Starting phenix.real_space_refine on Sun Jul 27 04:31:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7psd_13612/07_2025/7psd_13612.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psd_13612/07_2025/7psd_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_13612/07_2025/7psd_13612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psd_13612/07_2025/7psd_13612.map" model { file = "/net/cci-nas-00/data/ceres_data/7psd_13612/07_2025/7psd_13612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psd_13612/07_2025/7psd_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.98, per 1000 atoms: 0.99 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: 2.50 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: 0.94 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: 3.10 Time building geometry restraints manager: 2.88 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.530 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.050 ------------------------------------------------------------------------------- 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= 0.619 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 Details of bonding type rmsd hydrogen bonds : bond 0.14069 ( 612) hydrogen bonds : angle 6.27969 ( 1800) covalent geometry : bond 0.01502 ( 9196) covalent geometry : angle 1.11533 (12470) *********************** 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 : 1.022 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: 0.8390 time to fit residues: 114.2662 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 : 0.961 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.204031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118714 restraints weight = 9525.260| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.85 r_work: 0.3255 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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= 0.260 Angle : 0.694 7.597 12470 Z= 0.373 Chirality : 0.047 0.162 1464 Planarity : 0.005 0.050 1584 Dihedral : 5.262 22.240 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 Details of bonding type rmsd hydrogen bonds : bond 0.05751 ( 612) hydrogen bonds : angle 4.68025 ( 1800) covalent geometry : bond 0.00632 ( 9196) covalent geometry : angle 0.69354 (12470) *********************** 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 : 1.117 Fit side-chains REVERT: B 154 THR cc_start: 0.8101 (p) cc_final: 0.7898 (t) REVERT: B 632 LEU cc_start: 0.7888 (mp) cc_final: 0.7592 (mp) REVERT: A 305 ASP cc_start: 0.7968 (t70) cc_final: 0.7728 (t0) REVERT: A 595 ASP cc_start: 0.8020 (t0) cc_final: 0.7551 (p0) outliers start: 17 outliers final: 9 residues processed: 112 average time/residue: 0.7030 time to fit residues: 88.9749 Evaluate side-chains 103 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.206918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122135 restraints weight = 9565.518| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.87 r_work: 0.3307 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9196 Z= 0.154 Angle : 0.600 7.527 12470 Z= 0.320 Chirality : 0.043 0.158 1464 Planarity : 0.004 0.038 1584 Dihedral : 4.882 21.102 1268 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.08 % Allowed : 13.62 % 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: 0.57 (0.25), residues: 1156 helix: 1.05 (0.18), residues: 754 sheet: 0.05 (0.86), residues: 36 loop : -0.91 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 284 HIS 0.002 0.001 HIS B 211 PHE 0.030 0.002 PHE B 388 TYR 0.009 0.001 TYR A 136 ARG 0.002 0.000 ARG B 536 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 612) hydrogen bonds : angle 4.40107 ( 1800) covalent geometry : bond 0.00352 ( 9196) covalent geometry : angle 0.60007 (12470) *********************** 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 120 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: B 305 ASP cc_start: 0.7799 (t70) cc_final: 0.7581 (t0) REVERT: B 632 LEU cc_start: 0.8035 (mp) cc_final: 0.7784 (mp) REVERT: B 657 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7090 (pm20) REVERT: A 441 ILE cc_start: 0.8904 (mt) cc_final: 0.8510 (mm) REVERT: A 595 ASP cc_start: 0.8097 (t0) cc_final: 0.7599 (p0) REVERT: A 657 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7261 (pm20) outliers start: 20 outliers final: 12 residues processed: 111 average time/residue: 0.8223 time to fit residues: 101.1145 Evaluate side-chains 106 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 B residue 530 THR Chi-restraints excluded: chain B residue 657 GLU 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 556 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 4 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.207801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120030 restraints weight = 9536.725| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.98 r_work: 0.3287 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9196 Z= 0.143 Angle : 0.570 7.621 12470 Z= 0.301 Chirality : 0.042 0.156 1464 Planarity : 0.003 0.033 1584 Dihedral : 4.615 19.681 1268 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.29 % Allowed : 15.18 % Favored : 82.54 % 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: 0.97 (0.25), residues: 1156 helix: 1.38 (0.19), residues: 750 sheet: 0.31 (0.86), residues: 36 loop : -0.79 