Starting phenix.real_space_refine on Wed Aug 5 11:44:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yr2_39533/08_2026/8yr2_39533.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yr2_39533/08_2026/8yr2_39533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yr2_39533/08_2026/8yr2_39533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yr2_39533/08_2026/8yr2_39533.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yr2_39533/08_2026/8yr2_39533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yr2_39533/08_2026/8yr2_39533.map" } resolution = 2.89 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= 0.004 sd= 0.062 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 10 5.49 5 S 40 5.16 5 Cl 2 4.86 5 Na 4 4.78 5 C 6776 2.51 5 N 1414 2.21 5 O 1648 1.98 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9894 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "B" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 456 Unusual residues: {' CL': 1, ' NA': 2, '41U': 1, 'A1LX7': 2, 'CLR': 11, 'PIO': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "A" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 400 Unusual residues: {' CL': 1, ' NA': 2, '41U': 1, 'A1LX7': 2, 'CLR': 9, 'PIO': 1} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.20, per 1000 atoms: 0.22 Number of scatterers: 9894 At special positions: 0 Unit cell: (89.79, 114.61, 89.06, 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) Cl 2 17.00 S 40 16.00 P 10 15.00 Na 4 11.00 O 1648 8.00 N 1414 7.00 C 6776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 311.5 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 77.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 61 through 74 removed outlier: 3.688A pdb=" N PHE B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.718A pdb=" N VAL B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 107 removed outlier: 3.948A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Proline residue: B 97 - end of helix removed outlier: 3.674A pdb=" N LEU B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 134 through 165 removed outlier: 3.659A pdb=" N GLY B 138 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 151 " --> pdb=" O TYR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 234 through 253 Processing helix chain 'B' and resid 257 through 282 removed outlier: 3.873A pdb=" N LYS B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.618A pdb=" N GLY B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 4.008A pdb=" N LYS B 303 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA B 305 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 320 removed outlier: 3.544A pdb=" N ALA B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 331 removed outlier: 4.264A pdb=" N ILE B 327 " --> pdb=" O PHE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 373 removed outlier: 3.508A pdb=" N ASP B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 380 removed outlier: 3.836A pdb=" N VAL B 379 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 398 Proline residue: B 392 - end of helix Processing helix chain 'B' and resid 400 through 435 removed outlier: 3.520A pdb=" N TRP B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 441 removed outlier: 3.663A pdb=" N HIS B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 461 removed outlier: 3.766A pdb=" N PHE B 445 " --> pdb=" O HIS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 494 removed outlier: 4.007A pdb=" N VAL B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 509 removed outlier: 3.887A pdb=" N PHE B 501 " --> pdb=" O GLY B 497 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 502 " --> pdb=" O VAL B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 523 Processing helix chain 'B' and resid 523 through 539 Processing helix chain 'B' and resid 551 through 579 removed outlier: 4.040A pdb=" N ASN B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Proline residue: B 570 - end of helix Processing helix chain 'B' and resid 583 through 593 Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.746A pdb=" N ALA B 602 " --> pdb=" O HIS B 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.695A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.718A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.949A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix removed outlier: 3.675A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 165 removed outlier: 3.660A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 257 through 282 removed outlier: 3.868A pdb=" N LYS A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.605A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.985A pdb=" N LYS A 303 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 305 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 320 removed outlier: 3.504A pdb=" N ALA A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 removed outlier: 