Starting phenix.real_space_refine on Sat Dec 28 20:24:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7psd_13612/12_2024/7psd_13612.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psd_13612/12_2024/7psd_13612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7psd_13612/12_2024/7psd_13612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psd_13612/12_2024/7psd_13612.map" model { file = "/net/cci-nas-00/data/ceres_data/7psd_13612/12_2024/7psd_13612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psd_13612/12_2024/7psd_13612.cif" } resolution = 3.0 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= -0.001 sd= 0.102 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 24 5.16 5 C 5784 2.51 5 N 1574 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9032 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4516 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 17, 'TRANS': 562} Restraints were copied for chains: B Time building chain proxies: 8.37, per 1000 atoms: 0.93 Number of scatterers: 9032 At special positions: 0 Unit cell: (118.976, 75.712, 141.44, 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 24 16.00 O 1650 8.00 N 1574 7.00 C 5784 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: 2.21 Conformation dependent library (CDL) restraints added in 1.3 seconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 69.2% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.669A pdb=" N GLN B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 145 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 159 through 206 removed outlier: 3.750A pdb=" N GLN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 240 Processing helix chain 'B' and resid 240 through 259 Processing helix chain 'B' and resid 260 through 309 removed outlier: 3.824A pdb=" N ALA B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 318 through 371 removed outlier: 3.504A pdb=" N GLU B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 391 removed outlier: 3.662A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 398 removed outlier: 4.270A pdb=" N ASN B 395 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE B 396 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 397 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 398 " --> pdb=" O ASN B 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 392 through 398' Processing helix chain 'B' and resid 399 through 418 removed outlier: 3.742A pdb=" N ARG B 405 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 488 removed outlier: 4.653A pdb=" N ARG B 485 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 531 through 537 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 556 through 563 Processing helix chain 'B' and resid 565 through 568 removed outlier: 4.052A pdb=" N GLN B 568 " --> pdb=" O HIS B 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 565 through 568' Processing helix chain 'B' and resid 579 through 595 Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.937A pdb=" N ALA B 607 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 625 Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.922A pdb=" N TYR B 642 " --> pdb=" O ARG B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 666 removed outlier: 3.554A pdb=" N GLU B 666 " --> pdb=" O ARG B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 674 removed outlier: 4.033A pdb=" N GLU B 673 " --> pdb=" O VAL B 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 110 through 145 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 159 through 206 removed outlier: 3.749A pdb=" N GLN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 240 Processing helix chain 'A' and resid 240 through 259 Processing helix chain 'A' and resid 260 through 309 removed outlier: 3.823A pdb=" N ALA A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 318 through 371 removed outlier: 3.504A pdb=" N GLU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 removed outlier: 3.661A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 398 removed outlier: 4.271A pdb=" N ASN A 395 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE A 396 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 397 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 398' Processing helix chain 'A' and resid 399 through 418 removed outlier: 3.743A pdb=" N ARG A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 removed outlier: 4.653A pdb=" N ARG A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 565 through 568 removed outlier: 4.052A pdb=" N GLN A 568 " --> pdb=" O HIS A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 579 through 595 Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.937A pdb=" N ALA A 607 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 625 Processing helix chain 'A' and resid 637 through 642 removed outlier: 3.923A pdb=" N TYR A 642 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.555A pdb=" N GLU A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 removed outlier: 4.034A pdb=" N GLU A 673 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 457 through 464 removed outlier: 5.296A pdb=" N ARG B 458 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE B 448 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 462 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU B 444 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE B 464 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ARG B 442 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL B 446 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN B 495 " --> pdb=" O VAL B 446 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 517 through 519 removed outlier: 3.556A pdb=" N ILE B 647 " --> pdb=" O GLY B 659 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU B 657 " --> pdb=" O VAL B 649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 529 through 530 Processing sheet with id=AA4, first strand: chain 'A' and resid 457 through 464 removed outlier: 5.296A pdb=" N ARG A 458 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE A 448 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 462 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLU A 444 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE A 464 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ARG A 442 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A 446 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN A 495 " --> pdb=" O VAL A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 517 through 519 removed outlier: 3.556A pdb=" N ILE A 647 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU A 657 " --> pdb=" O VAL A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 530 612 hydrogen bonds defined for protein. 1800 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: 2.93 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2635 1.33 - 1.45: 1694 1.45 - 1.58: 4823 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 9196 Sorted by residual: bond pdb=" CB THR A 281 " pdb=" CG2 THR A 281 " ideal model delta sigma weight residual 1.521 1.391 0.130 3.30e-02 9.18e+02 1.54e+01 bond pdb=" CB THR B 281 " pdb=" CG2 THR B 281 " ideal model delta sigma weight residual 1.521 1.392 0.129 3.30e-02 9.18e+02 1.53e+01 bond pdb=" C SER B 156 " pdb=" N ALA B 157 " ideal model delta sigma weight residual 1.332 1.287 0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" C SER A 156 " pdb=" N ALA A 157 " ideal model delta sigma weight residual 1.332 1.288 0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" CG1 ILE A 192 " pdb=" CD1 ILE A 192 " ideal model delta sigma weight residual 1.513 1.392 0.121 3.90e-02 6.57e+02 9.60e+00 ... (remaining 9191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 11973 2.56 - 5.13: 436 5.13 - 7.69: 47 7.69 - 10.25: 10 10.25 - 12.81: 4 Bond angle restraints: 12470 Sorted by residual: angle pdb=" CA TRP A 284 " pdb=" CB TRP A 284 " pdb=" CG TRP A 284 " ideal model delta sigma weight residual 113.60 121.87 -8.27 1.90e+00 2.77e-01 1.89e+01 angle pdb=" CA TRP B 284 " pdb=" CB TRP B 284 " pdb=" CG TRP B 284 " ideal model delta sigma weight residual 113.60 121.84 -8.24 1.90e+00 2.77e-01 1.88e+01 angle pdb=" N VAL B 400 " pdb=" CA VAL B 400 " pdb=" C VAL B 400 " ideal model delta sigma weight residual 110.36 114.48 -4.12 1.05e+00 9.07e-01 1.54e+01 angle pdb=" N VAL A 400 " pdb=" CA VAL A 400 " pdb=" C VAL A 400 " ideal model delta sigma weight residual 110.36 114.48 -4.12 1.05e+00 9.07e-01 1.54e+01 angle pdb=" N VAL B 155 " pdb=" CA VAL B 155 " pdb=" C VAL B 155 " ideal model delta sigma weight residual 110.21 105.89 4.32 1.13e+00 7.83e-01 1.46e+01 ... (remaining 12465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 4918 17.12 - 34.24: 485 34.24 - 51.36: 89 51.36 - 68.48: 10 68.48 - 85.59: 14 Dihedral angle restraints: 5516 sinusoidal: 2156 harmonic: 3360 Sorted by residual: dihedral pdb=" CA TYR A 451 " pdb=" C TYR A 451 " pdb=" N PRO A 452 " pdb=" CA PRO A 452 " ideal model delta harmonic sigma weight residual -180.00 -154.36 -25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA TYR B 451 " pdb=" C TYR B 451 " pdb=" N PRO B 452 " pdb=" CA PRO B 452 " ideal model delta harmonic sigma weight residual 180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA SER B 399 " pdb=" C SER B 399 " pdb=" N VAL B 400 " pdb=" CA VAL B 400 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1365 0.118 - 0.235: 97 0.235 - 0.353: 0 0.353 - 0.470: 0 0.470 - 0.588: 2 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CB ILE A 192 " pdb=" CA ILE A 192 " pdb=" CG1 ILE A 192 " pdb=" CG2 ILE A 192 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.63e+00 chirality pdb=" CB ILE B 192 " pdb=" CA ILE B 192 " pdb=" CG1 ILE B 192 " pdb=" CG2 ILE B 192 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.61e+00 chirality pdb=" CA PHE A 355 " pdb=" N PHE A 355 " pdb=" C PHE A 355 " pdb=" CB PHE A 355 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1461 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 137 " 0.015 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE A 137 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 137 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE A 137 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 137 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 137 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 