Starting phenix.real_space_refine on Tue Mar 3 16:11:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cd0_16565/03_2026/8cd0_16565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cd0_16565/03_2026/8cd0_16565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cd0_16565/03_2026/8cd0_16565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cd0_16565/03_2026/8cd0_16565.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cd0_16565/03_2026/8cd0_16565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cd0_16565/03_2026/8cd0_16565.map" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 2 5.49 5 S 26 5.16 5 C 4426 2.51 5 N 1162 2.21 5 O 1243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6860 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5883 Classifications: {'peptide': 716} Link IDs: {'PCIS': 4, 'PTRANS': 32, 'TRANS': 679} Chain breaks: 6 Chain: "C" Number of atoms: 945 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 bond proxies already assigned to first conformer: 946 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'A3P': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.70, per 1000 atoms: 0.25 Number of scatterers: 6860 At special positions: 0 Unit cell: (78.11, 97.82, 102.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 26 16.00 P 2 15.00 O 1243 8.00 N 1162 7.00 C 4426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 818 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 103 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 222.2 milliseconds 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 42.7% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 148 through 163 Processing helix chain 'A' and resid 287 through 302 removed outlier: 3.849A pdb=" N THR A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 349 Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 401 through 420 removed outlier: 3.732A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.544A pdb=" N TYR A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.025A pdb=" N LEU A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 521 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.886A pdb=" N ARG A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 574 Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.649A pdb=" N LYS A 578 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP A 579 " --> pdb=" O GLU A 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 575 through 579' Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.517A pdb=" N PHE A 640 " --> pdb=" O SER A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 653 removed outlier: 3.905A pdb=" N TYR A 651 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS A 652 " --> pdb=" O HIS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 678 through 681 removed outlier: 3.758A pdb=" N PHE A 681 " --> pdb=" O ALA A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 678 through 681' Processing helix chain 'A' and resid 685 through 694 removed outlier: 3.572A pdb=" N ARG A 689 " --> pdb=" O VAL A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 720 Processing helix chain 'A' and resid 722 through 728 Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 742 through 753 Processing helix chain 'A' and resid 756 through 768 removed outlier: 3.842A pdb=" N HIS A 760 " --> pdb=" O TRP A 756 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 784 through 796 removed outlier: 4.291A pdb=" N VAL A 788 " --> pdb=" O GLU A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 808 removed outlier: 3.928A pdb=" N THR A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 808 " --> pdb=" O TYR A 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 803 through 808' Processing helix chain 'A' and resid 841 through 852 Processing helix chain 'A' and resid 853 through 866 Processing helix chain 'A' and resid 871 through 880 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.906A pdb=" N THR C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114 removed outlier: 6.602A pdb=" N ILE A 166 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 278 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 388 removed outlier: 5.415A pdb=" N LEU A 356 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ASN A 355 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 316 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLY A 357 