4.265A pdb=" N ILE A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.509A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.835A pdb=" N VAL A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 398 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.520A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.659A pdb=" N HIS A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 461 removed outlier: 3.781A pdb=" N PHE A 445 " --> pdb=" O HIS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 494 removed outlier: 4.008A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 removed outlier: 3.889A pdb=" N PHE A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 502 " --> pdb=" O VAL A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 579 removed outlier: 4.038A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.747A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1350 1.30 - 1.43: 2923 1.43 - 1.55: 5887 1.55 - 1.68: 16 1.68 - 1.81: 62 Bond restraints: 10238 Sorted by residual: bond pdb=" O 41U A 701 " pdb=" C7 41U A 701 " ideal model delta sigma weight residual 1.468 1.396 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" O 41U B 701 " pdb=" C7 41U B 701 " ideal model delta sigma weight residual 1.468 1.397 0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1B PIO A 702 " pdb=" O3C PIO A 702 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1A PIO A 702 " pdb=" O2C PIO A 702 " ideal model delta sigma weight residual 1.332 1.398 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1B PIO B 702 " pdb=" O3C PIO B 702 " ideal model delta sigma weight residual 1.331 1.396 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 10233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.73: 13971 5.73 - 11.46: 89 11.46 - 17.20: 8 17.20 - 22.93: 2 22.93 - 28.66: 2 Bond angle restraints: 14072 Sorted by residual: angle pdb=" C19 CLR B 717 " pdb=" C10 CLR B 717 " pdb=" C9 CLR B 717 " ideal model delta sigma weight residual 111.86 83.20 28.66 3.00e+00 1.11e-01 9.13e+01 angle pdb=" C1 CLR B 717 " pdb=" C10 CLR B 717 " pdb=" C19 CLR B 717 " ideal model delta sigma weight residual 109.60 82.51 27.09 3.00e+00 1.11e-01 8.15e+01 angle pdb=" C19 CLR B 717 " pdb=" C10 CLR B 717 " pdb=" C5 CLR B 717 " ideal model delta sigma weight residual 108.37 86.33 22.04 3.00e+00 1.11e-01 5.40e+01 angle pdb=" O23 A1LX7 A 711 " pdb=" P24 A1LX7 A 711 " pdb=" O26 A1LX7 A 711 " ideal model delta sigma weight residual 97.27 115.32 -18.05 3.00e+00 1.11e-01 3.62e+01 angle pdb=" O23 A1LX7 B 713 " pdb=" P24 A1LX7 B 713 " pdb=" O26 A1LX7 B 713 " ideal model delta sigma weight residual 97.27 113.42 -16.15 3.00e+00 1.11e-01 2.90e+01 ... (remaining 14067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 6490 35.08 - 70.16: 280 70.16 - 105.24: 19 105.24 - 140.32: 10 140.32 - 175.40: 9 Dihedral angle restraints: 6808 sinusoidal: 3544 harmonic: 3264 Sorted by residual: dihedral pdb=" C19 CLR B 717 " pdb=" C1 CLR B 717 " pdb=" C10 CLR B 717 " pdb=" C2 CLR B 717 " ideal model delta sinusoidal sigma weight residual 68.88 -115.72 -175.40 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C11 CLR B 717 " pdb=" C10 CLR B 717 " pdb=" C9 CLR B 717 " pdb=" C19 CLR B 717 " ideal model delta sinusoidal sigma weight residual 51.90 -109.43 161.33 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" N 41U B 701 " pdb=" C14 41U B 701 " pdb=" C15 41U B 701 " pdb=" C7 41U B 701 " ideal model delta sinusoidal sigma weight residual 298.27 139.98 158.29 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 6805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.379: 1621 0.379 - 0.759: 0 0.759 - 1.138: 0 1.138 - 1.518: 0 1.518 - 1.897: 1 Chirality restraints: 1622 Sorted by residual: chirality pdb=" C10 CLR B 717 " pdb=" C1 CLR B 717 " pdb=" C5 CLR B 717 " pdb=" C9 CLR B 717 " both_signs ideal model delta sigma weight residual False -2.85 -0.95 -1.90 2.00e-01 2.50e+01 9.00e+01 chirality pdb=" C10 CLR B 708 " pdb=" C1 CLR B 708 " pdb=" C5 CLR B 708 " pdb=" C9 CLR B 708 " both_signs ideal model delta sigma weight residual False -2.85 -2.54 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C20 CLR B 707 " pdb=" C17 CLR B 707 " pdb=" C21 CLR B 707 " pdb=" C22 CLR B 707 " both_signs ideal model delta sigma weight residual False 2.59 2.29 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 1619 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 104 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C ILE B 104 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE B 104 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA B 105 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 104 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C ILE A 104 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE A 104 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 105 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 103 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C