Starting phenix.real_space_refine on Wed Sep 17 11:52:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ikx_60662/09_2025/9ikx_60662.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ikx_60662/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ikx_60662/09_2025/9ikx_60662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ikx_60662/09_2025/9ikx_60662.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ikx_60662/09_2025/9ikx_60662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ikx_60662/09_2025/9ikx_60662.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.17, per 1000 atoms: 0.25 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: 0.66 Conformation dependent library (CDL) restraints added in 426.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.30 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: 1.30 Time building geometry restraints manager: 0.92 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: 0.02 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.350 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.690 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 600 TYR 0.011 0.001 TYR A 320 PHE 0.010 0.001 PHE B 163 TRP 0.009 0.001 TRP A 27 HIS 0.001 0.000 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8718) covalent geometry : angle 0.54414 (11856) hydrogen bonds : bond 0.14875 ( 525) hydrogen bonds : angle 5.07855 ( 1539) *********************** 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 : 0.385 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0655 time to fit residues: 8.6530 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 : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3212 r_free = 0.3212 target = 0.098302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.080867 restraints weight = 13838.764| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.16 r_work: 0.2824 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8718 Z= 0.096 Angle : 0.464 6.254 11856 Z= 0.241 Chirality : 0.039 0.130 1428 Planarity : 0.003 0.032 1448 Dihedral : 3.706 14.538 1172 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.13 % Favored : 94.69 % Rotamer: Outliers : 1.60 % Allowed : 13.25 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.27), residues: 1092 helix: 1.96 (0.21), residues: 724 sheet: 0.74 (0.88), residues: 34 loop : -1.70 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 600 TYR 0.010 0.001 TYR B 320 PHE 0.008 0.001 PHE A 104 TRP 0.008 0.001 TRP B 431 HIS 0.002 0.000 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 8718) covalent geometry : angle 0.46440 (11856) hydrogen bonds : bond 0.03762 ( 525) hydrogen bonds : angle 3.83220 ( 1539) *********************** 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 103 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.389 Fit side-chains outliers start: 15 outliers final: 3 residues processed: 101 average time/residue: 0.0615 time to fit residues: 10.2147 Evaluate side-chains 88 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 247 LEU 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 6 optimal weight: 3.9990 chunk 94 optimal weight: 0.0470 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 8 optimal weight: 5.9990 chunk 83 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.099145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.081530 restraints weight = 13627.854| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.13 r_work: 0.2837 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8718 Z= 0.093 Angle : 0.458 5.979 11856 Z= 0.236 Chirality : 0.039 0.132 1428 Planarity : 0.003 0.032 1448 Dihedral : 3.591 14.243 1172 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.58 % Favored : 95.24 % Rotamer: Outliers : 1.50 % Allowed : 13.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.27), residues: 1092 helix: 2.13 (0.21), residues: 728 sheet: 1.13 (0.95), residues: 34 loop : -1.72 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 600 TYR 0.009 0.001 TYR A 320 PHE 0.010 0.001 PHE A 104 TRP 0.007 0.001 TRP B 27 HIS 0.001 0.000 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 8718) covalent geometry : angle 0.45791 (11856) hydrogen bonds : bond 0.03442 ( 525) hydrogen bonds : angle 3.60295 ( 1539) *********************** 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 109 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.409 Fit side-chains REVERT: B 526 MET cc_start: 0.8686 (ttm) cc_final: 0.8417 (ttm) outliers start: 14 outliers final: 5 residues processed: 103 average time/residue: 0.0698 time to fit residues: 11.0359 Evaluate side-chains 92 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 524 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 257 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 60 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.3159 r_free = 0.3159 target = 0.094860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.077233 restraints weight = 14050.016| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.16 r_work: 0.2759 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8718 Z= 0.145 Angle : 0.505 6.109 11856 Z= 0.262 Chirality : 0.041 0.129 1428 Planarity : 0.003 0.030 1448 Dihedral : 3.800 15.784 1172 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.40 % Favored : 94.41 % Rotamer: Outliers : 1.28 % Allowed : 14.64 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.27), residues: 1092 helix: 2.09 (0.20), residues: 732 sheet: 1.49 (0.94), residues: 32 loop : -1.78 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 600 TYR 0.012 0.001 TYR B 90 PHE 0.008 0.001 PHE A 104 TRP 0.010 0.001 TRP B 27 HIS 0.002 0.000 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8718) covalent geometry : angle 0.50540 (11856) hydrogen bonds : bond 0.04392 ( 525) hydrogen bonds : angle 3.70868 ( 1539) *********************** 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 97 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.329 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 92 average time/residue: 