Starting phenix.real_space_refine on Sat May 10 21:45:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cd0_16565/05_2025/8cd0_16565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cd0_16565/05_2025/8cd0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cd0_16565/05_2025/8cd0_16565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cd0_16565/05_2025/8cd0_16565.map" model { file = "/net/cci-nas-00/data/ceres_data/8cd0_16565/05_2025/8cd0_16565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cd0_16565/05_2025/8cd0_16565.cif" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.51, per 1000 atoms: 1.09 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: 1.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.07 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: 2.34 Time building geometry restraints manager: 2.01 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: 7.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.350 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.003 TRP A 595 HIS 0.027 0.003 HIS A 400 PHE 0.058 0.004 PHE A 339 TYR 0.038 0.003 TYR A 680 ARG 0.010 0.001 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.19466 ( 265) hydrogen bonds : angle 8.09041 ( 759) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.96908 ( 8) covalent geometry : bond 0.00659 ( 7051) covalent geometry : angle 1.25305 ( 9565) *********************** 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 : 0.796 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: 0.5414 (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: 0.9983 time to fit residues: 140.3896 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 : 0.756 ------------------------------------------------------------------------------- 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 70 optimal weight: 0.9990 chunk 62 optimal weight: 0.0870 chunk 34 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 343 ASN A 400 HIS A 408 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 = 0.4408 r_free = 0.4408 target = 0.180372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.155370 restraints weight = 26082.410| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 3.52 r_work: 0.4013 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7055 Z= 0.127 Angle : 0.590 9.577 9573 Z= 0.309 Chirality : 0.043 0.162 1016 Planarity : 0.005 0.050 1212 Dihedral : 7.404 66.992 963 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.20 % Allowed : 21.27 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.28), residues: 820 helix: -1.24 (0.25), residues: 315 sheet: -0.99 (0.48), residues: 124 loop : -0.62 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 391 HIS 0.014 0.001 HIS A 400 PHE 0.014 0.001 PHE A 494 TYR 0.011 0.001 TYR C 59 ARG 0.006 0.001 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 265) hydrogen bonds : angle 5.48564 ( 759) SS BOND : bond 0.00198 ( 4) SS BOND : angle 0.77093 ( 8) covalent geometry : bond 0.00281 ( 7051) covalent geometry : angle 0.59001 ( 9565) *********************** 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 136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7708 (tp30) cc_final: 0.7432 (mm-30) REVERT: A 143 LYS cc_start: 0.6364 (mttp) cc_final: 0.6069 (mtpm) REVERT: A 203 LYS cc_start: 0.7174 (mptt) cc_final: 0.6890 (mttp) REVERT: A 308 LEU cc_start: 0.8226 (mt) cc_final: 0.7959 (tp) REVERT: A 413 LYS cc_start: 0.4886 (ttmt) cc_final: 0.4564 (ttmm) REVERT: A 452 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7839 (m) REVERT: A 688 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6932 (ptt-90) REVERT: A 708 ASP cc_start: 0.6472 (t70) cc_final: 0.6137 (t70) REVERT: A 743 LYS cc_start: 0.7875 (mttt) cc_final: 0.7250 (mptt) REVERT: A 784 GLU cc_start: 0.6334 (pp20) cc_final: 0.5836 (pp20) REVERT: A 853 ARG cc_start: 0.5518 (OUTLIER) cc_final: 0.5115 (ttm170) REVERT: A 864 TYR cc_start: 0.5948 (OUTLIER) cc_final: 0.5615 (m-80) outliers start: 31 outliers final: 12 residues processed: 122 average time/residue: 1.0097 time to fit residues: 131.8634 Evaluate side-chains 108 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 701 THR Chi-restraints excluded: chain A residue 716 HIS 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 Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 720 HIS A 769 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.173651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.148126 restraints weight = 20315.688| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.95 r_work: 0.3947 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3954 r_free = 0.3954 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3954 r_free = 0.3954 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7055 Z= 0.167 Angle : 0.633 8.850 9573 Z= 0.327 Chirality : 0.044 0.164 1016 Planarity : 0.005 0.041 1212 Dihedral : 7.076 63.176 952 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.88 % Allowed : 21.