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE A 318 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N ILE A 523 " --> pdb=" O VAL A 480 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE A 525 " --> pdb=" O PRO A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 458 removed outlier: 6.666A pdb=" N THR A 456 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG A 483 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR A 458 " --> pdb=" O ARG A 483 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N ILE A 523 " --> pdb=" O VAL A 480 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE A 525 " --> pdb=" O PRO A 482 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG A 312 " --> pdb=" O GLN A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 630 through 632 removed outlier: 6.893A pdb=" N LEU A 607 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N SER A 677 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 609 " --> pdb=" O SER A 677 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE A 702 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 809 through 811 removed outlier: 3.565A pdb=" N ALA A 809 " --> pdb=" O CYS A 818 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 811 " --> pdb=" O PHE A 816 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 816 " --> pdb=" O ASP A 811 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.584A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.885A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 91 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 121 " --> pdb=" O TYR C 93 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2039 1.34 - 1.46: 1607 1.46 - 1.58: 3357 1.58 - 1.70: 8 1.70 - 1.82: 40 Bond restraints: 7051 Sorted by residual: bond pdb=" C ALA A 430 " pdb=" N PRO A 431 " ideal model delta sigma weight residual 1.335 1.385 -0.050 1.30e-02 5.92e+03 1.48e+01 bond pdb=" CB PHE A 362 " pdb=" CG PHE A 362 " ideal model delta sigma weight residual 1.502 1.573 -0.071 2.30e-02 1.89e+03 9.64e+00 bond pdb=" C VAL A 429 " pdb=" N ALA A 430 " ideal model delta sigma weight residual 1.330 1.370 -0.040 1.37e-02 5.33e+03 8.51e+00 bond pdb=" CB PHE A 847 " pdb=" CG PHE A 847 " ideal model delta sigma weight residual 1.502 1.561 -0.059 2.30e-02 1.89e+03 6.53e+00 bond pdb=" C ALA A 686 " pdb=" N PRO A 687 " ideal model delta sigma weight residual 1.336 1.366 -0.031 1.23e-02 6.61e+03 6.16e+00 ... (remaining 7046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 9322 3.42 - 6.84: 189 6.84 - 10.26: 43 10.26 - 13.68: 9 13.68 - 17.11: 2 Bond angle restraints: 9565 Sorted by residual: angle pdb=" C THR A 485 " pdb=" N CYS A 486 " pdb=" CA CYS A 486 " ideal model delta sigma weight residual 121.54 132.61 -11.07 1.91e+00 2.74e-01 3.36e+01 angle pdb=" C PHE A 399 " pdb=" N HIS A 400 " pdb=" CA HIS A 400 " ideal model delta sigma weight residual 121.54 132.56 -11.02 1.91e+00 2.74e-01 3.33e+01 angle pdb=" CB GLU A 858 " pdb=" CG GLU A 858 " pdb=" CD GLU A 858 " ideal model delta sigma weight residual 112.60 121.92 -9.32 1.70e+00 3.46e-01 3.01e+01 angle pdb=" C SER A 213 " pdb=" N GLU A 214 " pdb=" CA GLU A 214 " ideal model delta sigma weight residual 121.70 131.18 -9.48 1.80e+00 3.09e-01 2.77e+01 angle pdb=" CG ARG C 74 " pdb=" CD ARG C 74 " pdb=" NE ARG C 74 " ideal model delta sigma weight residual 112.00 123.50 -11.50 2.20e+00 2.07e-01 2.73e+01 ... (remaining 9560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 3539 17.31 - 34.62: 433 34.62 - 51.93: 119 51.93 - 69.24: 41 69.24 - 86.55: 10 Dihedral angle restraints: 4142 sinusoidal: 1701 harmonic: 2441 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 165.46 -72.46 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CA ASN C 84 " pdb=" C ASN C 84 " pdb=" N LEU C 85 " pdb=" CA LEU C 85 " ideal model delta harmonic sigma weight residual 180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA SER C 11 " pdb=" C SER C 11 " pdb=" N VAL C 12 " pdb=" CA VAL C 12 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 4139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 858 0.080 - 0.161: 126 0.161 - 0.241: 24 0.241 - 0.322: 6 0.322 - 0.402: 2 Chirality restraints: 1016 Sorted by residual: chirality pdb=" CB ILE C 51 " pdb=" CA ILE C 51 " pdb=" CG1 ILE C 51 " pdb=" CG2 ILE C 51 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB THR C 90 " pdb=" CA THR C 90 " pdb=" OG1 THR C 90 " pdb=" CG2 THR C 90 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB ILE A 421 " pdb=" CA ILE A 421 " pdb=" CG1 ILE A 421 " pdb=" CG2 ILE A 421 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1013 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 643 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ILE A 643 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE A 643 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN A 644 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 339 " 0.024 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE A 339 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 339 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 339 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 339 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 339 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 339 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 627 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO A 628 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " -0.044 5.00e-02 4.00e+02 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 133 2.68 - 3.23: 5773 3.23 - 3.79: 11421 3.79 - 4.34: 15664 4.34 - 4.90: 25121 Nonbonded interactions: 58112 Sorted by model distance: nonbonded pdb="CA CA A 902 " pdb=" O HOH A1003 " model vdw 2.122 2.510 nonbonded pdb=" OD1 ASP A 320 " pdb="CA CA A 902 " model vdw 2.162 2.510 nonbonded pdb=" NE2 HIS A 393 " pdb="CA CA A 902 " model vdw 2.198 2.590 nonbonded pdb=" O GLU A 513 " pdb=" OG1 THR A 517 " model vdw 2.295 3.040 nonbonded pdb=" OG SER C 17 " pdb=" OD1 ASN C 83 " model vdw 2.335 3.040 ... (remaining 58107 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.25 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: 7.380 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.160 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 7055 Z= 0.319 Angle : 1.253 17.105 9573 Z= 0.679 Chirality : 0.065 0.402 1016 Planarity : 0.010 0.080 1212 Dihedral : 17.387 86.546 2564 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.03 % Allowed : 22.09 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.25), residues: 820 helix: -3.33 (0.17), residues: 300 sheet: -1.35 (0.45), residues: 133 loop : -1.10 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 557 TYR 0.038 0.003 TYR A 680 PHE 0.058 0.004 PHE A 339 TRP 0.026 0.003 TRP A 595 HIS 0.027 0.003 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00659 ( 7051) covalent geometry : angle 1.25305 ( 9565) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.96908 ( 8) hydrogen bonds : bond 0.19466 ( 265) hydrogen bonds : angle 8.09041 ( 759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7859 (tp30) cc_final: 0.7576 (mm-30) REVERT: A 137 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5649 (mt) REVERT: A 143 LYS cc_start: 0.6523 (mttp) cc_final: 0.6191 (mttm) REVERT: A 203 LYS cc_start: 0.7110 (mptt) cc_final: 0.6848 (mttm) REVERT: A 206 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6795 (mp) REVERT: A 208 TYR cc_start: 0.7867 (t80) cc_final: 0.7408 (t80) REVERT: A 308 LEU cc_start: 0.7927 (mt) cc_final: 0.7636 (tp) REVERT: A 400 HIS cc_start: 0.5718 (p-80) cc_final: 0.5413 (p90) REVERT: A 413 LYS cc_start: 0.4280 (ttmt) cc_final: 0.3836 (ttmm) REVERT: A 452 SER cc_start: 0.8106 (m) cc_final: 0.7894 (m) REVERT: A 536 ASP cc_start: 0.6909 (m-30) cc_final: 0.6348 (t0) REVERT: A 676 LYS cc_start: 0.7685 (tttt) cc_final: 0.7482 (tmtp) REVERT: A 688 ARG cc_start: 0.6999 (ttp-110) cc_final: 0.6556 (ptm160) REVERT: A 708 ASP cc_start: 0.6210 (t70) cc_final: 0.5944 (t70) REVERT: A 743 LYS cc_start: 0.7804 (mttt) cc_final: 0.7075 (mptt) REVERT: A 864 TYR cc_start: 0.5837 (OUTLIER) cc_final: 0.5160 (t80) REVERT: C 106 LYS cc_start: 0.7626 (pttt) cc_final: 0.7251 (tttm) outliers start: 15 outliers final: 7 residues processed: 132 average time/residue: 0.4667 time to fit residues: 65.3082 Evaluate side-chains 103 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.0010 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 overall best weight: 0.