Starting phenix.real_space_refine on Sat Jul 4 10:49:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3l_41005/07_2026/8t3l_41005_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3l_41005/07_2026/8t3l_41005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t3l_41005/07_2026/8t3l_41005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3l_41005/07_2026/8t3l_41005.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3l_41005/07_2026/8t3l_41005_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3l_41005/07_2026/8t3l_41005_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 70 5.16 5 Na 2 4.78 5 C 6715 2.51 5 N 1522 2.21 5 O 1753 1.98 5 H 10056 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20122 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 5059 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 296} Chain breaks: 1 Chain: "D" Number of atoms: 5078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 5078 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 298} Chain: "B" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4899 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 287} Chain breaks: 3 Chain: "C" Number of atoms: 4944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4944 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 288} Chain breaks: 1 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'8IJ': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'8IJ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'NKN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'NKN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.49, per 1000 atoms: 0.17 Number of scatterers: 20122 At special positions: 0 Unit cell: (112.725, 112.725, 81.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 70 16.00 P 4 15.00 Na 2 11.00 O 1753 8.00 N 1522 7.00 C 6715 6.00 H 10056 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 459.2 milliseconds 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.711A pdb=" N LEU A 413 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.555A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 504 through 508 removed outlier: 4.072A pdb=" N PHE A 507 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.873A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 689 Processing helix chain 'A' and resid 689 through 711 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.974A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 599 removed outlier: 4.062A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 4.056A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 670 Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 689 through 711 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 510 through 531 Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.999A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 575 Processing helix chain 'B' and resid 577 through 599 removed outlier: 3.803A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 640 removed outlier: 4.021A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 655 through 682 removed outlier: 3.541A pdb=" N PHE B 659 " --> pdb=" O PHE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 712 removed outlier: 3.679A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.654A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 499 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 552 Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.731A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 4.949A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 628 Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 655 through 686 removed outlier: 4.766A pdb=" N MET C 682 " --> pdb=" O LEU C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 711 removed outlier: 4.383A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2181 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.82 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10038 1.03 - 1.23: 80 1.23 - 1.42: 4413 1.42 - 1.62: 5706 1.62 - 1.82: 128 Bond restraints: 20365 Sorted by residual: bond pdb=" OAB NKN C 801 " pdb=" PAC NKN C 801 " ideal model delta sigma weight residual 1.668 1.457 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" OAB NKN B 801 " pdb=" PAC NKN B 801 " ideal model delta sigma weight residual 1.668 1.459 0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" OAA NKN B 801 " pdb=" PAC NKN B 801 " ideal model delta sigma weight residual 1.667 1.458 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" OAA NKN C 801 " pdb=" PAC NKN C 801 " ideal model delta sigma weight residual 1.667 1.460 0.207 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CAG NKN C 801 " pdb=" OAF NKN C 801 " ideal model delta sigma weight residual 1.467 1.397 0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 20360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.07: 36568 10.07 - 20.14: 6 20.14 - 30.22: 6 30.22 - 40.29: 0 40.29 - 50.36: 5 Bond angle restraints: 36585 Sorted by residual: angle pdb=" OAA NKN C 801 " pdb=" PAC NKN C 801 " pdb=" OAB NKN C 801 " ideal model delta sigma weight residual 54.49 104.85 -50.36 3.00e+00 1.11e-01 2.82e+02 angle pdb=" OAA NKN B 801 " pdb=" PAC NKN B 801 " pdb=" OAB NKN B 801 " ideal model delta sigma weight residual 54.49 104.48 -49.99 3.00e+00 1.11e-01 2.78e+02 angle pdb=" C23 8IJ A 801 " pdb=" C21 8IJ A 801 " pdb=" O20 8IJ A 801 " ideal model delta sigma weight residual 112.40 160.53 -48.13 3.00e+00 1.11e-01 2.57e+02 angle pdb=" O20 8IJ A 801 " pdb=" C21 8IJ A 801 " pdb=" O22 8IJ A 801 " ideal model delta sigma weight residual 123.25 77.61 45.64 3.00e+00 1.11e-01 2.31e+02 angle pdb=" C23 8IJ A 801 " pdb=" C21 8IJ A 801 " pdb=" O22 8IJ A 801 " ideal model delta sigma weight residual 124.34 82.92 41.42 3.00e+00 1.11e-01 1.91e+02 ... (remaining 36580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.12: 9288 31.12 - 62.23: 389 62.23 - 93.35: 35 93.35 - 124.47: 4 124.47 - 155.59: 3 Dihedral angle restraints: 9719 sinusoidal: 5139 harmonic: 4580 Sorted by residual: dihedral pdb=" CD ARG A 409 " pdb=" NE ARG A 409 " pdb=" CZ ARG A 409 " pdb=" NH1 ARG A 409 " ideal model delta sinusoidal sigma weight residual 0.00 -56.57 56.57 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CD ARG B 409 " pdb=" NE ARG B 409 " pdb=" CZ ARG B 409 " pdb=" NH1 ARG B 409 " ideal model delta sinusoidal sigma weight residual 0.00 -48.08 48.08 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" C49 8IJ D 801 " pdb=" C50 8IJ D 801 " pdb=" C51 8IJ D 801 " pdb=" C52 8IJ D 801 " ideal model delta sinusoidal sigma weight residual 171.66 -32.75 -155.59 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 9716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.036: 1558 1.036 - 2.072: 0 2.072 - 3.108: 0 3.108 - 4.144: 0 4.144 - 5.180: 2 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CAH NKN C 801 " pdb=" CAG NKN C 801 " pdb=" CAI NKN C 801 " pdb=" OAY NKN C 801 " both_signs ideal model delta sigma weight residual False -2.67 2.51 -5.18 2.00e-01 2.50e+01 6.71e+02 chirality pdb=" C18 8IJ A 801 " pdb=" C17 8IJ A 801 " pdb=" C19 8IJ A 801 " pdb=" O40 8IJ A 801 " both_signs ideal model delta sigma weight residual False -2.58 2.54 -5.12 2.00e-01 2.50e+01 6.55e+02 chirality pdb=" CA SER D 510 " pdb=" N SER D 510 " pdb=" C SER D 510 " pdb=" CB SER D 510 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1557 not shown) Planarity restraints: 2839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 474 " -0.613 9.50e-02 1.11e+02 2.68e-01 7.25e+02 pdb=" NE ARG D 474 " -0.137 2.00e-02 2.50e+03 pdb=" CZ ARG D 474 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG D 474 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 474 " 0.042 2.00e-02 2.50e+03 pdb="HH11 ARG D 474 " 0.362 2.00e-02 2.50e+03 pdb="HH12 ARG D 474 " -0.335 2.00e-02 2.50e+03 pdb="HH21 ARG D 474 " 0.059 2.00e-02 2.50e+03 pdb="HH22 ARG D 474 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 575 " -0.217 9.50e-02 1.11e+02 1.74e-01 5.73e+02 pdb=" NE ARG B 575 " -0.174 2.00e-02 2.50e+03 pdb=" CZ ARG B 575 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG B 575 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 575 " 0.034 2.00e-02 2.50e+03 pdb="HH11 ARG B 575 " 0.325 2.00e-02 2.50e+03 pdb="HH12 ARG B 575 " -0.261 2.00e-02 2.50e+03 pdb="HH21 ARG B 575 " 0.138 2.00e-02 2.50e+03 pdb="HH22 ARG B 575 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 455 " 0.509 9.50e-02 1.11e+02 2.09e-01 3.69e+02 pdb=" NE ARG B 455 " 0.082 2.00e-02 2.50e+03 pdb=" CZ ARG B 455 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG B 455 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 455 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG B 455 " -0.250 2.00e-02 2.50e+03 pdb="HH12 ARG B 455 " 0.241 2.00e-02 2.50e+03 pdb="HH21 ARG B 455 " -0.019 2.00e-02 2.50e+03 pdb="HH22 ARG B 455 " -0.079 2.00e-02 2.50e+03 ... (remaining 2836 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 1797 2.23 - 2.82: 43382 2.82 - 3.41: 54489 3.41 - 4.01: 69831 4.01 - 4.60: 107916 Nonbonded interactions: 277415 Sorted by model distance: nonbonded pdb="HD21 ASN B 408 " pdb=" OD2 ASP B 411 " model vdw 1.634 2.450 nonbonded pdb=" HZ3 LYS B 656 " pdb=" OH TYR C 631 " model vdw 1.638 2.450 nonbonded pdb=" OG SER B 402 " pdb=" HG1 THR B 406 " model vdw 1.647 2.450 nonbonded pdb=" OE1 GLN C 561 " pdb=" H GLN C 561 " model vdw 1.647 2.450 nonbonded pdb=" HH TYR D 463 " pdb=" OH TYR D 537 " model vdw 1.666 2.450 ... (remaining 277410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 392 through 456 or resid 461 through 463 or resid 467 thro \ ugh 683 or resid 688 through 712)) selection = (chain 'B' and resid 392 through 712) selection = (chain 'C' and (resid 392 through 456 or resid 461 through 463 or resid 467 thro \ ugh 683 or resid 688 through 712)) selection = (chain 'D' and (resid 392 through 456 or resid 461 through 463 or resid 467 thro \ ugh 683 or resid 688 through 712)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.440 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: 0.120 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 17.360 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 0.211 10309 Z= 0.378 Angle : 1.340 50.362 13911 Z= 0.626 Chirality : 0.189 5.180 1560 Planarity : 0.016 0.409 1673 Dihedral : 17.687 155.586 3831 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.64 % Allowed : 2.56 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1179 helix: 1.83 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -1.93 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 575 TYR 0.012 0.001 TYR B 627 PHE 0.021 0.001 PHE A 490 TRP 0.008 0.001 TRP B 697 HIS 0.002 0.001 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.38 (10309) covalent geometry : angle 1.34027 / 0.63 (13911) hydrogen bonds : bond 0.11347 / 6.92 ( 740) hydrogen bonds : angle 5.05073 / 3.63 ( 2181) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 301 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7420 (tm-30) REVERT: A 669 LEU cc_start: 0.8573 (mm) cc_final: 0.8264 (mm) REVERT: D 439 PHE cc_start: 0.7782 (t80) cc_final: 0.7204 (t80) REVERT: D 681 LEU cc_start: 0.8448 (mm) cc_final: 0.8220 (mm) REVERT: B 579 ARG cc_start: 0.7849 (ptm160) cc_final: 0.7045 (ptt180) REVERT: B 631 TYR cc_start: 0.7656 (t80) cc_final: 0.7211 (t80) outliers start: 7 outliers final: 3 residues processed: 306 average time/residue: 0.1883 time to fit residues: 81.2966 Evaluate side-chains 279 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 276 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 679 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.156235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.139327 restraints weight = 41712.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.143460 restraints weight = 17437.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.146049 restraints weight = 9972.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.147679 restraints weight = 6868.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.148802 restraints weight = 5299.446| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10309 Z= 0.199 Angle : 0.582 9.168 13911 Z= 0.317 Chirality : 0.036 0.193 1560 Planarity : 0.006 0.162 1673 Dihedral : 13.447 128.012 1513 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.56 % Allowed : 9.07 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.25), residues: 1179 helix: 2.04 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -2.03 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 575 TYR 0.009 0.001 TYR C 631 PHE 0.012 0.001 PHE C 439 TRP 0.007 0.001 TRP B 697 HIS 0.002 0.001 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (10309) covalent geometry : angle 0.58200 / 0.32 (13911) hydrogen bonds : bond 0.05571 / 3.64 ( 740) hydrogen bonds : angle 4.33272 / 3.07 ( 2181) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 274 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7511 (tm-30) REVERT: A 669 LEU cc_start: 0.8563 (mm) cc_final: 0.8262 (mm) REVERT: A 707 ASP cc_start: 0.7576 (m-30) cc_final: 0.7239 (t0) REVERT: D 439 PHE cc_start: 0.7787 (t80) cc_final: 0.7184 (t80) REVERT: D 681 LEU cc_start: 0.8494 (mm) cc_final: 0.8294 (mm) REVERT: B 579 ARG cc_start: 0.7566 (ptm160) cc_final: 0.7236 (ptm160) REVERT: B 631 TYR cc_start: 0.7695 (t80) cc_final: 0.7432 (t80) REVERT: C 471 ASP cc_start: 0.6359 (m-30) cc_final: 0.6143 (m-30) REVERT: C 652 ASN cc_start: 0.5301 (OUTLIER) cc_final: 0.4772 (m110) outliers start: 17 outliers final: 14 residues processed: 282 average time/residue: 0.2020 time to fit residues: 80.6262 Evaluate side-chains 279 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 264 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain D residue 519 GLN Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 682 MET Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 679 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 519 GLN C 410 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.150563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.133033 restraints weight = 42169.