Starting phenix.real_space_refine on Wed Feb 12 20:59:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6c_37320/02_2025/8w6c_37320.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6c_37320/02_2025/8w6c_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/cci-nas-00/data/ceres_data/8w6c_37320/02_2025/8w6c_37320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6c_37320/02_2025/8w6c_37320.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6c_37320/02_2025/8w6c_37320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6c_37320/02_2025/8w6c_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.61, per 1000 atoms: 0.91 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: 2.14 Conformation dependent library (CDL) restraints added in 1.0 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: 0.78 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: 2.22 Time building geometry restraints manager: 2.41 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: 1.410 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: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.500 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- 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 : 0.905 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: 1.2457 time to fit residues: 189.6935 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 : 0.967 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.125629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.101455 restraints weight = 8872.109| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.35 r_work: 0.2968 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9127 (mtp) cc_final: 0.8856 (mtm) REVERT: A 88 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8397 (mm) REVERT: A 129 MET cc_start: 0.9148 (mtp) cc_final: 0.8645 (mtp) REVERT: A 286 GLN cc_start: 0.8551 (tt0) cc_final: 0.8270 (tt0) REVERT: A 295 ARG cc_start: 0.7613 (mtp-110) cc_final: 0.6811 (mpt180) REVERT: A 313 CYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7666 (m) REVERT: A 433 LYS cc_start: 0.8741 (tptt) cc_final: 0.8340 (tptp) REVERT: A 446 ASN cc_start: 0.8723 (m-40) cc_final: 0.8522 (m-40) REVERT: A 514 MET cc_start: 0.9009 (mtm) cc_final: 0.8713 (mtm) REVERT: B 69 MET cc_start: 0.9129 (mtp) cc_final: 0.8857 (mtm) REVERT: B 88 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8469 (mm) REVERT: B 129 MET cc_start: 0.9145 (mtp) cc_final: 0.8626 (mtp) REVERT: B 295 ARG cc_start: 0.7642 (mtp-110) cc_final: 0.6783 (mmt180) REVERT: B 313 CYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7715 (m) REVERT: B 411 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8113 (mppt) REVERT: B 433 LYS cc_start: 0.8728 (tptt) cc_final: 0.8292 (tptm) REVERT: B 514 MET cc_start: 0.8996 (mtm) cc_final: 0.8730 (mtm) outliers start: 22 outliers final: 9 residues processed: 127 average time/residue: 1.2072 time to fit residues: 163.7639 Evaluate side-chains 124 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 313 CYS 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 313 CYS Chi-restraints excluded: chain B residue 411 LYS 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 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 84 optimal weight: 0.0070 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 286 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.132233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.108640 restraints weight = 8919.739| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.35 r_work: 0.2951 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1602 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= 0.168 Angle : 0.601 7.044 11724 Z= 0.290 Chirality : 0.041 0.154 1394 Planarity : 0.006 0.055 1414 Dihedral : 10.286 152.182 1332 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.49 % Allowed : 10.43 % Favored : 87.07 % 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: 0.51 (0.27), residues: 1052 helix: 1.27 (0.20), residues: 756 sheet: None (None), residues: 0 loop : -2.14 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 410 HIS 0.002 0.000 HIS B 497 PHE 0.011 0.001 PHE B 351 TYR 0.003 0.001 TYR A 312 ARG 0.001 0.000 ARG A 120 *********************** 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: 22 poor density : 113 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9110 (mtp) cc_final: 0.8870 (mtm) REVERT: A 88 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8498 (mm) REVERT: A 129 MET cc_start: 0.9148 (mtp) cc_final: 0.8670 (mtp) REVERT: A 295 ARG cc_start: 0.7765 (mtp-110) cc_final: 0.7023 (mpt180) REVERT: A 409 ASP cc_start: 0.8609 (p0) cc_final: 0.8324 (p0) REVERT: A 411 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8121 (tttt) REVERT: A 433 LYS cc_start: 0.8730 (tptt) cc_final: 0.8343 (tptp) REVERT: B 69 MET cc_start: 0.9109 (mtp) cc_final: 0.8875 (mtm) REVERT: B 88 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8505 (mm) REVERT: B 129 MET cc_start: 0.9144 (mtp) cc_final: 0.8654 (mtp) REVERT: B 295 ARG cc_start: 0.7768 (mtp-110) cc_final: 0.7015 (mpt180) REVERT: B 409 ASP cc_start: 0.8588 (p0) cc_final: 0.8306 (p0) REVERT: B 411 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8120 (tttt) REVERT: B 433 LYS cc_start: 0.8810 (tptt) cc_final: 0.8353 (tptm) outliers start: 22 outliers final: 10 residues processed: 121 average time/residue: 1.1999 time to fit residues: 154.9254 Evaluate side-chains 124 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU 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 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 161 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 103 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.124821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100175 restraints weight = 8940.748| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.38 r_work: 0.2850 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1720 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= 0.203 Angle : 0.632 7.643 11724 Z= 0.303 Chirality : 0.042 0.153 1394 Planarity : 0.006 0.052 1414 Dihedral : 10.367 152.450 1332 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.85 % Allowed : 10.66 % Favored : 85.49 % 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: 0.92 (0.28), residues: 1052 helix: 1.53 (0.20), residues: 760 sheet: None (None), residues: 0 loop : -1.93 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 410 HIS 0.001 0.000 HIS B 497 PHE 0.012 0.001 PHE B 350 TYR 0.007 0.001 TYR A 500 ARG 0.000 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 145 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9108 (mtp) cc_final: 0.8855 (mtm) REVERT: A 94 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8867 (mm) REVERT: A 101 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: A 129 MET cc_start: 0.9131 (mtp) cc_final: 0.8665 (mtp) REVERT: A 286 GLN cc_start: 0.8458 (tt0) cc_final: 0.8228 (tt0) REVERT: A 295 ARG cc_start: 0.7725 (mtp-110) cc_final: 0.6891 (mpt180) REVERT: A 409 ASP cc_start: 0.8708 (p0) cc_final: 0.8320 (p0) REVERT: A 433 LYS cc_start: 0.8674 (tptt) cc_final: 0.8273 (tptp) REVERT: B 69 MET cc_start: 0.9123 (mtp) cc_final: 0.8864 (mtm) REVERT: B 94 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8859 (mm) REVERT: B 101 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: B 129 MET cc_start: 0.9126 (mtp) cc_final: 0.8657 (mtp) REVERT: B 286 GLN cc_start: 0.8430 (tt0) cc_final: 0.8154 (tt0) REVERT: B 295 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.6913 (mpt180) REVERT: B 433 LYS cc_start: 0.8770 (tptt) cc_final: 0.8304 (tptm) outliers start: 34 outliers final: 19 residues processed: 133 average time/residue: 1.1290 time to fit residues: 160.3865 Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 147 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS 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 444 LEU 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 17 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.126597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.102134 restraints weight = 8879.656| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.38 r_work: 0.2875 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1857 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= 0.175 Angle : 0.600 7.463 11724 Z= 0.289 Chirality : 0.041 0.152 1394 Planarity : 0.005 0.051 1414 Dihedral : 10.303 151.930 1332 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.63 % Allowed : 12.36 % Favored : 84.01 % 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: 1.22 (0.28), residues: 1052 helix: 1.82 (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 0.017 0.001 TRP A 410 HIS 0.002 0.000 HIS A 497 PHE 0.012 0.001 PHE B 351 TYR 0.005 0.001 TYR A 500 ARG 0.001 0.000 ARG B 108 *********************** 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 146 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: A 69 MET cc_start: 0.9089 (mtp) cc_final: 0.8834 (mtm) REVERT: A 88 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8447 (mm) REVERT: A 101 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: A 129 MET cc_start: 0.9135 (mtp) cc_final: 0.8635 (mtp) REVERT: A 295 ARG cc_start: 0.7774 (mtp-110) cc_final: 0.6911 (mpt180) REVERT: A 352 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8107 (mp) REVERT: A 433 LYS cc_start: 0.8675 (tptt) cc_final: 0.8271 (tptp) REVERT: B 69 MET cc_start: 0.9103 (mtp) cc_final: 0.8845 (mtm) REVERT: B 88 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8451 (mm) REVERT: B 101 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: B 129 MET cc_start: 0.9130 (mtp) cc_final: 0.8625 (mtp) REVERT: B 286 GLN cc_start: 0.8381 (tt0) cc_final: 0.8164 (tt0) REVERT: B 295 ARG cc_start: 0.7752 (mtp-110) cc_final: 0.6893 (mpt180) REVERT: B 352 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8080 (mp) REVERT: B 433 LYS cc_start: 0.8754 (tptt) cc_final: 0.8287 (tptm) outliers start: 32 outliers final: 15 residues processed: 128 average time/residue: 1.2201 time to fit residues: 166.3926 Evaluate side-chains 132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU 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 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 86 SER Chi-restraints excluded: chain B residue 88 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 444 LEU Chi-restraints excluded: chain B residue 463 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 53 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.122655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.098243 restraints weight = 8889.965| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.35 r_work: 0.2800 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8584 Z= 0.286 Angle : 0.701 8.662 11724 Z= 0.337 Chirality : 0.046 0.154 1394 Planarity : 0.006 0.053 1414 Dihedral : 10.567 151.332 1332 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.63 % Allowed : 12.81 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.28), residues: 1052 helix: 1.52 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -1.74 (0.39), residues: 282 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 0.016 0.002 PHE A 350 TYR 0.010 0.002 TYR B 500 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 139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9146 (mtp) cc_final: 0.8850 (mtm) REVERT: A 101 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: A 129 MET cc_start: 0.9148 (mtp) cc_final: 0.8665 (mtp) REVERT: A 286 GLN cc_start: 0.8557 (tt0) cc_final: 0.8273 (tt0) REVERT: A 295 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.6884 (mpt180) REVERT: A 352 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8206 (mp) REVERT: A 409 ASP cc_start: 0.8773 (p0) cc_final: 0.8455 (p0) REVERT: A 433 LYS cc_start: 0.8754 (tptt) cc_final: 0.8357 (tptp) REVERT: B 69 MET cc_start: 0.9180 (mtp) cc_final: 0.8881 (mtm) REVERT: B 101 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: B 129 MET cc_start: 0.9146 (mtp) cc_final: 0.8663 (mtp) REVERT: B 286 GLN cc_start: 0.8515 (tt0) cc_final: 0.8241 (tt0) REVERT: B 295 ARG cc_start: 0.7808 (mtp-110) cc_final: 0.6862 (mpt180) REVERT: B 352 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8206 (mp) REVERT: B 433 LYS cc_start: 0.8764 (tptt) cc_final: 0.8348 (tptm) outliers start: 32 outliers final: 22 residues processed: 125 average time/residue: 1.2352 time to fit residues: 164.6271 Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 101 GLU Chi-restraints excluded: chain A residue 147 MET 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 411 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 6 GLN 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 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 444 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 16 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 98 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.129556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.105750 restraints weight = 8871.964| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.35 r_work: 0.2912 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1918 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 : 0.616 7.498 11724 Z= 0.298 Chirality : 0.042 0.152 1394 Planarity : 0.005 0.051 1414 Dihedral : 10.452 152.704 1332 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.85 % Allowed : 13.15 % Favored : 82.99 % 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: 1.37 (0.28), residues: 1052 helix: 1.93 (0.20), residues: 754 sheet: None (None), residues: 0 loop : -1.88 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 410 HIS 0.002 0.000 HIS B 497 PHE 0.012 0.001 PHE B 351 TYR 0.004 0.001 TYR A 500 ARG 0.001 0.000 ARG B 