137 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 137 " -0.015 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE B 137 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE B 137 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE B 137 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 137 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B 137 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 137 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 388 " -0.031 2.00e-02 2.50e+03 1.97e-02 6.78e+00 pdb=" CG PHE B 388 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 388 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 388 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 388 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 388 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 388 " -0.015 2.00e-02 2.50e+03 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 454 2.70 - 3.25: 9435 3.25 - 3.80: 14950 3.80 - 4.35: 18651 4.35 - 4.90: 31686 Nonbonded interactions: 75176 Sorted by model distance: nonbonded pdb=" O GLY A 566 " pdb=" OG1 THR A 569 " model vdw 2.146 3.040 nonbonded pdb=" O GLY B 566 " pdb=" OG1 THR B 569 " model vdw 2.146 3.040 nonbonded pdb=" O LEU A 586 " pdb=" OG SER A 589 " model vdw 2.290 3.040 nonbonded pdb=" O LEU B 586 " pdb=" OG SER B 589 " model vdw 2.290 3.040 nonbonded pdb=" O ARG B 637 " pdb=" OG1 THR B 640 " model vdw 2.302 3.040 ... (remaining 75171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 2.100 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.360 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.015 0.130 9196 Z= 0.967 Angle : 1.115 12.813 12470 Z= 0.626 Chirality : 0.069 0.588 1464 Planarity : 0.006 0.056 1584 Dihedral : 14.392 85.594 3352 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.23), residues: 1156 helix: -0.59 (0.17), residues: 750 sheet: -0.63 (0.68), residues: 56 loop : -1.37 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP B 284 HIS 0.004 0.001 HIS A 202 PHE 0.053 0.005 PHE A 137 TYR 0.017 0.003 TYR A 401 ARG 0.014 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.871 Fit side-chains REVERT: B 468 LYS cc_start: 0.7532 (mmmm) cc_final: 0.7306 (mmpt) REVERT: B 621 ASN cc_start: 0.9158 (m-40) cc_final: 0.8475 (m110) REVERT: B 632 LEU cc_start: 0.8247 (mp) cc_final: 0.7948 (mp) outliers start: 0 outliers final: 1 residues processed: 123 average time/residue: 0.8338 time to fit residues: 113.3404 Evaluate side-chains 103 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9196 Z= 0.407 Angle : 0.694 7.597 12470 Z= 0.373 Chirality : 0.047 0.162 1464 Planarity : 0.005 0.050 1584 Dihedral : 5.262 22.239 1268 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.77 % Allowed : 11.23 % Favored : 87.01 % 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: -0.24 (0.24), residues: 1156 helix: 0.38 (0.18), residues: 754 sheet: -0.52 (0.67), residues: 56 loop : -1.08 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 284 HIS 0.004 0.001 HIS B 211 PHE 0.035 0.003 PHE B 388 TYR 0.012 0.001 TYR B 136 ARG 0.006 0.001 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.073 Fit side-chains REVERT: B 632 LEU cc_start: 0.8366 (mp) cc_final: 0.8073 (mp) REVERT: A 595 ASP cc_start: 0.7615 (t0) cc_final: 0.7362 (p0) outliers start: 17 outliers final: 9 residues processed: 112 average time/residue: 0.7155 time to fit residues: 90.1656 Evaluate side-chains 102 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 556 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9196 Z= 0.215 Angle : 0.590 7.437 12470 Z= 0.314 Chirality : 0.043 0.166 1464 Planarity : 0.004 0.038 1584 Dihedral : 4.795 20.903 1268 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.77 % Allowed : 13.93 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1156 helix: 1.10 (0.19), residues: 758 sheet: 0.07 (0.86), residues: 36 loop : -0.96 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 284 HIS 0.003 0.001 HIS A 555 PHE 0.029 0.002 PHE B 388 TYR 0.009 0.001 TYR A 136 ARG 0.003 0.000 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: B 305 ASP cc_start: 0.7308 (t70) cc_final: 0.7104 (t0) REVERT: B 632 LEU cc_start: 0.8458 (mp) cc_final: 0.8200 (mp) REVERT: A 441 ILE cc_start: 0.9034 (mt) cc_final: 0.8672 (mm) REVERT: A 595 ASP cc_start: 0.7696 (t0) cc_final: 0.7431 (p0) outliers start: 17 outliers final: 10 residues processed: 109 average time/residue: 0.8523 time to fit residues: 102.8261 Evaluate side-chains 104 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 622 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.0470 chunk 112 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN B 621 ASN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9196 Z= 0.380 Angle : 0.640 7.653 12470 Z= 0.340 Chirality : 0.045 0.171 1464 Planarity : 0.004 0.047 1584 Dihedral : 4.755 19.673 1268 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 14.66 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1156 helix: 1.07 (0.18), residues: 760 sheet: 0.19 (0.85), residues: 36 loop : -0.92 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 284 HIS 0.003 0.001 HIS B 211 PHE 0.030 0.002 PHE B 388 TYR 0.012 0.001 