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.137215 restraints weight = 17692.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.139824 restraints weight = 10165.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.141492 restraints weight = 7030.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.142424 restraints weight = 5438.677| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10309 Z= 0.192 Angle : 0.549 5.610 13911 Z= 0.306 Chirality : 0.035 0.122 1560 Planarity : 0.004 0.095 1673 Dihedral : 12.235 103.685 1513 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.83 % Allowed : 12.73 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.25), residues: 1179 helix: 2.08 (0.17), residues: 911 sheet: None (None), residues: 0 loop : -2.24 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 432 TYR 0.011 0.001 TYR A 555 PHE 0.013 0.001 PHE C 439 TRP 0.007 0.001 TRP B 697 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (10309) covalent geometry : angle 0.54868 / 0.31 (13911) hydrogen bonds : bond 0.05457 / 3.58 ( 740) hydrogen bonds : angle 4.25576 / 3.02 ( 2181) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 669 LEU cc_start: 0.8558 (mm) cc_final: 0.8196 (mm) REVERT: A 707 ASP cc_start: 0.7572 (m-30) cc_final: 0.7268 (t0) REVERT: D 439 PHE cc_start: 0.7794 (t80) cc_final: 0.7184 (t80) REVERT: D 560 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6357 (pm20) REVERT: B 579 ARG cc_start: 0.7728 (ptm160) cc_final: 0.7426 (ptm160) REVERT: B 631 TYR cc_start: 0.7740 (t80) cc_final: 0.7433 (t80) REVERT: B 677 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6591 (ttp) outliers start: 20 outliers final: 14 residues processed: 279 average time/residue: 0.2026 time to fit residues: 79.7291 Evaluate side-chains 278 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 262 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 679 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 55 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.154294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136893 restraints weight = 42193.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.141028 restraints weight = 18017.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.143578 restraints weight = 10492.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.145238 restraints weight = 7359.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.146276 restraints weight = 5727.333| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10309 Z= 0.169 Angle : 0.529 5.579 13911 Z= 0.292 Chirality : 0.034 0.128 1560 Planarity : 0.004 0.078 1673 Dihedral : 11.618 82.011 1513 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.29 % Allowed : 13.55 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.25), residues: 1179 helix: 2.18 (0.17), residues: 911 sheet: None (None), residues: 0 loop : -2.30 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 534 TYR 0.010 0.001 TYR A 555 PHE 0.012 0.001 PHE C 439 TRP 0.007 0.001 TRP B 697 HIS 0.001 0.000 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (10309) covalent geometry : angle 0.52874 / 0.29 (13911) hydrogen bonds : bond 0.05204 / 3.44 ( 740) hydrogen bonds : angle 4.15615 / 2.95 ( 2181) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 267 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 GLN cc_start: 0.7247 (tp-100) cc_final: 0.6973 (tp40) REVERT: A 570 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 707 ASP cc_start: 0.7520 (m-30) cc_final: 0.7216 (t0) REVERT: D 439 PHE cc_start: 0.7773 (t80) cc_final: 0.7142 (t80) REVERT: D 560 GLN cc_start: 0.6711 (OUTLIER) cc_final: 0.6369 (pm20) REVERT: B 579 ARG cc_start: 0.7697 (ptm160) cc_final: 0.7356 (ptm160) REVERT: B 631 TYR cc_start: 0.7752 (t80) cc_final: 0.7440 (t80) REVERT: B 677 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6573 (ttp) outliers start: 25 outliers final: 18 residues processed: 281 average time/residue: 0.2066 time to fit residues: 82.3207 Evaluate side-chains 282 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 710 LYS Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 679 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 56 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 116 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.157385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.140429 restraints weight = 41296.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.144570 restraints weight = 17333.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.147123 restraints weight = 9944.