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 284 HIS 0.003 0.000 HIS B 211 PHE 0.027 0.002 PHE B 388 TYR 0.009 0.001 TYR A 232 ARG 0.002 0.000 ARG B 536 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 612) hydrogen bonds : angle 4.25916 ( 1800) covalent geometry : bond 0.00332 ( 9196) covalent geometry : angle 0.56991 (12470) *********************** 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 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: B 225 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7711 (mtt90) REVERT: B 632 LEU cc_start: 0.7941 (mp) cc_final: 0.7656 (mp) REVERT: A 225 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7603 (mtt90) REVERT: A 441 ILE cc_start: 0.8853 (mt) cc_final: 0.8416 (mm) REVERT: A 595 ASP cc_start: 0.8110 (t0) cc_final: 0.7668 (p0) REVERT: A 657 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7289 (pm20) outliers start: 22 outliers final: 14 residues processed: 116 average time/residue: 0.7469 time to fit residues: 96.9950 Evaluate side-chains 109 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 363 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 530 THR 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 363 MET Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 115 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 101 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 621 ASN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.208845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121546 restraints weight = 9575.802| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.00 r_work: 0.3308 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9196 Z= 0.126 Angle : 0.551 7.439 12470 Z= 0.291 Chirality : 0.041 0.153 1464 Planarity : 0.003 0.030 1584 Dihedral : 4.445 18.928 1268 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.49 % Allowed : 16.84 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1156 helix: 1.71 (0.19), residues: 742 sheet: 0.36 (0.86), residues: 36 loop : -0.64 (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 0.008 0.001 TYR A 232 ARG 0.002 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 612) hydrogen bonds : angle 4.15463 ( 1800) covalent geometry : bond 0.00279 ( 9196) covalent geometry : angle 0.55059 (12470) *********************** 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 122 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: B 355 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8036 (t80) REVERT: B 515 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8113 (ttmm) REVERT: B 632 LEU cc_start: 0.7913 (mp) cc_final: 0.7661 (mp) REVERT: A 225 ARG cc_start: 0.7845 (mtt90) cc_final: 0.7558 (mtt90) REVERT: A 355 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8007 (t80) REVERT: A 441 ILE cc_start: 0.8834 (mt) cc_final: 0.8419 (mm) REVERT: A 595 ASP cc_start: 0.8186 (t0) cc_final: 0.7765 (p0) REVERT: A 657 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7260 (pm20) outliers start: 24 outliers final: 12 residues processed: 114 average time/residue: 0.8344 time to fit residues: 107.1595 Evaluate side-chains 108 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 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 B residue 363 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 363 MET Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 0.0020 chunk 13 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 3 optimal weight: 0.0470 chunk 48 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.0170 chunk 86 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 overall best weight: 0.2524 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.211046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125217 restraints weight = 9510.946| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.00 r_work: 0.3315 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9196 Z= 0.111 Angle : 0.529 7.443 12470 Z= 0.278 Chirality : 0.041 0.197 1464 Planarity : 0.003 0.025 1584 Dihedral : 4.258 18.251 1268 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.18 % Allowed : 18.50 % Favored : 79.31 % 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: 1.69 (0.26), residues: 1156 helix: 1.98 (0.19), residues: 742 sheet: 0.49 (0.86), residues: 36 loop : -0.54 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 284 HIS 0.003 0.001 HIS B 211 PHE 0.025 0.002 PHE A 210 TYR 0.008 0.001 TYR B 232 ARG 0.002 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 612) hydrogen bonds : angle 4.03305 ( 1800) covalent geometry : bond 0.00238 ( 9196) covalent geometry : angle 0.52929 (12470) *********************** 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 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.068 Fit side-chains REVERT: B 221 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7381 (ttm110) REVERT: B 225 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7580 (mtt90) REVERT: B 250 MET cc_start: 0.8746 (mtt) cc_final: 0.8541 (mtm) REVERT: B 468 LYS cc_start: 0.7338 (mmmm) cc_final: 0.6982 (mmmm) REVERT: B 515 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8108 (ttmm) REVERT: B 632 LEU cc_start: 0.7918 (mp) cc_final: 0.7639 (mp) REVERT: A 221 ARG cc_start: 0.7601 (ttm110) cc_final: 0.7219 (ttm110) REVERT: A 225 ARG cc_start: 0.7774 (mtt90) cc_final: 0.7479 (mtt90) REVERT: A 441 ILE