Starting phenix.real_space_refine on Sat Jul 26 09:31:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ikx_60662/07_2025/9ikx_60662.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ikx_60662/07_2025/9ikx_60662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ikx_60662/07_2025/9ikx_60662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ikx_60662/07_2025/9ikx_60662.map" model { file = "/net/cci-nas-00/data/ceres_data/9ikx_60662/07_2025/9ikx_60662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ikx_60662/07_2025/9ikx_60662.cif" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5616 2.51 5 N 1358 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8526 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4263 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 21, 'TRANS': 532} Chain breaks: 3 Chain: "B" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4263 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 21, 'TRANS': 532} Chain breaks: 3 Time building chain proxies: 5.89, per 1000 atoms: 0.69 Number of scatterers: 8526 At special positions: 0 Unit cell: (101.091, 118.483, 100.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1486 8.00 N 1358 7.00 C 5616 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: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 72.2% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 32 through 37 removed outlier: 3.705A pdb=" N TRP A 37 " --> pdb=" O ILE A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 72 removed outlier: 4.000A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 94 removed outlier: 4.192A pdb=" N LEU A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Proline residue: A 86 - end of helix removed outlier: 3.834A pdb=" N ILE A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.620A pdb=" N SER A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.929A pdb=" N MET A 123 " --> pdb=" O PRO A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 165 removed outlier: 3.742A pdb=" N VAL A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.736A pdb=" N TYR A 216 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 226 removed outlier: 3.779A pdb=" N VAL A 226 " --> pdb=" O ILE A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 226' Processing helix chain 'A' and resid 227 through 251 removed outlier: 3.602A pdb=" N GLU A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 276 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 335 removed outlier: 3.743A pdb=" N TYR A 320 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 removed outlier: 3.725A pdb=" N LEU A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 365 through 376 removed outlier: 3.568A pdb=" N THR A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 397 removed outlier: 3.645A pdb=" N SER A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS A 387 " --> pdb=" O CYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.553A pdb=" N LEU A 401 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 402 " --> pdb=" O PRO A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 402' Processing helix chain 'A' and resid 405 through 417 removed outlier: 3.563A pdb=" N LEU A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 425 through 434 removed outlier: 4.228A pdb=" N LYS A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 452 through 472 removed outlier: 4.134A pdb=" N PHE A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 515 through 525 Processing helix chain 'A' and resid 583 through 600 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 633 through 642 Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 32 through 36 Processing helix chain 'B' and resid 47 through 72 removed outlier: 4.001A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 94 removed outlier: 4.214A pdb=" N LEU B 80 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Proline residue: B 86 - end of helix removed outlier: 3.834A pdb=" N ILE B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.622A pdb=" N SER B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.959A pdb=" N MET B 123 " --> pdb=" O PRO B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 165 removed outlier: 3.749A pdb=" N VAL B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.737A pdb=" N TYR B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.772A pdb=" N VAL B 226 " --> pdb=" O ILE B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 227 through 251 removed outlier: 3.603A pdb=" N GLU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 276 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 335 removed outlier: 3.743A pdb=" N TYR B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 355 removed outlier: 3.723A pdb=" N LEU B 345 " --> pdb=" O ASN B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 365 through 376 removed outlier: 3.564A pdb=" N THR B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 397 removed outlier: 3.645A pdb=" N SER B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS B 387 " --> pdb=" O CYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.547A pdb=" N LEU B 401 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 402 " --> pdb=" O PRO B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 398 through 402' Processing helix chain 'B' and resid 405 through 417 removed outlier: 3.565A pdb=" N LEU B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 425 through 434 removed outlier: 4.228A pdb=" N LYS B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 Processing helix chain 'B' and resid 452 through 472 removed outlier: 4.134A pdb=" N PHE B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 515 through 525 Processing helix chain 'B' and resid 583 through 600 Processing helix chain 'B' and resid 610 through 622 Processing helix chain 'B' and resid 633 through 642 Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA2, first strand: chain 'A' and resid 478 through 481 removed outlier: 4.692A pdb=" N ILE A 504 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS A 503 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP A 575 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 505 " --> pdb=" O ASP A 575 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'B' and resid 478 through 481 removed outlier: 4.689A pdb=" N ILE B 504 " --> pdb=" O LYS B 481 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS B 503 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASP B 575 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 505 " --> pdb=" O ASP B 575 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1539 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: 2.74 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2594 1.34 - 1.46: 1969 1.46 - 1.58: 4051 1.58 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 8718 Sorted by residual: bond pdb=" N GLY B 102 " pdb=" CA GLY B 102 " ideal model delta sigma weight residual 1.458 1.448 0.009 9.20e-03 1.18e+04 1.04e+00 bond pdb=" CB GLN B 124 " pdb=" CG GLN B 124 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.00e+00 bond pdb=" CB GLN A 124 " pdb=" CG GLN A 124 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.44e-01 bond pdb=" C ASN A 508 " pdb=" N ASN A 509 " ideal model delta sigma weight residual 1.331 1.351 -0.020 2.07e-02 2.33e+03 8.88e-01 bond pdb=" CA PHE A 104 " pdb=" C PHE A 104 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.73e-01 ... (remaining 8713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 11548 1.44 - 2.87: 250 2.87 - 4.31: 34 4.31 - 5.75: 20 5.75 - 7.18: 4 Bond angle restraints: 11856 Sorted by residual: angle pdb=" N VAL B 134 " pdb=" CA VAL B 134 " pdb=" C VAL B 134 " ideal model delta sigma weight residual 113.71 108.58 5.13 9.50e-01 1.11e+00 2.91e+01 angle pdb=" N VAL A 134 " pdb=" CA VAL A 134 " pdb=" C VAL A 134 " ideal model delta sigma weight residual 113.71 108.64 5.07 9.50e-01 1.11e+00 2.85e+01 angle pdb=" CA VAL A 134 " pdb=" C VAL A 134 " pdb=" N LEU A 135 " ideal model delta sigma weight residual 119.87 116.48 3.39 1.34e+00 5.57e-01 6.41e+00 angle pdb=" CA VAL B 134 " pdb=" C VAL B 134 " pdb=" N LEU B 135 " ideal model delta sigma weight residual 119.87 116.54 3.33 1.34e+00 5.57e-01 6.19e+00 angle pdb=" C ARG A 471 " pdb=" N PHE A 472 " pdb=" CA PHE A 472 " ideal model delta sigma weight residual 120.26 123.59 -3.33 1.34e+00 5.57e-01 6.16e+00 ... (remaining 11851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 4440 15.32 - 30.64: 511 30.64 - 45.97: 131 45.97 - 61.29: 30 61.29 - 76.61: 10 Dihedral angle restraints: 5122 sinusoidal: 1904 harmonic: 3218 Sorted by residual: dihedral pdb=" CB MET A 526 " pdb=" CG MET A 526 " pdb=" SD MET A 526 " pdb=" CE MET A 526 " ideal model delta sinusoidal sigma weight residual -180.00 -120.64 -59.36 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLU A 141 " pdb=" CB GLU A 141 " pdb=" CG GLU A 141 " pdb=" CD GLU A 141 " ideal model delta sinusoidal sigma weight residual -180.00 -121.08 -58.92 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N MET B 526 " pdb=" CA MET B 526 " pdb=" CB MET B 526 " pdb=" CG MET B 526 " ideal model delta sinusoidal sigma weight residual -60.00 -118.48 58.48 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 825 0.028 - 0.057: 396 0.057 - 0.085: 142 0.085 - 0.114: 57 0.114 - 0.142: 8 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA ILE B 505 " pdb=" N ILE B 505 " pdb=" C ILE B 505 " pdb=" CB ILE B 505 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE A 505 " pdb=" N ILE A 505 " pdb=" C ILE A 505 " pdb=" CB ILE A 505 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1425 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 398 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 399 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 399 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 399 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 398 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.58e+00 pdb=" N PRO B 399 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 399 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 399 