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.148780 restraints weight = 6879.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.149868 restraints weight = 5313.876| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10309 Z= 0.132 Angle : 0.493 5.226 13911 Z= 0.272 Chirality : 0.033 0.119 1560 Planarity : 0.003 0.057 1673 Dihedral : 11.082 83.228 1513 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.01 % Allowed : 15.48 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.26), residues: 1179 helix: 2.42 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -2.19 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 534 TYR 0.008 0.001 TYR A 555 PHE 0.010 0.001 PHE C 439 TRP 0.007 0.001 TRP B 697 HIS 0.001 0.000 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10309) covalent geometry : angle 0.49306 / 0.27 (13911) hydrogen bonds : bond 0.04836 / 3.20 ( 740) hydrogen bonds : angle 3.99934 / 2.83 ( 2181) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 ASP cc_start: 0.7525 (m-30) cc_final: 0.7222 (t0) REVERT: D 439 PHE cc_start: 0.7758 (t80) cc_final: 0.7143 (t80) REVERT: D 560 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6439 (pm20) REVERT: B 455 ARG cc_start: 0.7564 (ptt90) cc_final: 0.7324 (ptt90) REVERT: B 579 ARG cc_start: 0.7657 (ptm160) cc_final: 0.7426 (ptm160) REVERT: B 631 TYR cc_start: 0.7712 (t80) cc_final: 0.7408 (t80) REVERT: C 677 MET cc_start: 0.7298 (tmm) cc_final: 0.7070 (tmm) outliers start: 22 outliers final: 18 residues processed: 280 average time/residue: 0.2149 time to fit residues: 84.2639 Evaluate side-chains 285 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 266 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 710 LYS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.156228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.139241 restraints weight = 41680.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.143373 restraints weight = 17433.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.145944 restraints weight = 9994.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.147580 restraints weight = 6914.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.148695 restraints weight = 5352.852| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10309 Z= 0.150 Angle : 0.503 5.212 13911 Z= 0.278 Chirality : 0.033 0.126 1560 Planarity : 0.003 0.055 1673 Dihedral : 10.999 84.228 1513 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.38 % Allowed : 15.48 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.26), residues: 1179 helix: 2.48 (0.17), residues: 903 sheet: None (None), residues: 0 loop : -2.08 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 428 TYR 0.010 0.001 TYR A 555 PHE 0.010 0.001 PHE C 439 TRP 0.010 0.001 TRP A 697 HIS 0.001 0.000 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (10309) covalent geometry : angle 0.50316 / 0.28 (13911) hydrogen bonds : bond 0.04879 / 3.23 ( 740) hydrogen bonds : angle 4.02171 / 2.85 ( 2181) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.6480 (m-30) REVERT: A 707 ASP cc_start: 0.7532 (m-30) cc_final: 0.7261 (t0) REVERT: D 439 PHE cc_start: 0.7745 (t80) cc_final: 0.7143 (t80) REVERT: D 531 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: D 560 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: B 455 ARG cc_start: 0.7574 (ptt90) cc_final: 0.7315 (ptt90) REVERT: B 572 MET cc_start: 0.7136 (mtt) cc_final: 0.6802 (mtp) REVERT: B 579 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7380 (ptm160) REVERT: B 631 TYR cc_start: 0.7706 (t80) cc_final: 0.7401 (t80) outliers start: 26 outliers final: 20 residues processed: 279 average time/residue: 0.2000 time to fit residues: 78.1268 Evaluate side-chains 287 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 531 PHE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 710 LYS Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 679 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.152292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.134961 restraints weight = 41969.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.139036 restraints weight = 17864.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.141620 restraints weight = 10359.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.143248 restraints weight = 7201.