Starting phenix.real_space_refine on Fri Dec 27 22:54:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cd0_16565/12_2024/8cd0_16565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cd0_16565/12_2024/8cd0_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_16565/12_2024/8cd0_16565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cd0_16565/12_2024/8cd0_16565.map" model { file = "/net/cci-nas-00/data/ceres_data/8cd0_16565/12_2024/8cd0_16565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cd0_16565/12_2024/8cd0_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-5532/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: 6.08, per 1000 atoms: 0.89 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: 1.76 Conformation dependent library (CDL) restraints added in 1.1 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: 0.88 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: 2.32 Time building geometry restraints manager: 1.98 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: 6.340 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.660 Find NCS groups from input model: 0.060 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.150 ------------------------------------------------------------------------------- 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 7051 Z= 0.423 Angle : 1.253 17.105 9565 Z= 0.680 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 *********************** 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 : 0.798 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: 1.0439 time to fit residues: 146.7202 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 : 0.810 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 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 7051 Z= 0.182 Angle : 0.590 9.577 9565 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 *********************** 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 : 0.868 Fit side-chains revert: symmetry clash REVERT: A 95 GLN cc_start: 0.5962 (OUTLIER) cc_final: 0.5759 (pp30) REVERT: A 114 GLU cc_start: 0.7531 (tp30) cc_final: 0.7231 (mm-30) REVERT: A 143 LYS cc_start: 0.6328 (mttp) cc_final: 0.6008 (mtpm) REVERT: A 203 LYS cc_start: 0.7026 (mptt) cc_final: 0.6748 (mttp) REVERT: A 308 LEU cc_start: 0.8113 (mt) cc_final: 0.7838 (tp) REVERT: A 413 LYS cc_start: 0.4620 (ttmt) cc_final: 0.4212 (ttmm) REVERT: A 452 SER cc_start: 0.8019 (OUTLIER) cc_final: 0.7688 (m) REVERT: A 634 TYR cc_start: 0.6839 (m-80) cc_final: 0.6568 (m-80) REVERT: A 688 ARG cc_start: 0.6917 (ttp-110) cc_final: 0.6370 (ptt-90) REVERT: A 708 ASP cc_start: 0.6191 (t70) cc_final: 0.5836 (t70) REVERT: A 743 LYS cc_start: 0.7797 (mttt) cc_final: 0.7119 (mptt) REVERT: A 784 GLU cc_start: 0.6214 (pp20) cc_final: 0.5657 (pp20) REVERT: A 853 ARG cc_start: 0.4972 (OUTLIER) cc_final: 0.4725 (ttm170) REVERT: A 864 TYR cc_start: 0.5957 (OUTLIER) cc_final: 0.5614 (m-80) REVERT: C 106 LYS cc_start: 0.7540 (pttt) cc_final: 0.7171 (tttm) outliers start: 31 outliers final: 12 residues processed: 122 average time/residue: 1.0404 time to fit residues: 135.3945 Evaluate side-chains 110 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 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 41 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 400 HIS ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7051 Z= 0.205 Angle : 0.587 8.928 9565 Z= 0.305 Chirality : 0.043 0.159 1016 Planarity : 0.005 0.040 1212 Dihedral : 6.906 63.456 952 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.34 % Allowed : 22.22 % 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: -0.80 (0.29), residues: 820 helix: -0.35 (0.27), residues: 316 sheet: -0.80 (0.50), residues: 126 loop : -0.41 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 391 HIS 0.013 0.001 HIS A 400 PHE 0.019 0.002 PHE A 339 TYR 0.013 0.001 TYR C 32 ARG 0.003 0.001 ARG A 454 *********************** 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 131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.794 Fit side-chains REVERT: A 114 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7230 (mm-30) REVERT: A 143 LYS cc_start: 0.6349 (mttp) cc_final: 0.5976 (mttm) REVERT: A 203 LYS cc_start: 0.6974 (mptt) cc_final: 