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 400 HIS A 408 GLN A 583 GLN ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.184290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.159158 restraints weight = 27248.957| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 3.47 r_work: 0.4066 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4073 r_free = 0.4073 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4073 r_free = 0.4073 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7055 Z= 0.110 Angle : 0.563 8.927 9573 Z= 0.295 Chirality : 0.042 0.158 1016 Planarity : 0.005 0.048 1212 Dihedral : 7.300 66.383 963 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.25 % Allowed : 22.09 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.28), residues: 820 helix: -1.29 (0.25), residues: 319 sheet: -0.81 (0.48), residues: 124 loop : -0.77 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 557 TYR 0.013 0.001 TYR C 59 PHE 0.014 0.001 PHE A 494 TRP 0.010 0.001 TRP A 595 HIS 0.015 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7051) covalent geometry : angle 0.56299 ( 9565) SS BOND : bond 0.00101 ( 4) SS BOND : angle 0.55484 ( 8) hydrogen bonds : bond 0.03629 ( 265) hydrogen bonds : angle 5.49650 ( 759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.5998 (OUTLIER) cc_final: 0.5782 (pp30) REVERT: A 114 GLU cc_start: 0.7700 (tp30) cc_final: 0.7438 (mm-30) REVERT: A 143 LYS cc_start: 0.6383 (mttp) cc_final: 0.6131 (mtpm) REVERT: A 308 LEU cc_start: 0.8146 (mt) cc_final: 0.7921 (tp) REVERT: A 413 LYS cc_start: 0.4737 (ttmt) cc_final: 0.4421 (ttmm) REVERT: A 452 SER cc_start: 0.8002 (OUTLIER) cc_final: 0.7798 (m) REVERT: A 583 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6351 (mp10) REVERT: A 688 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.6853 (ptm160) REVERT: A 708 ASP cc_start: 0.6449 (t70) cc_final: 0.6176 (t70) REVERT: A 743 LYS cc_start: 0.7869 (mttt) cc_final: 0.7253 (mptt) REVERT: A 784 GLU cc_start: 0.6310 (pp20) cc_final: 0.5815 (pp20) REVERT: A 853 ARG cc_start: 0.5473 (OUTLIER) cc_final: 0.5075 (ttm170) REVERT: A 864 TYR cc_start: 0.5779 (OUTLIER) cc_final: 0.5465 (m-80) outliers start: 24 outliers final: 7 residues processed: 120 average time/residue: 0.4661 time to fit residues: 59.2316 Evaluate side-chains 109 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 864 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.175460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.149877 restraints weight = 26146.869| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.45 r_work: 0.3949 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7055 Z= 0.167 Angle : 0.612 8.724 9573 Z= 0.319 Chirality : 0.044 0.166 1016 Planarity : 0.005 0.041 1212 Dihedral : 6.970 64.755 952 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.01 % Allowed : 22.09 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.29), residues: 820 helix: -0.44 (0.27), residues: 316 sheet: -0.74 (0.50), residues: 126 loop : -0.42 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 557 TYR 0.015 0.002 TYR C 32 PHE 0.021 0.002 PHE A 339 TRP 0.025 0.002 TRP A 391 HIS 0.008 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7051) covalent geometry : angle 0.61219 ( 9565) SS BOND : bond 0.00293 ( 4) SS BOND : angle 0.87357 ( 8) hydrogen bonds : bond 0.04233 ( 265) hydrogen bonds : angle 5.24617 ( 759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: A 143 LYS cc_start: 0.6350 (mttp) cc_final: 0.6029 (mttm) REVERT: A 413 LYS cc_start: 0.4848 (ttmt) cc_final: 0.4522 (tptm) REVERT: A 447 TRP cc_start: 0.8043 (OUTLIER) cc_final: 0.7719 (m-10) REVERT: A 452 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7992 (m) REVERT: A 634 TYR cc_start: 0.7199 (m-80) cc_final: 0.6970 (m-80) REVERT: A 688 ARG cc_start: 0.7358 (ttp-110) cc_final: 0.7003 (ptt-90) REVERT: A 743 LYS cc_start: 0.7884 (mttt) cc_final: 0.7255 (mptt) REVERT: A 782 ARG cc_start: 0.5184 (OUTLIER) cc_final: 0.4551 (mtp85) REVERT: A 784 GLU cc_start: 0.6426 (pp20) cc_final: 0.5891 (pp20) REVERT: A 853 ARG cc_start: 0.5546 (OUTLIER) cc_final: 0.5092 (ttm170) REVERT: A 864 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5768 (m-80) outliers start: 37 outliers final: 13 residues processed: 123 average time/residue: 0.4280 time to fit residues: 56.1273 Evaluate side-chains 111 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 ARG Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 475 HIS ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.176917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.152991 restraints weight = 20684.877| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.32 r_work: 0.3979 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7055 