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.29), residues: 820 helix: -0.35 (0.27), residues: 316 sheet: -0.98 (0.50), residues: 118 loop : -0.44 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 391 HIS 0.013 0.002 HIS A 400 PHE 0.020 0.002 PHE C 108 TYR 0.016 0.002 TYR C 32 ARG 0.004 0.001 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 265) hydrogen bonds : angle 5.26172 ( 759) SS BOND : bond 0.00334 ( 4) SS BOND : angle 1.00015 ( 8) covalent geometry : bond 0.00378 ( 7051) covalent geometry : angle 0.63222 ( 9565) *********************** 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 137 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.797 Fit side-chains REVERT: A 98 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6903 (mm-40) REVERT: A 114 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7400 (mm-30) REVERT: A 143 LYS cc_start: 0.6427 (mttp) cc_final: 0.6073 (mttm) REVERT: A 203 LYS cc_start: 0.7130 (mptt) cc_final: 0.6895 (mttp) REVERT: A 413 LYS cc_start: 0.4821 (ttmt) cc_final: 0.4517 (ttmm) REVERT: A 447 TRP cc_start: 0.8004 (OUTLIER) cc_final: 0.7470 (m-10) REVERT: A 452 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7961 (m) REVERT: A 634 TYR cc_start: 0.7279 (m-80) cc_final: 0.7049 (m-80) REVERT: A 688 ARG cc_start: 0.7324 (ttp-110) cc_final: 0.7008 (ptt-90) REVERT: A 743 LYS cc_start: 0.7872 (mttt) cc_final: 0.7280 (mptt) REVERT: A 782 ARG cc_start: 0.5212 (OUTLIER) cc_final: 0.4546 (mtp85) REVERT: A 784 GLU cc_start: 0.6441 (pp20) cc_final: 0.5912 (pp20) REVERT: A 853 ARG cc_start: 0.5615 (OUTLIER) cc_final: 0.5098 (ttm170) REVERT: A 864 TYR cc_start: 0.6176 (OUTLIER) cc_final: 0.5802 (m-80) outliers start: 36 outliers final: 17 residues processed: 125 average time/residue: 0.9560 time to fit residues: 127.9878 Evaluate side-chains 113 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 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 400 HIS 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 29 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 85 LEU 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 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 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 = 0.4356 r_free = 0.4356 target = 0.175366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.149437 restraints weight = 25154.487| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 3.59 r_work: 0.3948 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2687 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= 0.124 Angle : 0.562 8.104 9573 Z= 0.289 Chirality : 0.042 0.158 1016 Planarity : 0.004 0.037 1212 Dihedral : 6.542 57.060 952 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.34 % Allowed : 22.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.29), residues: 820 helix: 0.10 (0.28), residues: 317 sheet: -1.05 (0.52), residues: 108 loop : -0.32 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 391 HIS 0.014 0.001 HIS A 400 PHE 0.016 0.001 PHE C 108 TYR 0.016 0.001 TYR C 32 ARG 0.004 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 265) hydrogen bonds : angle 5.01631 ( 759) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.55739 ( 8) covalent geometry : bond 0.00276 ( 7051) covalent geometry : angle 0.56175 ( 9565) *********************** 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 130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.740 Fit side-chains REVERT: A 89 VAL cc_start: 0.6356 (m) cc_final: 0.6082 (t) REVERT: A 114 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: A 143 LYS cc_start: 0.6368 (mttp) cc_final: 0.6024 (mttm) REVERT: A 203 LYS cc_start: 0.7101 (mptt) cc_final: 0.6894 (mttp) REVERT: A 208 TYR cc_start: 0.8207 (t80) cc_final: 0.7991 (t80) REVERT: A 413 LYS cc_start: 0.4699 (ttmt) cc_final: 0.4425 (ttmm) REVERT: A 447 TRP cc_start: 0.8003 (OUTLIER) cc_final: 0.7298 (m-10) REVERT: A 452 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7898 (m) REVERT: A 688 ARG cc_start: 