0.0646 time to fit residues: 9.5811 Evaluate side-chains 90 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 44 optimal weight: 0.0870 chunk 34 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.3212 r_free = 0.3212 target = 0.098182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.080452 restraints weight = 13896.651| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.17 r_work: 0.2814 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8718 Z= 0.095 Angle : 0.455 5.650 11856 Z= 0.235 Chirality : 0.039 0.129 1428 Planarity : 0.003 0.032 1448 Dihedral : 3.618 14.697 1172 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.85 % Favored : 94.96 % Rotamer: Outliers : 1.39 % Allowed : 14.74 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.27), residues: 1092 helix: 2.23 (0.20), residues: 728 sheet: 1.54 (0.94), residues: 32 loop : -1.66 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 253 TYR 0.009 0.001 TYR B 320 PHE 0.009 0.001 PHE A 104 TRP 0.007 0.001 TRP B 27 HIS 0.002 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 8718) covalent geometry : angle 0.45502 (11856) hydrogen bonds : bond 0.03438 ( 525) hydrogen bonds : angle 3.55596 ( 1539) *********************** 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 97 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.332 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 92 average time/residue: 0.0645 time to fit residues: 9.6060 Evaluate side-chains 87 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 480 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 79 optimal weight: 0.1980 chunk 67 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 overall best weight: 1.0524 ------------------------------------------------------------------------------- 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 = 0.3193 r_free = 0.3193 target = 0.096839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.079465 restraints weight = 13871.599| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.13 r_work: 0.2795 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1201 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= 0.110 Angle : 0.471 5.791 11856 Z= 0.243 Chirality : 0.040 0.128 1428 Planarity : 0.003 0.031 1448 Dihedral : 3.651 14.866 1172 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.22 % Favored : 94.60 % Rotamer: Outliers : 1.71 % Allowed : 14.64 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.27), residues: 1092 helix: 2.26 (0.20), residues: 728 sheet: 1.40 (0.95), residues: 32 loop : -1.65 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 600 TYR 0.010 0.001 TYR A 90 PHE 0.008 0.001 PHE A 104 TRP 0.008 0.001 TRP B 27 HIS 0.001 0.000 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8718) covalent geometry : angle 0.47080 (11856) hydrogen bonds : bond 0.03788 ( 525) hydrogen bonds : angle 3.57149 ( 1539) *********************** 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 101 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.326 Fit side-chains REVERT: A 302 MET cc_start: 0.8606 (mmt) cc_final: 0.8380 (mmt) REVERT: B 302 MET cc_start: 0.8560 (mmt) cc_final: 0.8345 (mmt) outliers start: 16 outliers final: 13 residues processed: 96 average time/residue: 0.0638 time to fit residues: 9.8974 Evaluate side-chains 97 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 255 ILE 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 B residue 103 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 480 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.0370 chunk 3 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.0050 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.6078 ------------------------------------------------------------------------------- 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 = 0.3153 r_free = 0.3153 target = 0.094371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.076916 restraints weight = 14144.089| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.15 r_work: 0.2753 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8718 Z= 0.143 Angle : 0.503 5.784 11856 Z= 0.262 Chirality : 0.040 0.128 1428 Planarity : 0.003 0.029 1448 Dihedral : 3.799 16.129 1172 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.77 % Favored : 94.05 % Rotamer: Outliers : 2.56 % Allowed : 13.57 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.27), residues: 1092 helix: 2.18 (0.20), residues: 732 sheet: 1.23 (0.95), residues: 32 loop : -1.72 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 600 TYR 0.011 0.001 TYR B 90 PHE 0.009 0.001 PHE A 104 TRP 0.009 0.001 TRP B 27 HIS 0.002 0.000 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8718) covalent geometry : angle 0.50332 (11856) hydrogen bonds : bond 0.04330 ( 525) hydrogen bonds : angle 3.66996 ( 1539) *********************** 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 105 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.327 Fit side-chains outliers start: 24 outliers final: 21 residues processed: 99 average time/residue: 0.0633 time to fit residues: 10.1461 Evaluate side-chains 101 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 257 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 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 106 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 255 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 14 optimal weight: 0.0020 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.095989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.078201 restraints weight = 13852.726| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.20 r_work: 0.2756 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1276 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= 0.128 Angle : 0.491 5.652 11856 Z= 0.254 Chirality : 0.040 0.133 1428 Planarity : 0.003 0.027 1448 Dihedral : 3.788 16.162 1172 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.31 % Favored : 94.51 % Rotamer: Outliers : 2.56 % Allowed : 13.57 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.27), residues: 