Z= 0.119 Angle : 0.549 8.153 9573 Z= 0.284 Chirality : 0.042 0.157 1016 Planarity : 0.004 0.036 1212 Dihedral : 6.564 58.987 952 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.93 % Allowed : 22.63 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.29), residues: 820 helix: 0.13 (0.29), residues: 317 sheet: -0.89 (0.54), residues: 104 loop : -0.30 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 557 TYR 0.016 0.001 TYR C 32 PHE 0.026 0.001 PHE A 339 TRP 0.015 0.001 TRP A 391 HIS 0.006 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7051) covalent geometry : angle 0.54937 ( 9565) SS BOND : bond 0.00183 ( 4) SS BOND : angle 0.55713 ( 8) hydrogen bonds : bond 0.03587 ( 265) hydrogen bonds : angle 4.99356 ( 759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 88 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.6208 (m-10) REVERT: A 89 VAL cc_start: 0.6425 (m) cc_final: 0.6133 (t) REVERT: A 95 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.6047 (pp30) REVERT: A 114 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: A 143 LYS cc_start: 0.6381 (mttp) cc_final: 0.6056 (mttm) REVERT: A 308 LEU cc_start: 0.8212 (mt) cc_final: 0.7947 (tp) REVERT: A 413 LYS cc_start: 0.4727 (ttmt) cc_final: 0.4419 (ttmm) REVERT: A 447 TRP cc_start: 0.7946 (OUTLIER) cc_final: 0.7294 (m-10) REVERT: A 452 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7928 (m) REVERT: A 634 TYR cc_start: 0.7239 (m-80) cc_final: 0.7014 (m-80) REVERT: A 688 ARG cc_start: 0.7327 (ttp-110) cc_final: 0.7036 (ptt-90) REVERT: A 743 LYS cc_start: 0.7867 (mttt) cc_final: 0.7260 (mptt) REVERT: A 784 GLU cc_start: 0.6422 (pp20) cc_final: 0.5875 (pp20) REVERT: A 853 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.5113 (ttm170) REVERT: A 864 TYR cc_start: 0.6080 (OUTLIER) cc_final: 0.5703 (m-80) outliers start: 29 outliers final: 14 residues processed: 117 average time/residue: 0.4396 time to fit residues: 54.8952 Evaluate side-chains 108 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.0370 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 0.0870 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 720 HIS A 769 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.177321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.151696 restraints weight = 24137.468| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 3.28 r_work: 0.3983 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3988 r_free = 0.3988 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3988 r_free = 0.3988 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7055 Z= 0.111 Angle : 0.538 8.021 9573 Z= 0.280 Chirality : 0.042 0.153 1016 Planarity : 0.004 0.033 1212 Dihedral : 6.418 56.135 952 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.93 % Allowed : 23.31 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.30), residues: 820 helix: 0.40 (0.29), residues: 317 sheet: -0.99 (0.53), residues: 108 loop : -0.26 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 557 TYR 0.017 0.001 TYR C 32 PHE 0.029 0.001 PHE A 339 TRP 0.024 0.002 TRP A 391 HIS 0.006 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7051) covalent geometry : angle 0.53763 ( 9565) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.48837 ( 8) hydrogen bonds : bond 0.03423 ( 265) hydrogen bonds : angle 4.85129 ( 759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: A 143 LYS cc_start: 0.6369 (mttp) cc_final: 0.6053 (mttm) REVERT: A 208 TYR cc_start: 0.8208 (t80) cc_final: 0.8008 (t80) REVERT: A 308 LEU cc_start: 0.8149 (mt) cc_final: 0.7901 (tp) REVERT: A 413 LYS cc_start: 0.4692 (ttmt) cc_final: 0.4254 (ttmm) REVERT: A 447 TRP cc_start: 0.7961 (OUTLIER) cc_final: 0.7413 (m-10) REVERT: A 452 SER cc_start: 0.8126 (OUTLIER) cc_final: 0.7878 (m) REVERT: A 634 TYR cc_start: 0.7220 (m-80) cc_final: 0.6983 (m-80) REVERT: A 688 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6990 (ptt-90) REVERT: A 743 LYS cc_start: 0.7862 (mttt) cc_final: 0.7264 (mptt) REVERT: A 784 GLU cc_start: 0.6467 (pp20) cc_final: 0.5942 (pp20) REVERT: A 853 ARG cc_start: 0.5514 (OUTLIER) cc_final: 0.5151 (ttm170) REVERT: A 864 TYR cc_start: 0.6007 (OUTLIER) cc_final: 0.5652 (m-80) outliers start: 29 outliers final: 14 residues processed: 117 average time/residue: 0.4104 time to fit residues: 51.3469 Evaluate side-chains 112 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 