0.7282 (ttp-110) cc_final: 0.6957 (ptt-90) REVERT: A 743 LYS cc_start: 0.7838 (mttt) cc_final: 0.7215 (mptt) REVERT: A 784 GLU cc_start: 0.6454 (pp20) cc_final: 0.5880 (pp20) REVERT: A 853 ARG cc_start: 0.5542 (OUTLIER) cc_final: 0.5113 (ttm170) REVERT: A 864 TYR cc_start: 0.6075 (OUTLIER) cc_final: 0.5728 (m-80) outliers start: 32 outliers final: 16 residues processed: 120 average time/residue: 0.9184 time to fit residues: 118.1281 Evaluate side-chains 111 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 148 ASP 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 583 GLN 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 853 ARG Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 82 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 17 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 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 = 0.4318 r_free = 0.4318 target = 0.171886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.146582 restraints weight = 19354.906| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.84 r_work: 0.3935 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3942 r_free = 0.3942 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3942 r_free = 0.3942 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7055 Z= 0.170 Angle : 0.613 7.646 9573 Z= 0.318 Chirality : 0.044 0.168 1016 Planarity : 0.004 0.035 1212 Dihedral : 6.720 57.320 952 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.28 % Allowed : 21.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.30), residues: 820 helix: 0.20 (0.29), residues: 316 sheet: -1.03 (0.53), residues: 106 loop : -0.22 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 391 HIS 0.014 0.002 HIS A 400 PHE 0.017 0.002 PHE A 543 TYR 0.019 0.002 TYR C 32 ARG 0.003 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 265) hydrogen bonds : angle 5.13676 ( 759) SS BOND : bond 0.00288 ( 4) SS BOND : angle 0.82818 ( 8) covalent geometry : bond 0.00385 ( 7051) covalent geometry : angle 0.61231 ( 9565) *********************** 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 132 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.790 Fit side-chains REVERT: A 98 GLN cc_start: 0.7325 (mm-40) cc_final: 0.6817 (mm110) REVERT: A 114 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: A 139 GLU cc_start: 0.7828 (mp0) cc_final: 0.7583 (mp0) REVERT: A 143 LYS cc_start: 0.6360 (mttp) cc_final: 0.5978 (mttm) REVERT: A 208 TYR cc_start: 0.8181 (t80) cc_final: 0.7946 (t80) REVERT: A 375 ASP cc_start: 0.6975 (m-30) cc_final: 0.6702 (m-30) REVERT: A 413 LYS cc_start: 0.4879 (ttmt) cc_final: 0.4604 (ttmm) REVERT: A 447 TRP cc_start: 0.8043 (OUTLIER) cc_final: 0.7393 (m-10) REVERT: A 452 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7998 (m) REVERT: A 688 ARG cc_start: 0.7275 (ttp-110) cc_final: 0.6942 (ptt-90) REVERT: A 743 LYS cc_start: 0.7844 (mttt) cc_final: 0.7260 (mptt) REVERT: A 782 ARG cc_start: 0.5213 (OUTLIER) cc_final: 0.4525 (mtp85) REVERT: A 784 GLU cc_start: 0.6428 (pp20) cc_final: 0.5850 (pp20) REVERT: A 853 ARG cc_start: 0.5628 (OUTLIER) cc_final: 0.5127 (ttm170) REVERT: A 864 TYR cc_start: 0.6225 (OUTLIER) cc_final: 0.5862 (m-80) outliers start: 39 outliers final: 18 residues processed: 121 average time/residue: 0.9329 time to fit residues: 120.6034 Evaluate side-chains 114 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 VAL 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 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 583 GLN 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 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 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 12 optimal weight: 0.0980 chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 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 = 0.4339 r_free = 0.4339 target = 0.174041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.148059 restraints weight = 24822.235| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.49 r_work: 0.3930 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7055 Z= 0.131 Angle : 0.570 7.681 9573 Z= 0.295 Chirality : 0.043 0.157 1016 Planarity : 0.004 0.034 1212 Dihedral : 6.497 55.534 952 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.01 % Allowed : 21.