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 360 " 0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO B 361 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 361 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 361 " 0.016 5.00e-02 4.00e+02 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2384 2.81 - 3.33: 8070 3.33 - 3.86: 13675 3.86 - 4.38: 15133 4.38 - 4.90: 27429 Nonbonded interactions: 66691 Sorted by model distance: nonbonded pdb=" OH TYR A 41 " pdb=" O ASN A 46 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR B 41 " pdb=" O ASN B 46 " model vdw 2.292 3.040 nonbonded pdb=" N ASP A 583 " pdb=" OD1 ASP A 583 " model vdw 2.346 3.120 nonbonded pdb=" N ASP B 583 " pdb=" OD1 ASP B 583 " model vdw 2.346 3.120 nonbonded pdb=" O SER A 72 " pdb=" OG SER A 72 " model vdw 2.353 3.040 ... (remaining 66686 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.170 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.910 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 0.002 0.030 8718 Z= 0.123 Angle : 0.544 7.182 11856 Z= 0.321 Chirality : 0.039 0.142 1428 Planarity : 0.003 0.032 1448 Dihedral : 14.714 76.610 3050 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.32 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 15.17 % Favored : 84.83 % 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: 1.02 (0.27), residues: 1092 helix: 1.87 (0.21), residues: 702 sheet: 0.45 (0.84), residues: 34 loop : -1.83 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 27 HIS 0.001 0.000 HIS B 347 PHE 0.010 0.001 PHE B 163 TYR 0.011 0.001 TYR A 320 ARG 0.002 0.000 ARG B 600 Details of bonding type rmsd hydrogen bonds : bond 0.14875 ( 525) hydrogen bonds : angle 5.07855 ( 1539) covalent geometry : bond 0.00237 ( 8718) covalent geometry : angle 0.54414 (11856) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1503 time to fit residues: 19.6152 Evaluate side-chains 78 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.080764 restraints weight = 13683.477| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.14 r_work: 0.2802 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8718 Z= 0.105 Angle : 0.475 6.271 11856 Z= 0.247 Chirality : 0.040 0.129 1428 Planarity : 0.003 0.032 1448 Dihedral : 3.757 14.967 1172 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.49 % Favored : 94.32 % Rotamer: Outliers : 1.50 % Allowed : 13.57 % Favored : 84.94 % 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: 1.27 (0.27), residues: 1092 helix: 1.94 (0.21), residues: 724 sheet: 0.72 (0.88), residues: 34 loop : -1.71 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 27 HIS 0.002 0.000 HIS A 146 PHE 0.008 0.001 PHE A 104 TYR 0.010 0.001 TYR B 320 ARG 0.001 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 525) hydrogen bonds : angle 3.86160 ( 1539) covalent geometry : bond 0.00222 ( 8718) covalent geometry : angle 0.47463 (11856) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.243 Fit side-chains outliers start: 14 outliers final: 2 residues processed: 101 average time/residue: 0.1598 time to fit residues: 25.9738 Evaluate side-chains 86 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 257 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.097895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.080163 restraints weight = 13813.365| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.17 r_work: 0.2796 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8718 Z= 0.108 Angle : 0.470 6.022 11856 Z= 0.245 Chirality : 0.040 0.131 1428 Planarity : 0.003 0.031 1448 Dihedral : 3.716 14.991 1172 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.04 % Favored : 94.78 % Rotamer: Outliers : 1.71 % Allowed : 13.57 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 1092 helix: 2.05 (0.20), residues: 728 sheet: 1.65 (0.92), residues: 32 loop : -1.81 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 27 HIS 0.002 0.000 HIS B 347 PHE 0.009 0.001 PHE A 104 TYR 0.010 0.001 TYR B 90 ARG 0.001 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 525) hydrogen bonds : angle 3.68911 ( 1539) covalent geometry : bond 0.00237 ( 8718) covalent geometry : angle 0.47032 (11856) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 1.148 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 96 average time/residue: 0.2067 time to fit residues: 31.5624 Evaluate side-chains 91 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 480 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.081391 restraints weight = 13719.483| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.17 r_work: 0.2817 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8718 Z= 0.098 Angle : 0.453 5.730 11856 Z= 0.236 Chirality : 0.039 0.131 1428 Planarity : 0.003 0.032 1448 Dihedral : 3.633 14.626 1172 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.22 % Favored : 94.60 % Rotamer: Outliers : 1.50 % Allowed : 14.10 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.27), residues: 1092 helix: 2.18 (0.20), residues: 728 sheet: 1.59 (0.93), residues: 32 loop : -1.73 