : 0.045 0.156 1394 Planarity : 0.006 0.053 1414 Dihedral : 10.581 151.457 1332 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.51 % Allowed : 13.04 % Favored : 83.45 % 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: 0.77 (0.27), residues: 1052 helix: 1.34 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -1.83 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 410 HIS 0.002 0.000 HIS A 106 PHE 0.015 0.002 PHE A 350 TYR 0.009 0.002 TYR A 500 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6648 (mp-120) REVERT: A 69 MET cc_start: 0.8835 (mtp) cc_final: 0.8574 (mtm) REVERT: A 94 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8851 (mm) REVERT: A 101 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: A 129 MET cc_start: 0.9000 (mtp) cc_final: 0.8473 (mtp) REVERT: A 295 ARG cc_start: 0.7301 (mtp-110) cc_final: 0.6915 (mpt180) REVERT: A 352 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8110 (mp) REVERT: A 433 LYS cc_start: 0.8553 (tptt) cc_final: 0.8224 (tptp) REVERT: B 69 MET cc_start: 0.8851 (mtp) cc_final: 0.8591 (mtm) REVERT: B 94 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8869 (mm) REVERT: B 101 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: B 129 MET cc_start: 0.9003 (mtp) cc_final: 0.8465 (mtp) REVERT: B 295 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.6890 (mpt180) REVERT: B 352 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8113 (mp) REVERT: B 433 LYS cc_start: 0.8539 (tptt) cc_final: 0.8186 (tptm) outliers start: 31 outliers final: 16 residues processed: 129 average time/residue: 1.2716 time to fit residues: 174.7409 Evaluate side-chains 131 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN B 6 GLN B 286 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8584 Z= 0.185 Angle : 0.616 7.499 11724 Z= 0.298 Chirality : 0.042 0.153 1394 Planarity : 0.006 0.052 1414 Dihedral : 10.475 152.560 1332 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.63 % Allowed : 13.95 % Favored : 82.43 % 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: 1.17 (0.28), residues: 1052 helix: 1.77 (0.20), residues: 756 sheet: None (None), residues: 0 loop : -1.95 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 410 HIS 0.002 0.000 HIS B 497 PHE 0.012 0.001 PHE A 351 TYR 0.005 0.001 TYR B 429 ARG 0.001 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8814 (mtp) cc_final: 0.8542 (mtm) REVERT: A 88 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8405 (mm) REVERT: A 101 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: A 129 MET cc_start: 0.8996 (mtp) cc_final: 0.8459 (mtp) REVERT: A 295 ARG cc_start: 0.7336 (mtp-110) cc_final: 0.6902 (mpt180) REVERT: A 352 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8104 (mp) REVERT: A 409 ASP cc_start: 0.8367 (p0) cc_final: 0.7997 (p0) REVERT: A 433 LYS cc_start: 0.8487 (tptt) cc_final: 0.8170 (tptp) REVERT: B 52 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7264 (mt-10) REVERT: B 69 MET cc_start: 0.8828 (mtp) cc_final: 0.8560 (mtm) REVERT: B 88 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8428 (mm) REVERT: B 94 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8776 (mm) REVERT: B 101 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: B 129 MET cc_start: 0.9000 (mtp) cc_final: 0.8462 (mtp) REVERT: B 295 ARG cc_start: 0.7320 (mtp-110) cc_final: 0.6874 (mpt180) REVERT: B 352 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8144 (mp) REVERT: B 409 ASP cc_start: 0.8336 (p0) cc_final: 0.7962 (p0) REVERT: B 433 LYS cc_start: 0.8555 (tptt) cc_final: 0.8199 (tptm) outliers start: 32 outliers final: 19 residues processed: 130 average time/residue: 1.2063 time to fit residues: 167.7064 Evaluate side-chains 135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.0370 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 286 GLN B 6 GLN B 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8584 Z= 0.172 Angle : 0.599 7.189 11724 Z= 0.289 Chirality : 0.041 0.153 1394 Planarity : 0.005 0.050 1414 Dihedral : 10.383 152.440 1332 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.63 % Allowed : 13.72 % Favored : 82.65 % 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: 1.36 (0.28), residues: 