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.30), residues: 820 helix: 0.36 (0.29), residues: 316 sheet: -1.07 (0.53), residues: 106 loop : -0.16 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 391 HIS 0.016 0.001 HIS A 400 PHE 0.014 0.001 PHE A 543 TYR 0.019 0.001 TYR C 32 ARG 0.002 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 265) hydrogen bonds : angle 4.94700 ( 759) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.57697 ( 8) covalent geometry : bond 0.00297 ( 7051) covalent geometry : angle 0.56996 ( 9565) *********************** 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: 37 poor density : 96 time to evaluate : 0.812 Fit side-chains REVERT: A 98 GLN cc_start: 0.7286 (mm-40) cc_final: 0.6826 (mm110) REVERT: A 114 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7483 (mm-30) REVERT: A 143 LYS cc_start: 0.6329 (mttp) cc_final: 0.5966 (mttm) REVERT: A 413 LYS cc_start: 0.4819 (ttmt) cc_final: 0.4538 (ttmm) REVERT: A 447 TRP cc_start: 0.8010 (OUTLIER) cc_final: 0.7375 (m-10) REVERT: A 452 SER cc_start: 0.8202 (OUTLIER) cc_final: 0.7954 (m) REVERT: A 504 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7340 (mm-30) REVERT: A 688 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6906 (ptt-90) REVERT: A 743 LYS cc_start: 0.7845 (mttt) cc_final: 0.7222 (mptt) REVERT: A 784 GLU cc_start: 0.6541 (pp20) cc_final: 0.5915 (pp20) REVERT: A 853 ARG cc_start: 0.5568 (OUTLIER) cc_final: 0.5192 (ttm170) REVERT: A 864 TYR cc_start: 0.6197 (OUTLIER) cc_final: 0.5837 (m-80) outliers start: 37 outliers final: 18 residues processed: 121 average time/residue: 0.9871 time to fit residues: 127.6158 Evaluate side-chains 113 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 128 LYS 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 583 GLN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN ** 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 = 0.4338 r_free = 0.4338 target = 0.174033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.148596 restraints weight = 35291.669| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 4.34 r_work: 0.3905 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7055 Z= 0.134 Angle : 0.579 7.234 9573 Z= 0.303 Chirality : 0.043 0.159 1016 Planarity : 0.004 0.034 1212 Dihedral : 6.435 55.273 952 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.74 % Allowed : 22.76 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.30), residues: 820 helix: 0.42 (0.29), residues: 317 sheet: -1.09 (0.52), residues: 108 loop : -0.15 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 391 HIS 0.006 0.001 HIS A 716 PHE 0.013 0.001 PHE A 543 TYR 0.019 0.002 TYR C 32 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 265) hydrogen bonds : angle 4.88525 ( 759) SS BOND : bond 0.00183 ( 4) SS BOND : angle 0.54106 ( 8) covalent geometry : bond 0.00303 ( 7051) covalent geometry : angle 0.57951 ( 9565) *********************** 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 129 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.832 Fit side-chains REVERT: A 98 GLN cc_start: 0.7291 (mm-40) cc_final: 0.6857 (mm-40) REVERT: A 114 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: A 143 LYS cc_start: 0.6289 (mttp) cc_final: 0.5928 (mttm) REVERT: A 208 TYR cc_start: 0.8282 (t80) cc_final: 0.7971 (t80) REVERT: A 375 ASP cc_start: 0.7071 (m-30) cc_final: 0.6759 (m-30) REVERT: A 413 LYS cc_start: 0.4819 (ttmt) cc_final: 0.4545 (ttmm) REVERT: A 447 TRP cc_start: 0.8049 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: A 452 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7983 (m) REVERT: A 504 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: A 688 ARG cc_start: 0.7267 (ttp-110) cc_final: 0.6977 (ptt-90) REVERT: A 743 LYS cc_start: 0.7837 (mttt) cc_final: 0.7227 (mptt) REVERT: A 782 ARG cc_start: 0.5165 (OUTLIER) cc_final: 0.4427 (mtp85) REVERT: A 784 GLU cc_start: 0.6580 (pp20) cc_final: 0.5930 (pp20) REVERT: A 853 ARG cc_start: 0.5592 (OUTLIER) cc_final: 0.5266 (ttm170) REVERT: A 864 TYR cc_start: 0.6192 (OUTLIER) cc_final: 0.5844 (m-80) outliers start: 35 outliers final: 18 residues processed: 118 average time/residue: 1.0004 time to fit residues: 126.0887 Evaluate side-chains 112 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 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 583 GLN 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 782 ARG 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 0.0170 chunk 57 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 389 HIS ** 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 = 0.4352 r_free = 0.4352 target = 0.175336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.149640 