TYR B 274 ARG 0.003 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.973 Fit side-chains REVERT: B 632 LEU cc_start: 0.8393 (mp) cc_final: 0.8069 (mp) REVERT: A 355 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7854 (t80) REVERT: A 441 ILE cc_start: 0.9023 (mt) cc_final: 0.8672 (mm) REVERT: A 595 ASP cc_start: 0.7713 (t0) cc_final: 0.7512 (p0) outliers start: 30 outliers final: 10 residues processed: 117 average time/residue: 0.7278 time to fit residues: 95.8709 Evaluate side-chains 103 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 530 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 0.0970 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9196 Z= 0.201 Angle : 0.572 8.804 12470 Z= 0.304 Chirality : 0.042 0.157 1464 Planarity : 0.003 0.032 1584 Dihedral : 4.539 18.739 1268 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.18 % Allowed : 17.46 % Favored : 80.35 % 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: 1.21 (0.25), residues: 1156 helix: 1.59 (0.19), residues: 738 sheet: 0.31 (0.85), residues: 36 loop : -0.66 (0.35), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 284 HIS 0.002 0.000 HIS A 211 PHE 0.026 0.002 PHE B 388 TYR 0.008 0.001 TYR A 232 ARG 0.006 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.969 Fit side-chains REVERT: B 225 ARG cc_start: 0.7712 (mtt90) cc_final: 0.7466 (mtt90) REVERT: B 355 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8017 (t80) REVERT: B 515 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8216 (ttmm) REVERT: B 632 LEU cc_start: 0.8479 (mp) cc_final: 0.8185 (mp) REVERT: A 225 ARG cc_start: 0.7653 (mtt90) cc_final: 0.7397 (mtt90) REVERT: A 355 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7905 (t80) REVERT: A 441 ILE cc_start: 0.9052 (mt) cc_final: 0.8628 (mm) outliers start: 21 outliers final: 10 residues processed: 117 average time/residue: 0.7443 time to fit residues: 97.4418 Evaluate side-chains 108 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 540 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 7.9990 chunk 100 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9196 Z= 0.347 Angle : 0.621 7.787 12470 Z= 0.328 Chirality : 0.045 0.185 1464 Planarity : 0.004 0.044 1584 Dihedral : 4.508 17.885 1268 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.22 % Allowed : 17.57 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1156 helix: 1.39 (0.19), residues: 750 sheet: 0.32 (0.84), residues: 36 loop : -0.73 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 284 HIS 0.003 0.001 HIS B 211 PHE 0.028 0.002 PHE B 388 TYR 0.012 0.001 TYR B 274 ARG 0.004 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 1.160 Fit side-chains REVERT: B 225 ARG cc_start: 0.7765 (mtt90) cc_final: 0.7536 (mtt90) REVERT: B 355 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8042 (t80) REVERT: B 468 LYS cc_start: 0.7680 (mmmm) cc_final: 0.7359 (mmmm) REVERT: B 515 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8199 (ttmm) REVERT: B 632 LEU cc_start: 0.8421 (mp) cc_final: 0.8101 (mp) REVERT: A 225 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7469 (mtt90) REVERT: A 355 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7878 (t80) outliers start: 31 outliers final: 18 residues processed: 116 average time/residue: 0.8181 time to fit residues: 105.3993 Evaluate side-chains 112 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 540 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9196 Z= 0.245 Angle : 0.594 7.565 12470 Z= 0.312 Chirality : 0.044 0.186 1464 Planarity : 0.003 0.034 1584 Dihedral : 4.388 17.559 1268 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.70 % Allowed : 19.02 % Favored : 78.27 % 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: 1.31 (0.25), residues: 1156 helix: 1.64 (0.19), residues: 740 sheet: 0.44 (0.85), residues: 36 loop : -0.57 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 284 HIS 0.003 0.000 HIS A 211 PHE 0.026 0.002 PHE A 388 TYR 0.009 0.001 TYR A 537 ARG 0.003 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.939 Fit side-chains REVERT: B 225 ARG cc_start: 0.7740 (mtt90) cc_final: 0.7513 (mtt90) REVERT: B 355 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8005 (t80) REVERT: B 468 LYS cc_start: 0.7676 (mmmm) cc_final: 0.7351 (mmmm) REVERT: B 515 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8187 (ttmm) REVERT: B 632 LEU cc_start: 0.8450 (mp) cc_final: 0.8122 (mp) REVERT: A 221 ARG cc_start: 0.7600 (ttm110) cc_final: 0.7334 (ttm110) REVERT: A 355 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7856 (t80) REVERT: A 515 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8316 (ttmm) outliers start: 26 outliers final: 16 residues processed: 116 average time/residue: 0.8595 time to fit residues: 110.2615 Evaluate side-chains 115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 602 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.0970 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9196 Z= 0.203 Angle : 0.583 7.669 12470 Z= 0.304 Chirality : 0.043 0.180 1464 Planarity : 0.003 0.035 1584 Dihedral : 4.334 17.313 1268 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.18 % Allowed : 20.27 