0.6751 (mttm) REVERT: A 330 MET cc_start: 0.4933 (mtp) cc_final: 0.4661 (mtt) REVERT: A 413 LYS cc_start: 0.4529 (ttmt) cc_final: 0.4168 (ttmm) REVERT: A 447 TRP cc_start: 0.8054 (OUTLIER) cc_final: 0.7600 (m-10) REVERT: A 452 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7777 (m) REVERT: A 634 TYR cc_start: 0.7138 (m-80) cc_final: 0.6826 (m-80) REVERT: A 688 ARG cc_start: 0.6959 (ttp-110) cc_final: 0.6424 (ptt-90) REVERT: A 743 LYS cc_start: 0.7789 (mttt) cc_final: 0.7105 (mptt) REVERT: A 784 GLU cc_start: 0.6244 (pp20) cc_final: 0.5656 (pp20) REVERT: A 853 ARG cc_start: 0.4943 (OUTLIER) cc_final: 0.4657 (ttm170) REVERT: A 864 TYR cc_start: 0.6087 (OUTLIER) cc_final: 0.5706 (m-80) REVERT: C 106 LYS cc_start: 0.7558 (pttt) cc_final: 0.7189 (tttm) outliers start: 32 outliers final: 13 residues processed: 118 average time/residue: 0.9062 time to fit residues: 115.1437 Evaluate side-chains 112 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 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 724 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7051 Z= 0.207 Angle : 0.578 8.282 9565 Z= 0.299 Chirality : 0.043 0.160 1016 Planarity : 0.004 0.039 1212 Dihedral : 6.675 58.618 952 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.74 % Allowed : 21.82 % 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: -0.52 (0.29), residues: 820 helix: 0.07 (0.28), residues: 316 sheet: -1.03 (0.52), residues: 108 loop : -0.35 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 391 HIS 0.015 0.002 HIS A 400 PHE 0.027 0.002 PHE A 339 TYR 0.017 0.002 TYR C 32 ARG 0.003 0.000 ARG A 709 *********************** 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 132 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.880 Fit side-chains REVERT: A 114 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: A 143 LYS cc_start: 0.6330 (mttp) cc_final: 0.5964 (mttm) REVERT: A 203 LYS cc_start: 0.6958 (mptt) cc_final: 0.6739 (mttp) REVERT: A 208 TYR cc_start: 0.8126 (t80) cc_final: 0.7852 (t80) REVERT: A 330 MET cc_start: 0.4967 (mtp) cc_final: 0.4743 (mtt) REVERT: A 413 LYS cc_start: 0.4451 (ttmt) cc_final: 0.4101 (ttmm) REVERT: A 447 TRP cc_start: 0.8035 (OUTLIER) cc_final: 0.7341 (m-10) REVERT: A 452 SER cc_start: 0.8108 (OUTLIER) cc_final: 0.7856 (m) REVERT: A 688 ARG cc_start: 0.6959 (ttp-110) cc_final: 0.6441 (ptt-90) REVERT: A 743 LYS cc_start: 0.7766 (mttt) cc_final: 0.7096 (mptt) REVERT: A 782 ARG cc_start: 0.5138 (OUTLIER) cc_final: 0.4424 (mtp85) REVERT: A 784 GLU cc_start: 0.6382 (pp20) cc_final: 0.5735 (pp20) REVERT: A 853 ARG cc_start: 0.4955 (OUTLIER) cc_final: 0.4630 (ttm170) REVERT: A 864 TYR cc_start: 0.6020 (OUTLIER) cc_final: 0.5641 (m-80) REVERT: C 106 LYS cc_start: 0.7635 (pttt) cc_final: 0.7244 (tttm) outliers start: 35 outliers final: 16 residues processed: 122 average time/residue: 0.9854 time to fit residues: 128.8009 Evaluate side-chains 114 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 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 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 862 LEU Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.0060 chunk 33 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 400 HIS ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7051 Z= 0.194 Angle : 0.571 7.988 9565 Z= 0.295 Chirality : 0.042 0.158 1016 Planarity : 0.004 0.035 1212 Dihedral : 6.510 56.078 952 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.47 % Allowed : 22.63 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.30), residues: 820 helix: 0.30 (0.29), residues: 317 sheet: -1.03 (0.53), residues: 108 loop : -0.26 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 447 HIS 0.015 0.001 HIS A 400 PHE 0.015 0.002 PHE C 108 TYR 0.018 0.001 TYR C 32 ARG 0.003 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 1.018 Fit side-chains REVERT: A 114 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: A 139 GLU cc_start: 0.7756 (mp0) cc_final: 0.7524 (mp0) REVERT: A 143 LYS cc_start: 0.6352 (mttp) cc_final: 0.5978 (mttm) REVERT: A 274 ASP cc_start: 0.6208 (p0) cc_final: 0.5997 (t0) REVERT: A 330 MET cc_start: 0.4991 (mtp) cc_final: 0.4731 (mtt) REVERT: A 413 LYS cc_start: 0.4464 (ttmt) cc_final: 0.4129 (ttmm) REVERT: A 447 TRP cc_start: 0.8042 (OUTLIER) cc_final: 0.7376 (m-10) REVERT: A 452 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7902 (m) REVERT: A 688 ARG cc_start: 0.6925 (ttp-110) cc_final: 0.6398 (ptt-90) REVERT: A 743 LYS cc_start: 0.7768 (mttt) cc_final: 0.7102 (mptt) REVERT: A 784 GLU cc_start: 0.6371 (pp20) cc_final: 0.5727 (pp20) REVERT: A 853 ARG cc_start: 0.4994 (OUTLIER) cc_final: 0.4688 (ttm170) REVERT: A 864 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.5705 (m-80) REVERT: C 106 LYS cc_start: 0.7619 (pttt) cc_final: 0.7218 (tttm) outliers start: 33 outliers final: 17 residues processed: 116 average time/residue: 1.0543 time to fit residues: 130.6201 Evaluate side-chains 111 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 148 ASP 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 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 829 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR 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 72 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 400 HIS A 475 HIS ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7051 Z= 0.161 Angle : 0.542 7.715 9565 Z= 0.281 Chirality : 0.042 0.154 1016 Planarity : 0.004 0.033 1212 Dihedral : 6.314 54.248 952 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.74 % Allowed : 21.68 % Favored : 73.58 % 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: -0.11 (0.30), residues: 820 helix: 0.54 (0.29), residues: 317 sheet: -1.05 (0.53), residues: 106 loop : -0.15 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 447 HIS 0.015 0.001 HIS A 400 PHE 0.014 0.001 PHE C 108 TYR 0.018 0.001 TYR C 32 ARG 0.002 0.000 ARG A 557 *********************** 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 134 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7226 (mm-30) REVERT: A 143 LYS cc_start: 0.6292 (mttp) cc_final: 0.5939 (mttm) REVERT: A 208 TYR cc_start: 0.8093 (t80) cc_final: 0.7825 (t80) REVERT: A 274 ASP cc_start: 0.6213 (p0) cc_final: 0.5935 (t0) REVERT: A 413 LYS cc_start: 0.4378 (ttmt) cc_final: 0.3978 (tptm) REVERT: A 447 TRP cc_start: 0.8013 (OUTLIER) cc_final: 0.7366 (m-10) REVERT: A 452 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7942 (m) REVERT: A 688 ARG cc_start: 0.6895 (ttp-110) cc_final: 0.6458 (ptt-90) REVERT: A 743 LYS cc_start: 0.7752 (mttt) cc_final: 0.7098 (mptt) REVERT: A 784 GLU cc_start: 0.6359 (pp20) cc_final: 0.5694 (pp20) REVERT: A 853 ARG cc_start: 0.5011 (OUTLIER) cc_final: 0.4800 (ttm170) REVERT: A 864 TYR cc_start: 0.6038 (OUTLIER) cc_final: 0.5683 (m-80) REVERT: C 106 LYS cc_start: 0.7573 (pttt) cc_final: 0.7213 (tttm) outliers start: 35 outliers final: 17 residues processed: 123 average time/residue: 1.0366 time to fit residues: 137.6440 Evaluate side-chains 118 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 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 617 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 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 9 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 400 HIS A 475 HIS ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7051 Z= 0.239 Angle : 0.608 6.924 9565 Z= 0.317 Chirality : 0.043 0.165 1016 Planarity : 0.004 0.035 1212 Dihedral : 6.541 55.421 952 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.88 % Allowed : 22.49 % Favored : 72.63 % 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: -0.18 (0.30), residues: 820 helix: 0.48 (0.29), residues: 316 sheet: -1.07 (0.53), residues: 108 loop : -0.18 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 391 HIS 0.017 0.002 HIS A 400 PHE 0.016 0.002 PHE A 543 TYR 0.021 0.002 TYR C 32 ARG 0.002 0.000 ARG A 108 *********************** 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 130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 1.974 Fit side-chains REVERT: A 98 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6596 (mm110) REVERT: A 114 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7273 (mm-30) REVERT: A 143 LYS cc_start: 0.6275 (mttp) cc_final: 0.5897 (mttm) REVERT: A 208 TYR cc_start: 0.8079 (t80) cc_final: 0.7875 (t80) REVERT: A 375 ASP cc_start: 0.7238 (m-30) cc_final: 0.6714 (m-30) REVERT: A 413 LYS cc_start: 0.4584 (ttmt) cc_final: 