1092 helix: 2.02 (0.20), residues: 758 sheet: 1.12 (0.93), residues: 32 loop : -1.70 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 600 TYR 0.010 0.001 TYR B 90 PHE 0.009 0.001 PHE A 104 TRP 0.008 0.001 TRP B 27 HIS 0.001 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8718) covalent geometry : angle 0.49070 (11856) hydrogen bonds : bond 0.04084 ( 525) hydrogen bonds : angle 3.64303 ( 1539) *********************** 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 107 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.311 Fit side-chains REVERT: A 525 ASN cc_start: 0.8577 (m-40) cc_final: 0.8302 (t0) outliers start: 24 outliers final: 21 residues processed: 103 average time/residue: 0.0633 time to fit residues: 10.5332 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 : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 GLU 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 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 175 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 255 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3182 r_free = 0.3182 target = 0.096200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.078730 restraints weight = 13839.322| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.13 r_work: 0.2781 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8718 Z= 0.113 Angle : 0.480 5.656 11856 Z= 0.248 Chirality : 0.040 0.134 1428 Planarity : 0.003 0.028 1448 Dihedral : 3.747 15.414 1172 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.13 % Favored : 94.69 % Rotamer: Outliers : 2.35 % Allowed : 14.00 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.27), residues: 1092 helix: 2.19 (0.20), residues: 744 sheet: 1.12 (0.92), residues: 32 loop : -1.76 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 600 TYR 0.009 0.001 TYR A 90 PHE 0.009 0.001 PHE A 104 TRP 0.007 0.001 TRP B 27 HIS 0.002 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8718) covalent geometry : angle 0.48016 (11856) hydrogen bonds : bond 0.03847 ( 525) hydrogen bonds : angle 3.59276 ( 1539) *********************** 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 107 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.324 Fit side-chains REVERT: A 302 MET cc_start: 0.8629 (mmt) cc_final: 0.8391 (mmt) REVERT: B 302 MET cc_start: 0.8640 (mmt) cc_final: 0.8406 (mmt) outliers start: 22 outliers final: 17 residues processed: 103 average time/residue: 0.0664 time to fit residues: 10.9074 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 : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 GLU 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 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 103 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 255 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 100 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3200 r_free = 0.3200 target = 0.097402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.079940 restraints weight = 13758.655| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.13 r_work: 0.2803 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1355 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= 0.103 Angle : 0.479 5.816 11856 Z= 0.251 Chirality : 0.039 0.132 1428 Planarity : 0.003 0.030 1448 Dihedral : 3.685 14.985 1172 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.04 % Favored : 94.78 % Rotamer: Outliers : 2.14 % Allowed : 14.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.27), residues: 1092 helix: 2.24 (0.20), residues: 742 sheet: 1.14 (0.92), residues: 32 loop : -1.70 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 600 TYR 0.010 0.001 TYR A 320 PHE 0.009 0.001 PHE A 104 TRP 0.008 0.001 TRP B 441 HIS 0.002 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8718) covalent geometry : angle 0.47909 (11856) hydrogen bonds : bond 0.03551 ( 525) hydrogen bonds : angle 3.54248 ( 1539) ********************** 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 101 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.325 Fit side-chains REVERT: A 302 MET cc_start: 0.8533 (mmt) cc_final: 0.8319 (mmt) REVERT: B 302 MET cc_start: 0.8552 (mmt) cc_final: 0.8343 (mmt) outliers start: 20 outliers final: 20 residues processed: 99 average time/residue: 0.0628 time to fit residues: 10.0949 Evaluate side-chains 102 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 GLU 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 468 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 593 VAL 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 255 ILE 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 525 ASN Chi-restraints excluded: chain B residue 593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 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 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 = 0.3195 r_free = 0.3195 target = 0.097105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.079580 restraints weight = 13799.847| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.14 r_work: 0.2794 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1369 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= 0.108 Angle : 0.478 5.758 11856 Z= 0.249 Chirality : 0.040 0.134 1428 Planarity : 0.003 0.029 1448 Dihedral : 3.665 14.864 1172 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.76 % Favored : 95.05 % Rotamer: Outliers : 2.14 % Allowed : 14.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.27), residues: 1092 helix: 2.31 (0.20), residues: 730 sheet: 1.10 (0.92), residues: 32 loop : -1.57 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 600 TYR 0.009 0.001 TYR B 320 PHE 0.008 0.001 PHE B 104 TRP 0.007 0.001 TRP B 441 HIS 0.002 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8718) covalent geometry : angle 0.47765 (11856) hydrogen bonds : bond 0.03647 ( 525) hydrogen bonds : angle 3.54217 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1971.24 seconds wall clock time: 34 minutes 36.64 seconds (2076.64 seconds total)