1052 helix: 1.92 (0.20), residues: 756 sheet: None (None), residues: 0 loop : -1.88 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 410 HIS 0.002 0.000 HIS B 497 PHE 0.012 0.001 PHE A 351 TYR 0.005 0.001 TYR A 500 ARG 0.001 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8800 (mtp) cc_final: 0.8551 (mtm) REVERT: A 88 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8338 (mm) REVERT: A 94 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8790 (mm) REVERT: A 101 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: A 129 MET cc_start: 0.9001 (mtp) cc_final: 0.8462 (mtp) REVERT: A 295 ARG cc_start: 0.7329 (mtp-110) cc_final: 0.6916 (mpt180) REVERT: A 433 LYS cc_start: 0.8488 (tptt) cc_final: 0.8180 (tptp) REVERT: B 52 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: B 69 MET cc_start: 0.8799 (mtp) cc_final: 0.8538 (mtm) REVERT: B 88 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8355 (mm) REVERT: B 94 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8766 (mm) REVERT: B 101 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: B 129 MET cc_start: 0.9005 (mtp) cc_final: 0.8491 (mtp) REVERT: B 295 ARG cc_start: 0.7294 (mtp-110) cc_final: 0.6876 (mpt180) REVERT: B 433 LYS cc_start: 0.8557 (tptt) cc_final: 0.8205 (tptm) outliers start: 32 outliers final: 19 residues processed: 132 average time/residue: 1.2618 time to fit residues: 177.8483 Evaluate side-chains 137 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 286 GLN B 6 GLN B 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8584 Z= 0.178 Angle : 0.602 7.285 11724 Z= 0.290 Chirality : 0.042 0.152 1394 Planarity : 0.005 0.051 1414 Dihedral : 10.328 152.232 1332 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.74 % Allowed : 13.83 % Favored : 82.43 % 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: 1.50 (0.28), residues: 1052 helix: 2.04 (0.20), residues: 752 sheet: None (None), residues: 0 loop : -1.82 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 410 HIS 0.002 0.000 HIS A 497 PHE 0.012 0.001 PHE B 351 TYR 0.006 0.001 TYR A 500 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8794 (mtp) cc_final: 0.8562 (mtm) REVERT: A 88 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8335 (mm) REVERT: A 94 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8790 (mm) REVERT: A 101 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: A 129 MET cc_start: 0.8995 (mtp) cc_final: 0.8479 (mtp) REVERT: A 295 ARG cc_start: 0.7347 (mtp-110) cc_final: 0.6904 (mpt180) REVERT: A 433 LYS cc_start: 0.8484 (tptt) cc_final: 0.8179 (tptp) REVERT: B 6 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6725 (mp-120) REVERT: B 52 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7265 (mt-10) REVERT: B 69 MET cc_start: 0.8824 (mtp) cc_final: 0.8569 (mtm) REVERT: B 88 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8357 (mm) REVERT: B 94 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8771 (mm) REVERT: B 101 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: B 129 MET cc_start: 0.9006 (mtp) cc_final: 0.8503 (mtp) REVERT: B 295 ARG cc_start: 0.7286 (mtp-110) cc_final: 0.6867 (mpt180) REVERT: B 433 LYS cc_start: 0.8559 (tptt) cc_final: 0.8214 (tptm) outliers start: 33 outliers final: 22 residues processed: 133 average time/residue: 1.2174 time to fit residues: 173.5102 Evaluate side-chains 139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 534 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 6 GLN B 286 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8584 Z= 0.179 Angle : 0.606 8.009 11724 Z= 0.292 Chirality : 0.042 0.152 1394 Planarity : 0.005 0.050 1414 Dihedral : 10.302 152.198 1332 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.63 % Allowed : 14.40 % Favored : 81.97 % 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: 1.58 (0.28), residues: 1052 helix: 2.08 (0.20), residues: 752 sheet: None (None), residues: 0 loop : -1.76 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 410 HIS 0.002 0.000 HIS A 497 PHE 0.011 0.001 PHE B 351 TYR 0.006 0.001 TYR A 500 ARG 0.001 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8802 (mtp) cc_final: 0.8570 (mtm) REVERT: A 88 