cc_start: 0.8800 (mt) cc_final: 0.8365 (mm) REVERT: A 595 ASP cc_start: 0.8151 (t0) cc_final: 0.7862 (p0) REVERT: A 657 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7357 (pm20) outliers start: 21 outliers final: 9 residues processed: 118 average time/residue: 0.9623 time to fit residues: 125.9547 Evaluate side-chains 102 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain A residue 155 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 657 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.209319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.122467 restraints weight = 9557.355| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.00 r_work: 0.3286 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9196 Z= 0.152 Angle : 0.561 7.754 12470 Z= 0.297 Chirality : 0.042 0.161 1464 Planarity : 0.003 0.033 1584 Dihedral : 4.252 17.216 1268 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.77 % Allowed : 19.75 % Favored : 78.48 % 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: 1.68 (0.26), residues: 1156 helix: 1.95 (0.19), residues: 740 sheet: 0.55 (0.87), residues: 36 loop : -0.48 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 284 HIS 0.002 0.001 HIS B 211 PHE 0.024 0.002 PHE A 388 TYR 0.010 0.001 TYR B 274 ARG 0.002 0.000 ARG B 138 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 612) hydrogen bonds : angle 4.10550 ( 1800) covalent geometry : bond 0.00359 ( 9196) covalent geometry : angle 0.56078 (12470) *********************** 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 117 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.945 Fit side-chains REVERT: B 221 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7424 (ttm110) REVERT: B 225 ARG cc_start: 0.7980 (mtt90) cc_final: 0.7721 (mtt90) REVERT: B 468 LYS cc_start: 0.7410 (mmmm) cc_final: 0.7047 (mmmm) REVERT: B 515 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8112 (ttmm) REVERT: B 632 LEU cc_start: 0.8022 (mp) cc_final: 0.7764 (mp) REVERT: A 221 ARG cc_start: 0.7655 (ttm110) cc_final: 0.7359 (ttm110) REVERT: A 595 ASP cc_start: 0.8190 (t0) cc_final: 0.7922 (p0) REVERT: A 657 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7367 (pm20) outliers start: 17 outliers final: 12 residues processed: 112 average time/residue: 0.8638 time to fit residues: 106.8240 Evaluate side-chains 109 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 371 LEU 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 293 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 57 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.207873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122687 restraints weight = 9572.624| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.93 r_work: 0.3298 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2491 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= 0.145 Angle : 0.568 7.398 12470 Z= 0.297 Chirality : 0.042 0.193 1464 Planarity : 0.003 0.036 1584 Dihedral : 4.230 17.016 1268 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.81 % Allowed : 19.23 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.26), residues: 1156 helix: 1.97 (0.19), residues: 740 sheet: 0.60 (0.88), residues: 36 loop : -0.46 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 284 HIS 0.002 0.000 HIS B 211 PHE 0.026 0.002 PHE A 210 TYR 0.018 0.001 TYR B 537 ARG 0.002 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 612) hydrogen bonds : angle 4.07649 ( 1800) covalent geometry : bond 0.00338 ( 9196) covalent geometry : angle 0.56831 (12470) *********************** 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 124 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: B 221 ARG cc_start: 0.7695 (ttm110) cc_final: 0.7341 (ttm110) REVERT: B 225 ARG cc_start: 0.7935 (mtt90) cc_final: 0.7668 (mtt90) REVERT: B 331 GLN cc_start: 0.7984 (tt0) cc_final: 0.7602 (mt0) REVERT: B 355 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8026 (t80) REVERT: B 468 LYS cc_start: 0.7423 (mmmm) cc_final: 0.7064 (mmmm) REVERT: B 515 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8166 (ttmm) REVERT: B 632 LEU cc_start: 0.8014 (mp) cc_final: 0.7757 (mp) REVERT: A 355 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8012 (t80) REVERT: A 595 ASP cc_start: 0.8218 (t0) cc_final: 0.7957 (p0) REVERT: A 657 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7373 (pm20) outliers start: 27 outliers final: 14 residues processed: 116 average time/residue: 1.3428 time to fit residues: 171.8367 Evaluate side-chains 112 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 155 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 B residue 371 LEU 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 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 540 VAL Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.207559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.122216 restraints weight = 9463.545| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.92 r_work: 0.3297 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2594 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= 0.147 Angle : 0.579 10.045 12470 Z= 0.305 Chirality : 0.043 0.197 1464 Planarity : 0.003 0.036 1584 Dihedral : 4.231 16.833 1268 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.39 % Allowed : 20.27 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.26), residues: 