restraints weight = 28922.024| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.57 r_work: 0.3949 rms_B_bonded: 3.88 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 = 0.28 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 = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3174 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= 0.119 Angle : 0.568 7.136 9573 Z= 0.296 Chirality : 0.042 0.154 1016 Planarity : 0.004 0.040 1212 Dihedral : 6.283 53.761 952 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.61 % Allowed : 23.58 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.30), residues: 820 helix: 0.55 (0.29), residues: 318 sheet: -1.11 (0.52), residues: 108 loop : -0.16 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 447 HIS 0.006 0.001 HIS A 716 PHE 0.013 0.001 PHE C 108 TYR 0.018 0.001 TYR C 32 ARG 0.004 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 265) hydrogen bonds : angle 4.78622 ( 759) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.42155 ( 8) covalent geometry : bond 0.00268 ( 7051) covalent geometry : angle 0.56777 ( 9565) *********************** 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 125 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.711 Fit side-chains REVERT: A 98 GLN cc_start: 0.7277 (mm-40) cc_final: 0.6830 (mm110) REVERT: A 114 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: A 143 LYS cc_start: 0.6387 (mttp) cc_final: 0.6031 (mttm) REVERT: A 208 TYR cc_start: 0.8252 (t80) cc_final: 0.8048 (t80) REVERT: A 413 LYS cc_start: 0.4768 (ttmt) cc_final: 0.4494 (ttmm) REVERT: A 447 TRP cc_start: 0.7960 (OUTLIER) cc_final: 0.7500 (m-10) REVERT: A 452 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.8042 (m) REVERT: A 504 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7340 (mm-30) REVERT: A 688 ARG cc_start: 0.7211 (ttp-110) cc_final: 0.6979 (ptt-90) REVERT: A 743 LYS cc_start: 0.7831 (mttt) cc_final: 0.7257 (mptt) REVERT: A 784 GLU cc_start: 0.6582 (pp20) cc_final: 0.5851 (pp20) REVERT: A 853 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.5257 (ttm170) REVERT: A 858 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6183 (mp0) REVERT: A 864 TYR cc_start: 0.6116 (OUTLIER) cc_final: 0.5791 (m-80) outliers start: 34 outliers final: 15 residues processed: 113 average time/residue: 0.9302 time to fit residues: 112.7317 Evaluate side-chains 112 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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 583 GLN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 67 optimal weight: 0.0000 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 19 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.4242 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.177051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.151707 restraints weight = 28178.094| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 3.52 r_work: 0.3975 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3980 r_free = 0.3980 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3980 r_free = 0.3980 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7055 Z= 0.111 Angle : 0.554 7.243 9573 Z= 0.290 Chirality : 0.042 0.152 1016 Planarity : 0.004 0.041 1212 Dihedral : 6.091 51.412 952 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.39 % Allowed : 24.39 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.30), residues: 820 helix: 0.66 (0.29), residues: 318 sheet: -0.97 (0.52), residues: 106 loop : -0.10 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 447 HIS 0.006 0.001 HIS A 716 PHE 0.020 0.001 PHE A 543 TYR 0.020 0.001 TYR A 680 ARG 0.005 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 265) hydrogen bonds : angle 4.66282 ( 759) SS BOND : bond 0.00102 ( 4) SS BOND : angle 0.37305 ( 8) covalent geometry : bond 0.00250 ( 7051) covalent geometry : angle 0.55429 ( 9565) *********************** 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 119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.810 Fit side-chains REVERT: A 98 GLN cc_start: 0.7274 (mm-40) cc_final: 0.6835 (mm110) REVERT: A 114 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: A 143 LYS cc_start: 0.6324 (mttp) cc_final: 0.5983 (mttm) REVERT: A 413 LYS cc_start: 0.4755 (ttmt) cc_final: 0.4503 (ttmm) REVERT: A 447 TRP cc_start: 0.7924 (OUTLIER) cc_final: 0.7618 (m-10) REVERT: A 504 GLU cc_start: 0.7510 (tp30) cc_final: 0.7279 (mm-30) REVERT: A 688 ARG cc_start: 