40 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 720 HIS A 769 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.176569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.151474 restraints weight = 35593.416| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 4.35 r_work: 0.3942 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7055 Z= 0.118 Angle : 0.550 7.671 9573 Z= 0.286 Chirality : 0.042 0.158 1016 Planarity : 0.004 0.034 1212 Dihedral : 6.366 54.463 952 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.74 % Allowed : 22.09 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.30), residues: 820 helix: 0.58 (0.29), residues: 317 sheet: -1.02 (0.53), residues: 108 loop : -0.19 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.019 0.001 TYR C 32 PHE 0.032 0.001 PHE A 339 TRP 0.023 0.002 TRP A 391 HIS 0.005 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7051) covalent geometry : angle 0.55018 ( 9565) SS BOND : bond 0.00177 ( 4) SS BOND : angle 0.54948 ( 8) hydrogen bonds : bond 0.03444 ( 265) hydrogen bonds : angle 4.77771 ( 759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 87 VAL cc_start: 0.7122 (m) cc_final: 0.6721 (t) REVERT: A 110 LYS cc_start: 0.6722 (mmmt) cc_final: 0.6175 (mptt) REVERT: A 114 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: A 139 GLU cc_start: 0.7881 (mp0) cc_final: 0.7591 (mp0) REVERT: A 143 LYS cc_start: 0.6329 (mttp) cc_final: 0.6019 (mttm) REVERT: A 274 ASP cc_start: 0.5967 (p0) cc_final: 0.5742 (t0) REVERT: A 308 LEU cc_start: 0.8208 (mt) cc_final: 0.7917 (tp) REVERT: A 413 LYS cc_start: 0.4690 (ttmt) cc_final: 0.4363 (tptm) REVERT: A 447 TRP cc_start: 0.7998 (OUTLIER) cc_final: 0.7429 (m-10) REVERT: A 452 SER cc_start: 0.8175 (OUTLIER) cc_final: 0.7947 (m) REVERT: A 504 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: A 688 ARG cc_start: 0.7303 (ttp-110) cc_final: 0.7011 (ptt-90) REVERT: A 708 ASP cc_start: 0.5981 (t70) cc_final: 0.5770 (t0) REVERT: A 743 LYS cc_start: 0.7861 (mttt) cc_final: 0.7246 (mptt) REVERT: A 784 GLU cc_start: 0.6480 (pp20) cc_final: 0.5842 (pp20) REVERT: A 853 ARG cc_start: 0.5535 (OUTLIER) cc_final: 0.5188 (ttm170) REVERT: A 864 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.5726 (m-80) outliers start: 35 outliers final: 15 residues processed: 121 average time/residue: 0.4218 time to fit residues: 54.5537 Evaluate side-chains 115 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 58 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 70 optimal weight: 0.0980 chunk 66 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.176917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.154370 restraints weight = 15910.190| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.44 r_work: 0.4013 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7055 Z= 0.116 Angle : 0.544 7.347 9573 Z= 0.284 Chirality : 0.042 0.159 1016 Planarity : 0.004 0.034 1212 Dihedral : 6.287 53.671 952 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.07 % Allowed : 23.17 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.30), residues: 820 helix: 0.69 (0.29), residues: 317 sheet: -1.06 (0.52), residues: 108 loop : -0.12 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.017 0.001 TYR C 32 PHE 0.035 0.001 PHE A 339 TRP 0.025 0.002 TRP A 391 HIS 0.005 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7051) covalent geometry : angle 0.54431 ( 9565) SS BOND : bond 0.00150 ( 4) SS BOND : angle 0.43467 ( 8) hydrogen bonds : bond 0.03359 ( 265) hydrogen bonds : angle 4.73177 ( 759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 88 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.6149 (m-10) REVERT: A 114 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: A 143 LYS cc_start: 0.6339 (mttp) cc_final: 0.6057 (mtpm) REVERT: A 208 TYR cc_start: 0.8214 (t80) cc_final: 0.8001 (t80) REVERT: A 274 ASP cc_start: 0.5808 (p0) cc_final: 0.5581 (t0) REVERT: A 413 LYS cc_start: 0.4712 (ttmt) cc_final: 0.4384 (tptm) REVERT: A 447 TRP cc_start: 0.7906 (OUTLIER) cc_final: 0.7416 (m-10) REVERT: A 688 ARG cc_start: 0.7214 (ttp-110) cc_final: 0.6940 (ptt-90) REVERT: A 743 LYS cc_start: 0.7834 (mttt) cc_final: 0.7255 (mptt) REVERT: A 784 GLU cc_start: 0.6398 (pp20) cc_final: 0.6033 (pp20) REVERT: A 853 ARG cc_start: 0.5515 (OUTLIER) cc_final: 0.5163 (ttm170) REVERT: A 864 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.5727 (m-80) outliers start: 30 outliers final: 16 residues processed: 116 average time/residue: 0.4438 time to fit residues: 54.7716 Evaluate side-chains 115 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.176397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.150306 restraints weight = 26054.795| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 3.39 r_work: 0.3963 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7055 Z= 0.124 Angle : 0.566 8.501 9573 Z= 0.295 Chirality : 0.042 0.155 1016 Planarity : 0.004 0.034 1212 Dihedral : 6.286 53.329 952 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.93 % Allowed : 23.04 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.30), residues: 820 helix: 0.72 (0.29), residues: 318 sheet: -1.03 (0.53), residues: 108 loop : -0.12 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 709 TYR 0.018 0.001 TYR C 32 PHE 0.037 0.001 PHE A 339 TRP 0.029 0.002 TRP A 391 HIS 0.005 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7051) covalent geometry : angle 0.56572 ( 9565) SS BOND : bond 0.00162 ( 4) SS BOND : angle 0.45571 ( 8) hydrogen bonds : bond 0.03443 ( 265) hydrogen bonds : angle 4.70456 ( 759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 88 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.6209 (m-10) REVERT: A 110 LYS cc_start: 0.6792 (mmmt) cc_final: 0.6231 (mptt) REVERT: A 114 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: A 143 LYS cc_start: 0.6350 (mttp) cc_final: 0.6072 (mtpm) REVERT: A 208 TYR cc_start: 0.8248 (t80) cc_final: 0.8028 (t80) REVERT: A 274 ASP cc_start: 0.5831 (p0) cc_final: 0.5589 (t0) REVERT: A 308 LEU cc_start: 0.8234 (mt) cc_final: 0.7928 (tp) REVERT: A 413 LYS cc_start: 0.4723 (ttmt) cc_final: 0.4383 (tptm) REVERT: A 447 TRP cc_start: 0.7969 (OUTLIER) cc_final: 0.7600 (m-10) REVERT: A 688 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6956 (ptt-90) REVERT: A 743 LYS cc_start: 0.7829 (mttt) cc_final: 0.7252 (mptt) REVERT: A 784 GLU cc_start: 0.6506 (pp20) cc_final: 0.6093 (pp20) REVERT: A 853 ARG cc_start: 0.5481 (OUTLIER) cc_final: 0.5156 (ttm170) REVERT: A 858 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6062 (mp0) REVERT: A 864 TYR cc_start: 0.6067 (OUTLIER) cc_final: 0.5706 (m-80) outliers start: 29 outliers final: 20 residues processed: 110 average time/residue: 0.4272 time to fit residues: 50.0280 Evaluate side-chains 117 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 24 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.0670 chunk 64 optimal weight: 2.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.176418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.150629 restraints weight = 31695.096| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.73 r_work: 0.3956 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3961 r_free = 0.3961 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3961 r_free = 0.3961 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7055 Z= 0.122 Angle : 0.566 7.136 9573 Z= 0.295 Chirality : 0.042 0.150 1016 Planarity : 0.004 0.034 1212 Dihedral : 6.250 51.908 952 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.34 % Allowed : 22.63 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.30), residues: 820 helix: 0.78 (0.29), residues: 317 sheet: -1.11 (0.50), residues: 117 loop : -0.02 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.020 0.001 TYR A 680 PHE 0.040 0.001 PHE A 339 TRP 0.034 0.002 TRP A 391 HIS 0.006 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7051) covalent geometry : angle 0.56602 ( 9565) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.42794 ( 8) hydrogen bonds : bond 0.03384 ( 265) hydrogen bonds : angle 4.68378 ( 759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 88 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.6224 (m-10) REVERT: A 98 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6832 (mm-40) REVERT: A 114 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: A 143 LYS cc_start: 0.6323 (mttp) cc_final: 0.6049 (mtpm) REVERT: A 208 TYR cc_start: 0.8275 (t80) cc_final: 0.8048 (t80) REVERT: A 274 ASP cc_start: 0.5838 (p0) cc_final: 0.5584 (t0) REVERT: A 308 LEU cc_start: 0.8224 (mt) cc_final: 0.7887 (tp) REVERT: A 413 LYS cc_start: 0.4766 (ttmt) cc_final: 0.4508 (ttmm) REVERT: A 447 TRP cc_start: 0.7958 (OUTLIER) cc_final: 0.7647 (m-10) REVERT: A 504 GLU cc_start: 0.7479 (tp30) cc_final: 