1156 helix: 1.88 (0.19), residues: 750 sheet: 0.63 (0.88), residues: 36 loop : -0.46 (0.36), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 284 HIS 0.003 0.000 HIS A 211 PHE 0.024 0.002 PHE A 388 TYR 0.020 0.001 TYR B 537 ARG 0.007 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 612) hydrogen bonds : angle 4.07938 ( 1800) covalent geometry : bond 0.00344 ( 9196) covalent geometry : angle 0.57880 (12470) *********************** 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 120 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.944 Fit side-chains REVERT: B 221 ARG cc_start: 0.7699 (ttm110) cc_final: 0.7350 (ttm110) REVERT: B 225 ARG cc_start: 0.7935 (mtt90) cc_final: 0.7677 (mtt90) REVERT: B 331 GLN cc_start: 0.7988 (tt0) cc_final: 0.7611 (mt0) REVERT: B 355 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8015 (t80) REVERT: B 468 LYS cc_start: 0.7416 (mmmm) cc_final: 0.7065 (mmmm) REVERT: B 515 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8149 (ttmm) REVERT: B 632 LEU cc_start: 0.7967 (mp) cc_final: 0.7719 (mp) REVERT: A 355 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8011 (t80) REVERT: A 595 ASP cc_start: 0.8216 (t0) cc_final: 0.7956 (p0) REVERT: A 657 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7348 (pm20) outliers start: 23 outliers final: 16 residues processed: 113 average time/residue: 0.8198 time to fit residues: 102.6560 Evaluate side-chains 115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 238 VAL Chi-restraints excluded: chain B residue 293 ASN 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 371 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 111 optimal weight: 0.0270 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 GLN B 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.209577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122536 restraints weight = 9768.444| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.03 r_work: 0.3268 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2675 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= 0.137 Angle : 0.589 11.318 12470 Z= 0.310 Chirality : 0.043 0.207 1464 Planarity : 0.003 0.034 1584 Dihedral : 4.211 17.988 1268 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.87 % Allowed : 21.21 % Favored : 76.92 % 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: 1.80 (0.26), residues: 1156 helix: 2.02 (0.19), residues: 740 sheet: 0.59 (0.88), residues: 36 loop : -0.38 (0.36), residues: 380 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 0.027 0.002 PHE A 210 TYR 0.021 0.001 TYR A 537 ARG 0.007 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 612) hydrogen bonds : angle 4.03128 ( 1800) covalent geometry : bond 0.00314 ( 9196) covalent geometry : angle 0.58927 (12470) ********************** 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 115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: B 221 ARG cc_start: 0.7645 (ttm110) cc_final: 0.7284 (ttm110) REVERT: B 225 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7567 (mtt90) REVERT: B 331 GLN cc_start: 0.7924 (tt0) cc_final: 0.7557 (mt0) REVERT: B 355 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7972 (t80) REVERT: B 468 LYS cc_start: 0.7404 (mmmm) cc_final: 0.7060 (mmmm) REVERT: B 515 LYS cc_start: 0.8353 (ttpt) cc_final: 0.8121 (ttmm) REVERT: B 632 LEU cc_start: 0.7915 (mp) cc_final: 0.7631 (mp) REVERT: A 355 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.7969 (t80) REVERT: A 416 ASP cc_start: 0.7678 (m-30) cc_final: 0.7189 (p0) REVERT: A 595 ASP cc_start: 0.8238 (t0) cc_final: 0.7973 (p0) REVERT: A 657 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7337 (pm20) outliers start: 18 outliers final: 15 residues processed: 112 average time/residue: 0.9573 time to fit residues: 118.7454 Evaluate side-chains 113 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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 238 VAL Chi-restraints excluded: chain B residue 293 ASN 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 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 371 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 110 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.208609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122886 restraints weight = 9535.954| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.96 r_work: 0.3265 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2745 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= 0.143 Angle : 0.582 11.001 12470 Z= 0.308 Chirality : 0.043 0.201 1464 Planarity : 0.003 0.039 1584 Dihedral : 4.215 21.419 1268 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.77 % Allowed : 21.62 % Favored : 76.61 % 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: 1.80 (0.26), residues: 1156 helix: 2.02 (0.19), residues: 740 sheet: 0.58 (0.88), residues: 36 loop : -0.37 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 284 HIS 0.003 0.000 HIS B 211 PHE 0.023 0.002 PHE A 388 TYR 0.020 0.001 TYR A 537 ARG 0.007 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 612) hydrogen bonds : angle 4.03812 ( 1800) covalent geometry : bond 0.00334 ( 9196) covalent geometry : angle 0.58241 (12470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8899.99 seconds wall clock time: 158 minutes 51.19 seconds (9531.19 seconds total)