0.7147 (ttp-110) cc_final: 0.6909 (ptt-90) REVERT: A 708 ASP cc_start: 0.5957 (t70) cc_final: 0.5747 (t70) REVERT: A 743 LYS cc_start: 0.7822 (mttt) cc_final: 0.7250 (mptt) REVERT: A 784 GLU cc_start: 0.6522 (pp20) cc_final: 0.6146 (pp20) REVERT: A 853 ARG cc_start: 0.5573 (OUTLIER) cc_final: 0.5268 (ttm170) REVERT: A 858 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6121 (mp0) outliers start: 25 outliers final: 16 residues processed: 112 average time/residue: 0.9593 time to fit residues: 115.1868 Evaluate side-chains 104 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 148 ASP 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 583 GLN 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 853 ARG Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 862 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 0.0470 chunk 14 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4350 r_free = 0.4350 target = 0.175322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.152406 restraints weight = 16715.097| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.55 r_work: 0.3991 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7055 Z= 0.135 Angle : 0.596 9.168 9573 Z= 0.311 Chirality : 0.044 0.192 1016 Planarity : 0.004 0.044 1212 Dihedral : 5.970 52.076 950 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.98 % Allowed : 24.80 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.30), residues: 820 helix: 0.67 (0.29), residues: 317 sheet: -1.09 (0.53), residues: 106 loop : -0.03 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 451 HIS 0.006 0.001 HIS A 716 PHE 0.042 0.002 PHE A 339 TYR 0.025 0.002 TYR A 680 ARG 0.005 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 265) hydrogen bonds : angle 4.76647 ( 759) SS BOND : bond 0.00174 ( 4) SS BOND : angle 0.46606 ( 8) covalent geometry : bond 0.00313 ( 7051) covalent geometry : angle 0.59657 ( 9565) ********************** 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 112 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.748 Fit side-chains REVERT: A 98 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6818 (mm-40) REVERT: A 110 LYS cc_start: 0.6701 (mmmt) cc_final: 0.6108 (mptt) REVERT: A 114 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7310 (mm-30) REVERT: A 143 LYS cc_start: 0.6256 (mttp) cc_final: 0.5917 (mttm) REVERT: A 413 LYS cc_start: 0.4809 (ttmt) cc_final: 0.4542 (ttmm) REVERT: A 504 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: A 688 ARG cc_start: 0.7156 (ttp-110) cc_final: 0.6877 (ptt-90) REVERT: A 708 ASP cc_start: 0.5866 (t70) cc_final: 0.5652 (t70) REVERT: A 743 LYS cc_start: 0.7813 (mttt) cc_final: 0.7239 (mptt) REVERT: A 784 GLU cc_start: 0.6500 (pp20) cc_final: 0.6082 (pp20) REVERT: A 853 ARG cc_start: 0.5595 (OUTLIER) cc_final: 0.5279 (ttm170) REVERT: A 858 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6095 (mp0) outliers start: 22 outliers final: 16 residues processed: 105 average time/residue: 0.9661 time to fit residues: 108.4936 Evaluate side-chains 111 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 583 GLN 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 853 ARG Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 862 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS ** 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 = 0.4342 r_free = 0.4342 target = 0.174570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.148653 restraints weight = 25030.188| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.50 r_work: 0.3934 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7055 Z= 0.148 Angle : 0.614 7.758 9573 Z= 0.321 Chirality : 0.044 0.176 1016 Planarity : 0.004 0.044 1212 Dihedral : 6.023 51.151 950 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.98 % Allowed : 24.93 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.30), residues: 820 helix: 0.60 (0.29), residues: 317 sheet: -0.97 (0.53), residues: 104 loop : -0.09 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 447 HIS 0.007 0.001 HIS A 389 PHE 0.044 0.002 PHE A 339 TYR 0.033 0.002 TYR A 680 ARG 0.004 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 265) hydrogen bonds : angle 4.82388 ( 759) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.49909 ( 8) covalent geometry : bond 0.00343 ( 7051) covalent geometry : angle 0.61400 ( 9565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6310.44 seconds wall clock time: 109 minutes 21.91 seconds (6561.91 seconds total)