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 27 HIS 0.002 0.000 HIS A 347 PHE 0.009 0.001 PHE A 104 TYR 0.009 0.001 TYR B 320 ARG 0.001 0.000 ARG B 600 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 525) hydrogen bonds : angle 3.58878 ( 1539) covalent geometry : bond 0.00209 ( 8718) covalent geometry : angle 0.45281 (11856) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.936 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 94 average time/residue: 0.1812 time to fit residues: 25.8092 Evaluate side-chains 89 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 257 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3122 r_free = 0.3122 target = 0.092439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.074894 restraints weight = 13993.574| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.16 r_work: 0.2696 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8718 Z= 0.226 Angle : 0.567 6.268 11856 Z= 0.298 Chirality : 0.043 0.129 1428 Planarity : 0.003 0.034 1448 Dihedral : 4.073 17.377 1172 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.23 % Favored : 93.59 % Rotamer: Outliers : 2.88 % Allowed : 13.78 % Favored : 83.33 % 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: 1.32 (0.27), residues: 1092 helix: 1.90 (0.20), residues: 748 sheet: 1.10 (0.93), residues: 32 loop : -1.79 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 27 HIS 0.002 0.001 HIS B 640 PHE 0.009 0.002 PHE A 85 TYR 0.014 0.001 TYR B 90 ARG 0.001 0.000 ARG B 600 Details of bonding type rmsd hydrogen bonds : bond 0.05300 ( 525) hydrogen bonds : angle 3.89661 ( 1539) covalent geometry : bond 0.00549 ( 8718) covalent geometry : angle 0.56696 (11856) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.922 Fit side-chains outliers start: 27 outliers final: 21 residues processed: 104 average time/residue: 0.1346 time to fit residues: 22.5197 Evaluate side-chains 94 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 593 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3191 r_free = 0.3191 target = 0.096678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.079576 restraints weight = 13709.005| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.10 r_work: 0.2785 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8718 Z= 0.098 Angle : 0.460 5.622 11856 Z= 0.241 Chirality : 0.040 0.132 1428 Planarity : 0.003 0.035 1448 Dihedral : 3.788 15.329 1172 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.13 % Favored : 94.69 % Rotamer: Outliers : 1.92 % Allowed : 14.64 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 1092 helix: 2.12 (0.20), residues: 744 sheet: 1.09 (0.92), residues: 32 loop : -1.88 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 441 HIS 0.002 0.000 HIS A 347 PHE 0.009 0.001 PHE B 104 TYR 0.012 0.001 TYR A 320 ARG 0.001 0.000 ARG B 253 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 525) hydrogen bonds : angle 3.64489 ( 1539) covalent geometry : bond 0.00207 ( 8718) covalent geometry : angle 0.46004 (11856) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.951 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 94 average time/residue: 0.1473 time to fit residues: 22.0309 Evaluate side-chains 95 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 617 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3181 r_free = 0.3181 target = 0.096011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.078608 restraints weight = 13863.091| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.14 r_work: 0.2782 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8718 Z= 0.111 Angle : 0.468 5.735 11856 Z= 0.244 Chirality : 0.040 0.128 1428 Planarity : 0.003 0.035 1448 Dihedral : 3.739 15.459 1172 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.59 % Favored : 94.23 % Rotamer: Outliers : 2.24 % Allowed : 14.74 % Favored : 83.01 % 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: 1.62 (0.27), residues: 1092 helix: 2.24 (0.20), residues: 728 sheet: 1.05 (0.92), residues: 32 loop : -1.70 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 27 HIS 0.002 0.000 HIS B 347 PHE 0.009 0.001 PHE A 104 TYR 0.011 0.001 TYR B 320 ARG 0.001 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 525) hydrogen bonds : angle 3.61068 ( 1539) covalent geometry : bond 0.00249 ( 8718) covalent geometry : angle 0.46837 (11856) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.898 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 97 average time/residue: 0.1328 time to fit residues: 20.6511 Evaluate side-chains 96 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 593 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 48 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.097871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.080635 restraints weight = 14046.573| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.15 r_work: 0.2818 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8718 Z= 0.095 Angle : 0.451 5.563 11856 Z= 0.235 Chirality : 0.039 0.130 1428 Planarity : 0.003 0.037 1448 Dihedral : 3.631 16.405 1172 