0.7258 (mm-30) REVERT: A 688 ARG cc_start: 0.7230 (ttp-110) cc_final: 0.6971 (ptt-90) REVERT: A 743 LYS cc_start: 0.7821 (mttt) cc_final: 0.7241 (mptt) REVERT: A 781 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7086 (tt) REVERT: A 784 GLU cc_start: 0.6578 (pp20) cc_final: 0.6164 (pp20) REVERT: A 853 ARG cc_start: 0.5571 (OUTLIER) cc_final: 0.5248 (ttm170) REVERT: A 858 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6082 (mp0) REVERT: A 864 TYR cc_start: 0.6065 (OUTLIER) cc_final: 0.5735 (m-80) outliers start: 32 outliers final: 16 residues processed: 116 average time/residue: 0.4387 time to fit residues: 54.2868 Evaluate side-chains 114 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 447 TRP Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 475 HIS ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.175821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.150283 restraints weight = 27467.098| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 3.57 r_work: 0.3952 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3958 r_free = 0.3958 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3958 r_free = 0.3958 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7055 Z= 0.132 Angle : 0.585 7.231 9573 Z= 0.305 Chirality : 0.043 0.194 1016 Planarity : 0.004 0.034 1212 Dihedral : 6.312 51.859 952 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.39 % Allowed : 23.31 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.30), residues: 820 helix: 0.80 (0.30), residues: 317 sheet: -1.10 (0.51), residues: 117 loop : -0.01 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.026 0.002 TYR A 680 PHE 0.046 0.002 PHE A 339 TRP 0.044 0.002 TRP A 391 HIS 0.006 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7051) covalent geometry : angle 0.58489 ( 9565) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.45648 ( 8) hydrogen bonds : bond 0.03531 ( 265) hydrogen bonds : angle 4.75174 ( 759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 88 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.6250 (m-10) REVERT: A 98 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6785 (mm110) REVERT: A 110 LYS cc_start: 0.6779 (mmmt) cc_final: 0.6130 (mptt) REVERT: A 114 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: A 143 LYS cc_start: 0.6287 (mttp) cc_final: 0.6005 (mtpm) REVERT: A 208 TYR cc_start: 0.8278 (t80) cc_final: 0.8037 (t80) REVERT: A 274 ASP cc_start: 0.5835 (p0) cc_final: 0.5593 (t0) REVERT: A 413 LYS cc_start: 0.4779 (ttmt) cc_final: 0.4508 (ttmm) REVERT: A 504 GLU cc_start: 0.7531 (tp30) cc_final: 0.7308 (mm-30) REVERT: A 688 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.6996 (ptt-90) REVERT: A 743 LYS cc_start: 0.7819 (mttt) cc_final: 0.7243 (mptt) REVERT: A 784 GLU cc_start: 0.6554 (pp20) cc_final: 0.6142 (pp20) REVERT: A 853 ARG cc_start: 0.5608 (OUTLIER) cc_final: 0.5280 (ttm170) REVERT: A 858 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6138 (mp0) REVERT: A 864 TYR cc_start: 0.6038 (OUTLIER) cc_final: 0.5726 (m-80) outliers start: 25 outliers final: 17 residues processed: 113 average time/residue: 0.4841 time to fit residues: 58.0632 Evaluate side-chains 114 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 475 HIS ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.176823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.151236 restraints weight = 29181.335| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 3.69 r_work: 0.3962 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7055 Z= 0.122 Angle : 0.588 7.682 9573 Z= 0.308 Chirality : 0.043 0.172 1016 Planarity : 0.004 0.034 1212 Dihedral : 6.157 50.005 952 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.85 % Allowed : 24.25 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.30), residues: 820 helix: 0.75 (0.29), residues: 318 sheet: -1.07 (0.51), residues: 117 loop : 0.00 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 38 TYR 0.029 0.001 TYR A 680 PHE 0.014 0.001 PHE A 362 TRP 0.051 0.002 TRP A 391 HIS 0.007 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7051) covalent geometry : angle 0.58852 ( 9565) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.36485 ( 8) hydrogen bonds : bond 0.03417 ( 265) hydrogen bonds : angle 4.72801 ( 759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.84 seconds wall clock time: 54 minutes 55.96 seconds (3295.96 seconds total)