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 145 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9142 (mtp) cc_final: 0.8886 (mtm) REVERT: A 88 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8532 (mm) REVERT: A 101 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: A 129 MET cc_start: 0.9149 (mtp) cc_final: 0.8665 (mtp) REVERT: A 286 GLN cc_start: 0.8478 (tt0) cc_final: 0.8193 (tt0) REVERT: A 295 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.6959 (mpt180) REVERT: A 409 ASP cc_start: 0.8649 (p0) cc_final: 0.8310 (p0) REVERT: A 433 LYS cc_start: 0.8698 (tptt) cc_final: 0.8312 (tptp) REVERT: B 52 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: B 69 MET cc_start: 0.9155 (mtp) cc_final: 0.8904 (mtm) REVERT: B 88 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8535 (mm) REVERT: B 101 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: B 129 MET cc_start: 0.9145 (mtp) cc_final: 0.8661 (mtp) REVERT: B 286 GLN cc_start: 0.8449 (tt0) cc_final: 0.8182 (tt0) REVERT: B 295 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.6907 (mpt180) REVERT: B 409 ASP cc_start: 0.8647 (p0) cc_final: 0.8300 (p0) REVERT: B 433 LYS cc_start: 0.8785 (tptt) cc_final: 0.8346 (tptm) outliers start: 34 outliers final: 16 residues processed: 130 average time/residue: 1.1746 time to fit residues: 163.0809 Evaluate side-chains 130 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 444 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 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 444 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 55 optimal weight: 0.0170 chunk 84 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 0.0000 chunk 90 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.5422 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.127992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.103693 restraints weight = 8989.474| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.37 r_work: 0.2940 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8584 Z= 0.160 Angle : 0.586 7.664 11724 Z= 0.282 Chirality : 0.041 0.151 1394 Planarity : 0.005 0.050 1414 Dihedral : 10.279 152.374 1332 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.17 % Allowed : 13.95 % Favored : 82.88 % 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: 1.65 (0.28), residues: 1052 helix: 2.16 (0.20), residues: 752 sheet: None (None), residues: 0 loop : -1.81 (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 B 497 PHE 0.012 0.001 PHE B 351 TYR 0.005 0.001 TYR B 500 ARG 0.000 0.000 ARG A 12 *********************** 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 138 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: A 69 MET cc_start: 0.9128 (mtp) cc_final: 0.8875 (mtm) REVERT: A 88 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8453 (mm) REVERT: A 101 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: A 129 MET cc_start: 0.9158 (mtp) cc_final: 0.8713 (mtp) REVERT: A 286 GLN cc_start: 0.8442 (tt0) cc_final: 0.8201 (tt0) REVERT: A 295 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.6956 (mpt180) REVERT: A 433 LYS cc_start: 0.8692 (tptt) cc_final: 0.8309 (tptp) REVERT: B 52 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: B 69 MET cc_start: 0.9124 (mtp) cc_final: 0.8893 (mtm) REVERT: B 88 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8456 (mm) REVERT: B 101 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: B 129 MET cc_start: 0.9152 (mtp) cc_final: 0.8656 (mtp) REVERT: B 286 GLN cc_start: 0.8404 (tt0) cc_final: 0.8183 (tt0) REVERT: B 295 ARG cc_start: 0.7777 (mtp-110) cc_final: 0.6941 (mpt180) REVERT: B 433 LYS cc_start: 0.8788 (tptt) cc_final: 0.8342 (tptm) outliers start: 28 outliers final: 16 residues processed: 125 average time/residue: 1.1971 time to fit residues: 159.7956 Evaluate side-chains 130 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 304 MET Chi-restraints excluded: chain A residue 321 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 101 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.126112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.101633 restraints weight = 9029.007| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.37 r_work: 0.2917 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8584 Z= 0.198 Angle : 0.624 7.965 11724 Z= 0.300 Chirality : 0.043 0.152 1394 Planarity : 0.005 0.051 1414 Dihedral : 10.320 152.185 1332 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.06 % Allowed : 14.17 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.28), residues: 1052 helix: 2.10 (0.20), residues: 