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.04 % Favored : 94.78 % Rotamer: Outliers : 2.03 % Allowed : 14.74 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.27), residues: 1092 helix: 2.29 (0.20), residues: 728 sheet: 1.14 (0.92), residues: 32 loop : -1.64 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 441 HIS 0.002 0.000 HIS B 347 PHE 0.009 0.001 PHE A 104 TYR 0.011 0.001 TYR B 320 ARG 0.001 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 525) hydrogen bonds : angle 3.53186 ( 1539) covalent geometry : bond 0.00202 ( 8718) covalent geometry : angle 0.45107 (11856) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 1.028 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 99 average time/residue: 0.1420 time to fit residues: 22.4352 Evaluate side-chains 90 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 480 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 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 525 ASN B 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.080825 restraints weight = 13756.143| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.12 r_work: 0.2823 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8718 Z= 0.100 Angle : 0.465 5.633 11856 Z= 0.245 Chirality : 0.039 0.131 1428 Planarity : 0.003 0.038 1448 Dihedral : 3.629 14.718 1172 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.58 % Favored : 95.24 % Rotamer: Outliers : 1.60 % Allowed : 15.28 % Favored : 83.12 % 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: 1.76 (0.27), residues: 1092 helix: 2.33 (0.20), residues: 728 sheet: 1.13 (0.93), residues: 32 loop : -1.62 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 441 HIS 0.002 0.000 HIS B 347 PHE 0.009 0.001 PHE A 104 TYR 0.009 0.001 TYR B 320 ARG 0.001 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 525) hydrogen bonds : angle 3.50707 ( 1539) covalent geometry : bond 0.00213 ( 8718) covalent geometry : angle 0.46474 (11856) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 1.010 Fit side-chains REVERT: A 302 MET cc_start: 0.8636 (mmt) cc_final: 0.8414 (mmt) REVERT: B 302 MET cc_start: 0.8642 (mmt) cc_final: 0.8424 (mmt) outliers start: 15 outliers final: 15 residues processed: 90 average time/residue: 0.1452 time to fit residues: 21.0386 Evaluate side-chains 94 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 617 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 65 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.098598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.081028 restraints weight = 13790.322| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.13 r_work: 0.2812 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8718 Z= 0.104 Angle : 0.464 5.654 11856 Z= 0.244 Chirality : 0.039 0.133 1428 Planarity : 0.003 0.037 1448 Dihedral : 3.621 14.986 1172 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.76 % Favored : 95.05 % Rotamer: Outliers : 1.82 % Allowed : 15.38 % Favored : 82.80 % 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: 1.78 (0.27), residues: 1092 helix: 2.35 (0.20), residues: 728 sheet: 1.10 (0.93), residues: 32 loop : -1.62 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 441 HIS 0.001 0.000 HIS B 347 PHE 0.008 0.001 PHE A 104 TYR 0.011 0.001 TYR A 320 ARG 0.001 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 525) hydrogen bonds : angle 3.51830 ( 1539) covalent geometry : bond 0.00228 ( 8718) covalent geometry : angle 0.46433 (11856) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 1.000 Fit side-chains REVERT: A 302 MET cc_start: 0.8611 (mmt) cc_final: 0.8390 (mmt) REVERT: B 302 MET cc_start: 0.8621 (mmt) cc_final: 0.8405 (mmt) outliers start: 17 outliers final: 17 residues processed: 94 average time/residue: 0.1435 time to fit residues: 21.5784 Evaluate side-chains 94 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 617 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3180 r_free = 0.3180 target = 0.096099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.078809 restraints weight = 13934.828| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.12 r_work: 0.2781 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8718 Z= 0.124 Angle : 0.484 5.763 11856 Z= 0.254 Chirality : 0.040 0.130 1428 Planarity : 0.003 0.036 1448 Dihedral : 3.717 15.849 1172 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.67 % Favored : 95.15 % Rotamer: Outliers : 2.03 % Allowed : 14.96 % Favored : 83.01 % 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: 1.75 (0.27), residues: 1092 helix: 2.33 (0.20), residues: 728 sheet: 1.02 (0.93), residues: 32 loop : -1.62 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 27 HIS 0.001 0.000 HIS A 640 PHE 0.008 0.001 PHE A 104 TYR 0.009 0.001 TYR B 90 ARG 0.001 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 525) hydrogen bonds : angle 3.58575 ( 1539) covalent geometry : bond 0.00286 ( 8718) covalent geometry : angle 0.48399 (11856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4278.70 seconds wall clock time: 76 minutes 43.60 seconds (4603.60 seconds total)