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8332 (mm) REVERT: A 94 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8786 (mm) REVERT: A 101 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: A 129 MET cc_start: 0.8997 (mtp) cc_final: 0.8485 (mtp) REVERT: A 295 ARG cc_start: 0.7343 (mtp-110) cc_final: 0.6856 (mpt180) REVERT: A 433 LYS cc_start: 0.8485 (tptt) cc_final: 0.8176 (tptp) REVERT: B 52 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: B 69 MET cc_start: 0.8819 (mtp) cc_final: 0.8569 (mtm) REVERT: B 88 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8358 (mm) REVERT: B 94 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8766 (mm) REVERT: B 101 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: B 129 MET cc_start: 0.9006 (mtp) cc_final: 0.8506 (mtp) REVERT: B 295 ARG cc_start: 0.7283 (mtp-110) cc_final: 0.6865 (mpt180) REVERT: B 433 LYS cc_start: 0.8562 (tptt) cc_final: 0.8219 (tptm) outliers start: 32 outliers final: 22 residues processed: 128 average time/residue: 1.2215 time to fit residues: 166.5749 Evaluate side-chains 137 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 534 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 4.9990 chunk 47 optimal weight: 0.2980 chunk 69 optimal weight: 0.0870 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.0570 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 286 GLN B 6 GLN B 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8584 Z= 0.152 Angle : 0.577 8.599 11724 Z= 0.278 Chirality : 0.040 0.151 1394 Planarity : 0.005 0.050 1414 Dihedral : 10.155 151.995 1332 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.95 % Allowed : 14.85 % Favored : 82.20 % 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: 1.79 (0.28), residues: 1052 helix: 2.20 (0.20), residues: 754 sheet: None (None), residues: 0 loop : -1.60 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 410 HIS 0.002 0.000 HIS B 497 PHE 0.011 0.001 PHE A 351 TYR 0.004 0.001 TYR B 40 ARG 0.001 0.000 ARG B 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7083 (mt-10) REVERT: A 69 MET cc_start: 0.8796 (mtp) cc_final: 0.8553 (mtm) REVERT: A 88 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8305 (mm) REVERT: A 94 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8721 (mm) REVERT: A 129 MET cc_start: 0.9003 (mtp) cc_final: 0.8501 (mtp) REVERT: A 295 ARG cc_start: 0.7277 (mtp-110) cc_final: 0.6797 (mpt180) REVERT: A 433 LYS cc_start: 0.8501 (tptt) cc_final: 0.8198 (tptp) REVERT: B 52 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: B 69 MET cc_start: 0.8792 (mtp) cc_final: 0.8580 (mtm) REVERT: B 88 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8312 (mm) REVERT: B 94 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8730 (mm) REVERT: B 129 MET cc_start: 0.9014 (mtp) cc_final: 0.8533 (mtp) REVERT: B 295 ARG cc_start: 0.7232 (mtp-110) cc_final: 0.6860 (mpt180) REVERT: B 433 LYS cc_start: 0.8520 (tptt) cc_final: 0.8213 (tptp) REVERT: B 538 ARG cc_start: 0.8326 (ttp80) cc_final: 0.8120 (ttm110) outliers start: 26 outliers final: 17 residues processed: 126 average time/residue: 1.1654 time to fit residues: 156.8519 Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 534 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 6 GLN B 256 GLN B 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.132461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.108593 restraints weight = 8783.204| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.35 r_work: 0.3003 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8584 Z= 0.180 Angle : 0.602 8.859 11724 Z= 0.289 Chirality : 0.041 0.150 1394 Planarity : 0.005 0.050 1414 Dihedral : 10.162 151.854 1332 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.72 % Allowed : 15.08 % Favored : 82.20 % 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: 1.77 (0.28), residues: 1052 helix: 2.19 (0.20), residues: 752 sheet: None (None), residues: 0 loop : -1.58 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 410 HIS 0.002 0.000 HIS B 497 PHE 0.011 0.001 PHE A 351 TYR 0.006 0.001 TYR A 500 ARG 0.000 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3313.07 seconds wall clock time: 60 minutes 19.61 seconds (3619.61 seconds total)