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1156 helix: 1.76 (0.19), residues: 742 sheet: 0.49 (0.85), residues: 36 loop : -0.55 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 284 HIS 0.003 0.000 HIS A 211 PHE 0.025 0.002 PHE B 388 TYR 0.019 0.001 TYR A 537 ARG 0.005 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.970 Fit side-chains REVERT: B 355 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8014 (t80) REVERT: B 468 LYS cc_start: 0.7677 (mmmm) cc_final: 0.7347 (mmmm) REVERT: B 515 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8175 (ttmm) REVERT: B 632 LEU cc_start: 0.8482 (mp) cc_final: 0.8197 (mp) REVERT: A 355 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.7891 (t80) REVERT: A 515 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8323 (ttmm) outliers start: 21 outliers final: 17 residues processed: 111 average time/residue: 0.7241 time to fit residues: 90.2861 Evaluate side-chains 111 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 602 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 0.0060 chunk 98 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 GLN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9196 Z= 0.239 Angle : 0.590 7.679 12470 Z= 0.308 Chirality : 0.043 0.174 1464 Planarity : 0.003 0.037 1584 Dihedral : 4.273 16.936 1268 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.01 % Allowed : 20.17 % Favored : 76.82 % 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: 1.53 (0.25), residues: 1156 helix: 1.80 (0.19), residues: 742 sheet: 0.53 (0.87), residues: 36 loop : -0.49 (0.36), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 284 HIS 0.003 0.001 HIS A 211 PHE 0.025 0.002 PHE A 388 TYR 0.019 0.001 TYR A 537 ARG 0.004 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 1.223 Fit side-chains REVERT: B 355 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8030 (t80) REVERT: B 468 LYS cc_start: 0.7700 (mmmm) cc_final: 0.7373 (mmmm) REVERT: B 515 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8194 (ttmm) REVERT: B 632 LEU cc_start: 0.8493 (mp) cc_final: 0.8202 (mp) REVERT: A 355 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7909 (t80) REVERT: A 515 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8306 (ttmm) outliers start: 29 outliers final: 19 residues processed: 118 average time/residue: 0.8286 time to fit residues: 108.3979 Evaluate side-chains 115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 602 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 0.0980 chunk 106 optimal weight: 10.0000 chunk 92 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 0.0470 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN A 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9196 Z= 0.176 Angle : 0.576 7.800 12470 Z= 0.299 Chirality : 0.042 0.175 1464 Planarity : 0.003 0.039 1584 Dihedral : 4.185 16.795 1266 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.29 % Allowed : 21.31 % Favored : 76.40 % 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: 1.76 (0.26), residues: 1156 helix: 1.99 (0.19), residues: 742 sheet: 0.55 (0.88), residues: 36 loop : -0.42 (0.36), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 284 HIS 0.003 0.000 HIS A 211 PHE 0.026 0.002 PHE A 210 TYR 0.018 0.001 TYR A 537 ARG 0.008 0.000 ARG A 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.011 Fit side-chains REVERT: B 355 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8046 (t80) REVERT: B 468 LYS cc_start: 0.7682 (mmmm) cc_final: 0.7364 (mmmm) REVERT: B 515 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8180 (ttmm) REVERT: B 632 LEU cc_start: 0.8493 (mp) cc_final: 0.8237 (mp) REVERT: A 355 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7897 (t80) REVERT: A 515 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8306 (ttmm) outliers start: 22 outliers final: 17 residues processed: 113 average time/residue: 0.7460 time to fit residues: 94.6786 Evaluate side-chains 109 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 602 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 38 optimal weight: 0.0570 chunk 94 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.0030 chunk 66 optimal weight: 0.8980 overall best weight: 0.4708 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.210013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.123386 restraints weight = 9578.924| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.01 r_work: 0.3282 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9196 Z= 0.186 Angle : 0.568 7.843 12470 Z= 0.294 Chirality : 0.042 0.174 1464 Planarity : 0.003 0.039 1584 Dihedral : 4.124 16.408 1266 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.29 % Allowed : 22.14 % Favored : 75.57 % 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: 1.88 (0.26), residues: 1156 helix: 2.07 (0.19), residues: 742 sheet: 0.65 (0.89), residues: 36 loop : -0.35 (0.36), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 284 HIS 0.003 0.000 HIS B 211 PHE 0.031 0.002 PHE B 210 TYR 0.021 0.001 TYR B 537 ARG 0.008 0.000 ARG A 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2727.28 seconds wall clock time: 50 minutes 34.38 seconds (3034.38 seconds total)