0.4230 (ttmm) REVERT: A 447 TRP cc_start: 0.8080 (OUTLIER) cc_final: 0.7555 (m-10) REVERT: A 452 SER cc_start: 0.8156 (OUTLIER) cc_final: 0.7905 (m) REVERT: A 504 GLU cc_start: 0.7817 (tp30) cc_final: 0.7539 (mm-30) REVERT: A 688 ARG cc_start: 0.6875 (ttp-110) cc_final: 0.6447 (ptt-90) REVERT: A 743 LYS cc_start: 0.7757 (mttt) cc_final: 0.7089 (mptt) REVERT: A 782 ARG cc_start: 0.5088 (OUTLIER) cc_final: 0.4355 (mtp85) REVERT: A 784 GLU cc_start: 0.6567 (pp20) cc_final: 0.5816 (pp20) REVERT: A 787 LYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6262 (tptp) REVERT: A 853 ARG cc_start: 0.4987 (OUTLIER) cc_final: 0.4730 (ttm170) REVERT: A 864 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5753 (m-80) outliers start: 36 outliers final: 16 residues processed: 121 average time/residue: 1.2243 time to fit residues: 157.9756 Evaluate side-chains 116 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 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 583 GLN 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 782 ARG Chi-restraints excluded: chain A residue 787 LYS 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 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 72 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 400 HIS A 408 GLN A 475 HIS ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7051 Z= 0.179 Angle : 0.573 7.308 9565 Z= 0.298 Chirality : 0.042 0.154 1016 Planarity : 0.004 0.044 1212 Dihedral : 6.337 53.379 952 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.07 % Allowed : 23.58 % Favored : 72.36 % 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: -0.09 (0.30), residues: 820 helix: 0.57 (0.29), residues: 317 sheet: -1.11 (0.52), residues: 108 loop : -0.11 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 391 HIS 0.017 0.001 HIS A 400 PHE 0.013 0.001 PHE C 108 TYR 0.018 0.001 TYR C 32 ARG 0.005 0.000 ARG A 709 *********************** 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 122 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.843 Fit side-chains REVERT: A 98 GLN cc_start: 0.7161 (mm-40) cc_final: 0.6658 (mm-40) REVERT: A 114 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7180 (mm-30) REVERT: A 143 LYS cc_start: 0.6260 (mttp) cc_final: 0.5890 (mttm) REVERT: A 208 TYR cc_start: 0.8102 (t80) cc_final: 0.7863 (t80) REVERT: A 413 LYS cc_start: 0.4445 (ttmt) cc_final: 0.4119 (ttmm) REVERT: A 447 TRP cc_start: 0.8025 (OUTLIER) cc_final: 0.7480 (m-10) REVERT: A 452 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7908 (m) REVERT: A 504 GLU cc_start: 0.7746 (tp30) cc_final: 0.7464 (mm-30) REVERT: A 688 ARG cc_start: 0.6881 (ttp-110) cc_final: 0.6455 (ptt-90) REVERT: A 743 LYS cc_start: 0.7749 (mttt) cc_final: 0.7110 (mptt) REVERT: A 784 GLU cc_start: 0.6505 (pp20) cc_final: 0.5681 (pp20) REVERT: A 858 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5896 (mp0) REVERT: A 864 TYR cc_start: 0.6071 (OUTLIER) cc_final: 0.5709 (m-80) outliers start: 30 outliers final: 17 residues processed: 114 average time/residue: 0.9951 time to fit residues: 121.8685 Evaluate side-chains 115 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 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 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 74 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 : 0.003 0.036 7051 Z= 0.192 Angle : 0.586 7.144 9565 Z= 0.305 Chirality : 0.043 0.157 1016 Planarity : 0.004 0.047 1212 Dihedral : 6.326 53.384 952 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.93 % Allowed : 23.85 % 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: -0.07 (0.30), residues: 820 helix: 0.57 (0.29), residues: 317 sheet: -1.11 (0.52), residues: 108 loop : -0.09 (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 0.021 0.001 TYR A 680 ARG 0.005 0.000 ARG A 709 *********************** 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 123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.812 Fit side-chains REVERT: A 98 GLN cc_start: 0.7164 (mm-40) cc_final: 0.6593 (mm110) REVERT: A 114 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7176 (mm-30) REVERT: A 143 LYS cc_start: 0.6237 (mttp) cc_final: 0.5874 (mttm) REVERT: A 208 TYR cc_start: 0.8085 (t80) cc_final: 0.7794 (t80) REVERT: A 413 LYS cc_start: 0.4514 (ttmt) cc_final: 0.4179 (ttmm) REVERT: A 447 TRP cc_start: 0.8045 (OUTLIER) cc_final: 0.7617 (m-10) REVERT: A 504 GLU cc_start: 0.7738 (tp30) cc_final: 0.7456 (mm-30) REVERT: A 688 ARG cc_start: 0.6873 (ttp-110) cc_final: 0.6436 (ptt-90) REVERT: A 743 LYS cc_start: 0.7755 (mttt) cc_final: 0.7111 (mptt) REVERT: A 782 ARG cc_start: 0.5214 (OUTLIER) cc_final: 0.4441 (mtp85) REVERT: A 784 GLU cc_start: 0.6511 (pp20) cc_final: 0.5992 (pp20) REVERT: A 858 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.5920 (mp0) REVERT: A 864 TYR cc_start: 0.6071 (OUTLIER) cc_final: 0.5726 (m-80) outliers start: 29 outliers final: 17 residues processed: 115 average time/residue: 1.0065 time to fit residues: 123.8242 Evaluate side-chains 110 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 765 LEU Chi-restraints excluded: chain A residue 782 ARG Chi-restraints excluded: chain A residue 829 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 0.0470 chunk 65 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 20 optimal weight: 0.0470 chunk 60 optimal weight: 3.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7051 Z= 0.154 Angle : 0.554 7.280 9565 Z= 0.290 Chirality : 0.042 0.152 1016 Planarity : 0.004 0.038 1212 Dihedral : 6.077 51.017 952 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.25 % Allowed : 24.53 % 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: 0.06 (0.30), residues: 820 helix: 0.74 (0.30), residues: 317 sheet: -1.09 (0.52), residues: 108 loop : -0.07 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 391 HIS 0.005 0.001 HIS A 720 PHE 0.041 0.001 PHE A 339 TYR 0.022 0.001 TYR A 680 ARG 0.005 0.000 ARG A 709 ********************** 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 122 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7121 (mm-40) cc_final: 0.6690 (mm-40) REVERT: A 110 LYS cc_start: 0.6727 (mmmt) cc_final: 0.6053 (mptt) REVERT: A 114 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7131 (mm-30) REVERT: A 143 LYS cc_start: 0.6256 (mttp) cc_final: 0.5949 (mtpm) REVERT: A 208 TYR cc_start: 0.8097 (t80) cc_final: 0.7844 (t80) REVERT: A 413 LYS cc_start: 0.4439 (ttmt) cc_final: 0.4112 (ttmm) REVERT: A 504 GLU cc_start: 0.7641 (tp30) cc_final: 0.7358 (mm-30) REVERT: A 688 ARG cc_start: 0.6804 (ttp-110) cc_final: 0.6372 (ptt-90) REVERT: A 708 ASP cc_start: 0.5629 (t70) cc_final: 0.5427 (t70) REVERT: A 743 LYS cc_start: 0.7740 (mttt) cc_final: 0.7107 (mptt) REVERT: A 781 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6873 (tt) REVERT: A 784 GLU cc_start: 0.6502 (pp20) cc_final: 0.5968 (pp20) REVERT: A 858 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5948 (mp0) outliers start: 24 outliers final: 16 residues processed: 114 average time/residue: 0.9755 time to fit residues: 119.5676 Evaluate side-chains 109 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 267 VAL Chi-restraints excluded: chain A residue 323 VAL 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 781 LEU Chi-restraints excluded: chain A residue 847 PHE 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 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.177045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.153284 restraints weight = 17631.897| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 2.67 r_work: 0.4006 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4012 r_free = 0.4012 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4012 r_free = 0.4012 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7051 Z= 0.180 Angle : 0.569 6.802 9565 Z= 0.299 Chirality : 0.043 0.170 1016 Planarity : 0.004 0.051 1212 Dihedral : 5.856 51.290 950 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.85 % Allowed : 25.47 % Favored : 71.68 % 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: 0.03 (0.30), residues: 820 helix: 0.66 (0.29), residues: 317 sheet: -1.09 (0.52), residues: 108 loop : -0.03 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 447 HIS 0.006 0.001 HIS A 716 PHE 0.046 0.002 PHE A 339 TYR 0.030 0.001 TYR A 680 ARG 0.006 0.000 ARG A 709 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3147.01 seconds wall clock time: 57 minutes 58.93 seconds (3478.93 seconds total)