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.144336 restraints weight = 5602.399| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10309 Z= 0.152 Angle : 0.507 5.216 13911 Z= 0.279 Chirality : 0.033 0.130 1560 Planarity : 0.003 0.052 1673 Dihedral : 10.836 84.750 1513 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.56 % Allowed : 16.12 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.26), residues: 1179 helix: 2.40 (0.17), residues: 911 sheet: None (None), residues: 0 loop : -2.27 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 534 TYR 0.011 0.001 TYR B 401 PHE 0.011 0.001 PHE C 439 TRP 0.010 0.001 TRP A 697 HIS 0.001 0.000 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (10309) covalent geometry : angle 0.50742 / 0.28 (13911) hydrogen bonds : bond 0.04859 / 3.22 ( 740) hydrogen bonds : angle 4.01396 / 2.84 ( 2181) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 267 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 439 PHE cc_start: 0.7718 (t80) cc_final: 0.7141 (t80) REVERT: D 531 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: D 560 GLN cc_start: 0.6786 (OUTLIER) cc_final: 0.6471 (pm20) REVERT: B 455 ARG cc_start: 0.7554 (ptt90) cc_final: 0.7304 (ptt90) REVERT: B 631 TYR cc_start: 0.7689 (t80) cc_final: 0.7370 (t80) REVERT: B 658 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7840 (m) REVERT: C 677 MET cc_start: 0.7340 (tmm) cc_final: 0.7123 (tmm) outliers start: 28 outliers final: 21 residues processed: 282 average time/residue: 0.1995 time to fit residues: 78.8706 Evaluate side-chains 285 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 531 PHE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 90 optimal weight: 0.0670 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 96 optimal weight: 0.0980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.159875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.142604 restraints weight = 41473.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.146767 restraints weight = 17591.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.149365 restraints weight = 10196.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.151043 restraints weight = 7111.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.152185 restraints weight = 5518.165| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10309 Z= 0.115 Angle : 0.480 5.119 13911 Z= 0.262 Chirality : 0.032 0.138 1560 Planarity : 0.003 0.042 1673 Dihedral : 10.503 84.416 1513 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.01 % Allowed : 16.85 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.26), residues: 1179 helix: 2.61 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -2.08 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 534 TYR 0.007 0.001 TYR C 666 PHE 0.011 0.001 PHE C 496 TRP 0.010 0.001 TRP A 697 HIS 0.001 0.000 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (10309) covalent geometry : angle 0.47984 / 0.26 (13911) hydrogen bonds : bond 0.04474 / 2.97 ( 740) hydrogen bonds : angle 3.86608 / 2.74 ( 2181) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 273 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6545 (m-30) REVERT: A 707 ASP cc_start: 0.7564 (m-30) cc_final: 0.7252 (t0) REVERT: D 439 PHE cc_start: 0.7583 (t80) cc_final: 0.6972 (t80) REVERT: D 531 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: B 455 ARG cc_start: 0.7574 (ptt90) cc_final: 0.7336 (ptt90) REVERT: B 572 MET cc_start: 0.7025 (mtt) cc_final: 0.6792 (mtp) REVERT: B 631 TYR cc_start: 0.7652 (t80) cc_final: 0.7368 (t80) REVERT: B 658 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7857 (m) REVERT: B 677 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6711 (ttp) REVERT: C 496 PHE cc_start: 0.6586 (m-80) cc_final: 0.6359 (m-80) REVERT: C 677 MET cc_start: 0.7353 (tmm) cc_final: 0.7152 (tmm) outliers start: 22 outliers final: 16 residues processed: 285 average time/residue: 0.1935 time to fit residues: 77.4284 Evaluate side-chains 283 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 531 PHE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 26 optimal weight: 0.0770 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.151873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.134354 restraints weight = 41838.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.138487 restraints weight = 17717.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.141060 restraints weight = 10268.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.142689 restraints weight = 7165.