752 sheet: None (None), residues: 0 loop : -1.74 (0.37), 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 0.012 0.001 PHE B 350 TYR 0.007 0.001 TYR B 500 ARG 0.001 0.000 ARG B 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 137 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9144 (mtp) cc_final: 0.8889 (mtm) REVERT: A 88 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8455 (mm) REVERT: A 101 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: A 129 MET cc_start: 0.9150 (mtp) cc_final: 0.8696 (mtp) REVERT: A 286 GLN cc_start: 0.8456 (tt0) cc_final: 0.8213 (tt0) REVERT: A 295 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.6986 (mpt180) REVERT: A 433 LYS cc_start: 0.8679 (tptt) cc_final: 0.8283 (tptp) REVERT: B 69 MET cc_start: 0.9152 (mtp) cc_final: 0.8884 (mtm) REVERT: B 88 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8454 (mm) REVERT: B 101 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: B 129 MET cc_start: 0.9148 (mtp) cc_final: 0.8695 (mtp) REVERT: B 286 GLN cc_start: 0.8428 (tt0) cc_final: 0.8186 (tt0) REVERT: B 295 ARG cc_start: 0.7762 (mtp-110) cc_final: 0.6909 (mpt180) REVERT: B 433 LYS cc_start: 0.8767 (tptt) cc_final: 0.8319 (tptm) outliers start: 27 outliers final: 18 residues processed: 125 average time/residue: 1.2335 time to fit residues: 164.2645 Evaluate side-chains 129 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 304 MET 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 B residue 6 GLN 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 224 CYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.104686 restraints weight = 8911.649| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.34 r_work: 0.2922 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2049 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= 0.190 Angle : 0.618 8.434 11724 Z= 0.298 Chirality : 0.042 0.151 1394 Planarity : 0.005 0.051 1414 Dihedral : 10.310 152.282 1332 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.61 % Allowed : 14.51 % Favored : 82.88 % 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: 1.64 (0.28), residues: 1052 helix: 2.12 (0.20), residues: 752 sheet: None (None), residues: 0 loop : -1.71 (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 A 497 PHE 0.012 0.001 PHE B 351 TYR 0.007 0.001 TYR A 500 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 130 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9138 (mtp) cc_final: 0.8870 (mtm) REVERT: A 88 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8455 (mm) REVERT: A 101 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: A 129 MET cc_start: 0.9147 (mtp) cc_final: 0.8692 (mtp) REVERT: A 286 GLN cc_start: 0.8461 (tt0) cc_final: 0.8212 (tt0) REVERT: A 295 ARG cc_start: 0.7751 (mtp-110) cc_final: 0.6982 (mpt180) REVERT: A 409 ASP cc_start: 0.8632 (p0) cc_final: 0.8329 (p0) REVERT: B 69 MET cc_start: 0.9142 (mtp) cc_final: 0.8873 (mtm) REVERT: B 88 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8452 (mm) REVERT: B 101 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: B 129 MET cc_start: 0.9144 (mtp) cc_final: 0.8692 (mtp) REVERT: B 286 GLN cc_start: 0.8434 (tt0) cc_final: 0.8194 (tt0) REVERT: B 295 ARG cc_start: 0.7751 (mtp-110) cc_final: 0.6902 (mpt180) REVERT: B 433 LYS cc_start: 0.8761 (tptt) cc_final: 0.8313 (tptm) outliers start: 23 outliers final: 16 residues processed: 122 average time/residue: 1.2430 time to fit residues: 161.8163 Evaluate side-chains 127 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 339 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 101 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 78 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.132345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.108513 restraints weight = 9003.511| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.37 r_work: 0.2951 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2141 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= 0.165 Angle : 0.591 8.915 11724 Z= 0.284 Chirality : 0.041 0.151 1394 Planarity : 0.005 0.051 1414 Dihedral : 10.204 152.400 1332 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.06 % Allowed : 13.95 % Favored : 82.99 % 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: 2.22 (0.20), residues: 752 sheet: None (None), residues: 0 loop : -1.62 (0.38), 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 A 351 TYR 0.005 0.001 TYR A 500 ARG 0.001 0.000 ARG B 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5962.47 seconds wall clock time: 105 minutes 50.13 seconds (6350.13 seconds total)