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.143775 restraints weight = 5591.170| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10309 Z= 0.223 Angle : 0.571 5.947 13911 Z= 0.317 Chirality : 0.036 0.132 1560 Planarity : 0.004 0.058 1673 Dihedral : 10.746 88.501 1513 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.20 % Allowed : 16.85 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.25), residues: 1179 helix: 2.16 (0.17), residues: 911 sheet: None (None), residues: 0 loop : -2.37 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 534 TYR 0.019 0.002 TYR C 671 PHE 0.020 0.002 PHE C 591 TRP 0.006 0.001 TRP B 549 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (10309) covalent geometry : angle 0.57075 / 0.32 (13911) hydrogen bonds : bond 0.05294 / 3.48 ( 740) hydrogen bonds : angle 4.18389 / 2.97 ( 2181) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 271 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6597 (m-30) REVERT: A 570 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 707 ASP cc_start: 0.7572 (m-30) cc_final: 0.7276 (t0) REVERT: D 439 PHE cc_start: 0.7810 (t80) cc_final: 0.7209 (t80) REVERT: D 531 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: B 631 TYR cc_start: 0.7705 (t80) cc_final: 0.7357 (t80) REVERT: B 677 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6698 (ttp) REVERT: C 496 PHE cc_start: 0.6682 (m-80) cc_final: 0.6439 (m-80) outliers start: 24 outliers final: 19 residues processed: 283 average time/residue: 0.1858 time to fit residues: 74.7335 Evaluate side-chains 287 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 531 PHE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.151077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133701 restraints weight = 41902.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137786 restraints weight = 17891.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.140378 restraints weight = 10382.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.142015 restraints weight = 7211.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.143082 restraints weight = 5605.069| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10309 Z= 0.166 Angle : 0.531 6.115 13911 Z= 0.293 Chirality : 0.034 0.145 1560 Planarity : 0.003 0.050 1673 Dihedral : 10.579 88.602 1513 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.29 % Allowed : 16.67 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.25), residues: 1179 helix: 2.24 (0.17), residues: 911 sheet: None (None), residues: 0 loop : -2.32 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 534 TYR 0.012 0.001 TYR A 554 PHE 0.013 0.001 PHE C 591 TRP 0.006 0.001 TRP A 697 HIS 0.001 0.000 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (10309) covalent geometry : angle 0.53139 / 0.29 (13911) hydrogen bonds : bond 0.05028 / 3.32 ( 740) hydrogen bonds : angle 4.08840 / 2.90 ( 2181) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6580 (m-30) REVERT: A 570 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7697 (tm-30) REVERT: A 707 ASP cc_start: 0.7574 (m-30) cc_final: 0.7279 (t0) REVERT: D 439 PHE cc_start: 0.7694 (t80) cc_final: 0.7098 (t80) REVERT: D 531 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: D 560 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6283 (pm20) REVERT: B 631 TYR cc_start: 0.7699 (t80) cc_final: 0.7354 (t80) REVERT: B 658 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7738 (m) REVERT: C 496 PHE cc_start: 0.6703 (m-80) cc_final: 0.6426 (m-80) outliers start: 25 outliers final: 21 residues processed: 281 average time/residue: 0.1971 time to fit residues: 78.2069 Evaluate side-chains 289 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 264 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 531 PHE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.151165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.133791 restraints weight = 41806.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.137891 restraints weight = 17823.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.140509 restraints weight = 10318.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.142156 restraints weight = 7144.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.143285 restraints weight = 5539.088| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10309 Z= 0.180 Angle : 0.547 7.370 13911 Z= 0.300 Chirality : 0.034 0.147 1560 Planarity : 0.004 0.052 1673 Dihedral : 10.551 89.631 1513 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.56 % Allowed : 16.76 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.25), residues: 1179 helix: 2.17 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.41 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 534 TYR 0.015 0.001 TYR C 671 PHE 0.017 0.001 PHE D 438 TRP 0.005 0.001 TRP A 697 HIS 0.001 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (10309) covalent geometry : angle 0.54692 / 0.30 (13911) hydrogen bonds : bond 0.05090 / 3.36 ( 740) hydrogen bonds : angle 4.12770 / 2.93 ( 2181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3144.87 seconds wall clock time: 54 minutes 15.35 seconds (3255.35 seconds total)