ILE B 103 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE B 103 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE B 104 " -0.012 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.34: 29 2.34 - 2.98: 5375 2.98 - 3.62: 15412 3.62 - 4.26: 24286 4.26 - 4.90: 39959 Nonbonded interactions: 85061 Sorted by model distance: nonbonded pdb=" O MET A 566 " pdb=" C27 CLR A 713 " model vdw 1.706 3.460 nonbonded pdb=" O ALA A 73 " pdb="NA NA A 703 " model vdw 1.707 2.470 nonbonded pdb=" O ILE B 227 " pdb=" O1 CLR B 709 " model vdw 1.785 3.040 nonbonded pdb=" OD1 ASP A 418 " pdb="NA NA A 704 " model vdw 1.789 2.470 nonbonded pdb=" O MET B 566 " pdb=" C27 CLR B 718 " model vdw 1.900 3.460 ... (remaining 85056 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 53 through 710 or resid 715 through 716)) selection = (chain 'B' and (resid 53 through 710 or resid 715 through 716)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.440 Find NCS groups from input model: 0.210 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 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 : 0.008 0.446 10242 Z= 0.595 Angle : 1.178 28.659 14072 Z= 0.465 Chirality : 0.076 1.897 1622 Planarity : 0.004 0.041 1568 Dihedral : 17.922 175.403 4732 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.36 % Allowed : 8.93 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.38 (0.23), residues: 1126 helix: -0.48 (0.17), residues: 748 sheet: None (None), residues: 0 loop : -1.60 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 512 TYR 0.013 0.001 TYR B 151 PHE 0.012 0.001 PHE B 362 TRP 0.006 0.001 TRP A 553 HIS 0.001 0.000 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.31 (10238) covalent geometry : angle 1.17765 / 0.46 (14072) hydrogen bonds : bond 0.13886 / 9.26 ( 584) hydrogen bonds : angle 6.37306 / 4.48 ( 1734) Misc. bond : bond 0.25651 / 12.72 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 281 time to evaluate : 0.315 Fit side-chains REVERT: B 126 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.7720 (p) REVERT: B 153 ASN cc_start: 0.7171 (m110) cc_final: 0.6784 (m110) REVERT: B 215 GLU cc_start: 0.7191 (pt0) cc_final: 0.6912 (mt-10) REVERT: B 242 MET cc_start: 0.6503 (mtp) cc_final: 0.5750 (ptt) REVERT: B 420 SER cc_start: 0.7516 (t) cc_final: 0.7256 (m) REVERT: B 519 LEU cc_start: 0.8635 (mt) cc_final: 0.8383 (mm) REVERT: B 609 PHE cc_start: 0.7464 (m-10) cc_final: 0.6104 (m-80) REVERT: A 126 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.7640 (p) REVERT: A 153 ASN cc_start: 0.7179 (m110) cc_final: 0.6806 (m110) REVERT: A 215 GLU cc_start: 0.7193 (pt0) cc_final: 0.6930 (mt-10) REVERT: A 242 MET cc_start: 0.6492 (mtp) cc_final: 0.5743 (ptt) REVERT: A 391 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: A 420 SER cc_start: 0.7546 (t) cc_final: 0.7301 (m) REVERT: A 609 PHE cc_start: 0.7471 (m-10) cc_final: 0.6122 (m-80) outliers start: 51 outliers final: 10 residues processed: 313 average time/residue: 0.3196 time to fit residues: 111.1553 Evaluate side-chains 178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.190577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.158134 restraints weight = 12220.579| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.36 r_work: 0.3796 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10242 Z= 0.199 Angle : 0.883 28.727 14072 Z= 0.377 Chirality : 0.067 1.949 1622 Planarity : 0.005 0.038 1568 Dihedral : 17.021 177.430 2836 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.88 % Allowed : 17.02 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1126 helix: 0.61 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -1.22 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 587 TYR 0.019 0.002 TYR A 572 PHE 0.018 0.002 PHE B 362 TRP 0.019 0.002 TRP A 585 HIS 0.004 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (10238) covalent geometry : angle 0.88345 / 0.38 (14072) hydrogen bonds : bond 0.05913 / 3.83 ( 584) hydrogen bonds : angle 5.15918 / 3.61 ( 1734) Misc. bond : bond 0.00358 / 0.17 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 0.250 Fit side-chains REVERT: B 126 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8272 (p) REVERT: B 215 GLU cc_start: 0.7636 (pt0) cc_final: 0.7432 (mt-10) REVERT: B 280 HIS cc_start: 0.7187 (t-90) cc_final: 0.6579 (t70) REVERT: B 337 ASN cc_start: 0.8170 (t0) cc_final: 0.7705 (t0) REVERT: B 425 GLU cc_start: 0.8229 (tm-30) cc_final: 0.8024 (tm-30) REVERT: B 436 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7314 (mm-40) REVERT: B 439 LYS cc_start: 0.6581 (tttt) cc_final: 0.6255 (ttpt) REVERT: A 122 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6364 (pt0) REVERT: A 126 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8206 (p) REVERT: A 264 TRP cc_start: 0.6456 (t-100) cc_final: 0.6254 (t-100) REVERT: A 280 HIS cc_start: 0.7146 (t-90) cc_final: 0.6523 (t70) REVERT: A 337 ASN cc_start: 0.8091 (t0) cc_final: 0.7607 (t0) REVERT: A 425 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 439 LYS cc_start: 0.6520 (tttt) cc_final: 0.6212 (ttpt) REVERT: A 587 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5189 (mpt-90) outliers start: 56 outliers final: 24 residues processed: 206 average time/residue: 0.2753 time to fit residues: 63.6925 Evaluate side-chains 173 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 13 optimal weight: 0.0980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.188302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.154965 restraints weight = 12180.414| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.37 r_work: 0.3760 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10242 Z= 0.151 Angle : 0.839 27.643 14072 Z= 0.354 Chirality : 0.066 1.967 1622 Planarity : 0.004 0.037 1568 Dihedral : 15.987 175.601 2828 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.04 % Allowed : 17.96 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1126 helix: 1.17 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -1.00 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.013 0.002 TYR A 572 PHE 0.016 0.002 PHE B 362 TRP 0.021 0.001 TRP A 585 HIS 0.003 0.000 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10238) covalent geometry : angle 0.83918 / 0.35 (14072) hydrogen bonds : bond 0.05590 / 3.58 ( 584) hydrogen bonds : angle 5.02622 / 3.52 ( 1734) Misc. bond : bond 0.00441 / 0.21 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.334 Fit side-chains REVERT: B 81 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7917 (mmm160) REVERT: B 122 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6541 (pt0) REVERT: B 126 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8114 (p) REVERT: B 207 PHE cc_start: 0.8236 (m-80) cc_final: 0.8014 (m-10) REVERT: B 215 GLU cc_start: 0.7582 (pt0) cc_final: 0.7371 (mt-10) REVERT: B 280 HIS cc_start: 0.7200 (t-90) cc_final: 0.6607 (t70) REVERT: B 337 ASN cc_start: 0.8092 (t0) cc_final: 0.7668 (t0) REVERT: B 425 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 81 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7883 (mmm160) REVERT: A 126 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8279 (p) REVERT: A 207 PHE cc_start: 0.8192 (m-80) cc_final: 0.7972 (m-10) REVERT: A 215 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7556 (mt-10) REVERT: A 264 TRP cc_start: 0.6445 (t-100) cc_final: 0.6238 (t-100) REVERT: A 280 HIS cc_start: 0.7190 (t-90) cc_final: 0.6580 (t70) REVERT: A 337 ASN cc_start: 0.8064 (t0) cc_final: 0.7629 (t0) REVERT: A 425 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7731 (tm-30) REVERT: A 587 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.5114 (mpt-90) outliers start: 48 outliers final: 25 residues processed: 180 average time/residue: 0.3058 time to fit residues: 61.4771 Evaluate side-chains 166 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 111 optimal weight: 0.0040 chunk 88 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.188221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.154878 restraints weight = 12225.974| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.37 r_work: 0.3747 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10242 Z= 0.140 Angle : 0.835 27.620 14072 Z= 0.348 Chirality : 0.066 2.001 1622 Planarity : 0.004 0.040 1568 Dihedral : 15.506 177.875 2828 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.25 % Allowed : 17.65 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.25), residues: 1126 helix: 1.35 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -0.73 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.020 0.001 TYR A 249 PHE 0.016 0.001 PHE B 362 TRP 0.022 0.001 TRP A 585 HIS 0.004 0.000 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (10238) covalent geometry : angle 0.83482 / 0.35 (14072) hydrogen bonds : bond 0.05388 / 3.43 ( 584) hydrogen bonds : angle 4.93596 / 3.47 ( 1734) Misc. bond : bond 0.00469 / 0.23 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 0.335 Fit side-chains REVERT: B 126 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 180 TRP cc_start: 0.4787 (OUTLIER) cc_final: 0.4298 (t60) REVERT: B 280 HIS cc_start: 0.7185 (t-90) cc_final: 0.6549 (t70) REVERT: B 337 ASN cc_start: 0.8071 (t0) cc_final: 0.7647 (t0) REVERT: B 425 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7778 (tm-30) REVERT: B 587 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.5426 (mtt-85) REVERT: A 81 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7943 (mmm160) REVERT: A 126 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8329 (p) REVERT: A 168 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7455 (p) REVERT: A 180 TRP cc_start: 0.4689 (OUTLIER) cc_final: 0.4201 (t60) REVERT: A 215 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 264 TRP cc_start: 0.6448 (t-100) cc_final: 0.6201 (t-100) REVERT: A 280 HIS cc_start: 0.7212 (t-90) cc_final: 0.6561 (t70) REVERT: A 337 ASN cc_start: 0.8052 (t0) cc_final: 0.7658 (t0) REVERT: A 425 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7786 (tm-30) REVERT: A 587 ARG cc_start: 0.5848 (OUTLIER) cc_final: 0.5182 (mpt-90) REVERT: A 612 GLN cc_start: 0.7527 (mp-120) cc_final: 0.7023 (tm-30) outliers start: 50 outliers final: 27 residues processed: 180 average time/residue: 0.2909 time to fit residues: 58.8940 Evaluate side-chains 177 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 587 ARG Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 5 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.176230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143274 restraints weight = 12161.908| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.06 r_work: 0.3576 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10242 Z= 0.176 Angle : 0.820 28.074 14072 Z= 0.352 Chirality : 0.065 1.917 1622 Planarity : 0.004 0.041 1568 Dihedral : 15.509 176.777 2828 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.36 % Allowed : 18.70 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1126 helix: 1.29 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -0.74 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 81 TYR 0.022 0.002 TYR A 249 PHE 0.021 0.002 PHE B 362 TRP 0.026 0.002 TRP A 585 HIS 0.002 0.000 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (10238) covalent geometry : angle 0.81967 / 0.35 (14072) hydrogen bonds : bond 0.06228 / 3.96 ( 584) hydrogen bonds : angle 5.12173 / 3.60 ( 1734) Misc. bond : bond 0.00486 / 0.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 138 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8286 (mmm160) REVERT: B 168 THR cc_start: 0.7854 (OUTLIER) cc_final: 0.7506 (p) REVERT: B 180 TRP cc_start: 0.4968 (OUTLIER) cc_final: 0.4447 (t60) REVERT: B 189 LYS cc_start: 0.6298 (mttt) cc_final: 0.5740 (mmtp) REVERT: B 215 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7828 (mt-10) REVERT: B 236 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6755 (pm20) REVERT: B 280 HIS cc_start: 0.7342 (t-90) cc_final: 0.6665 (t70) REVERT: B 337 ASN cc_start: 0.8272 (t0) cc_final: 0.7824 (t0) REVERT: B 425 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8150 (tm-30) REVERT: B 584 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7360 (tp) REVERT: B 587 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.5656 (mtt-85) REVERT: B 612 GLN cc_start: 0.7596 (mp-120) cc_final: 0.7119 (tm-30) REVERT: A 81 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8280 (mmm160) REVERT: A 126 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8525 (p) REVERT: A 168 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7754 (p) REVERT: A 180 TRP cc_start: 0.4951 (OUTLIER) cc_final: 0.4406 (t60) REVERT: A 189 LYS cc_start: 0.6309 (mttt) cc_final: 0.5744 (mmtp) REVERT: A 215 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7974 (mt-10) REVERT: A 234 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7604 (mt0) REVERT: A 264 TRP cc_start: 0.6749 (t-100) cc_final: 0.6516 (t-100) REVERT: A 280 HIS cc_start: 0.7319 (t-90) cc_final: 0.6681 (t70) REVERT: A 337 ASN cc_start: 0.8168 (t0) cc_final: 0.7795 (t0) REVERT: A 425 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8147 (tm-30) REVERT: A 587 ARG cc_start: 0.6071 (OUTLIER) cc_final: 0.5363 (mpt-90) REVERT: A 610 GLN cc_start: 0.7932 (mp10) cc_final: 0.7388 (pm20) REVERT: A 612 GLN cc_start: 0.7610 (mp-120) cc_final: 0.7120 (tm-30) outliers start: 51 outliers final: 29 residues processed: 175 average time/residue: 0.3198 time to fit residues: 62.4587 Evaluate side-chains 170 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 587 ARG Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.182807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.148641 restraints weight = 12347.409| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.38 r_work: 0.3672 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10242 Z= 0.145 Angle : 0.785 28.055 14072 Z= 0.334 Chirality : 0.064 1.922 1622 Planarity : 0.004 0.041 1568 Dihedral : 15.221 175.455 2826 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.46 % Allowed : 20.17 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.25), residues: 1126 helix: 1.48 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.68 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.017 0.001 TYR A 249 PHE 0.016 0.001 PHE A 362 TRP 0.027 0.001 TRP A 585 HIS 0.002 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (10238) covalent geometry : angle 0.78492 / 0.33 (14072) hydrogen bonds : bond 0.05758 / 3.65 ( 584) hydrogen bonds : angle 5.03053 / 3.54 ( 1734) Misc. bond : bond 0.00392 / 0.19 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 129 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7986 (tp) REVERT: B 168 THR cc_start: 0.7947 (OUTLIER) cc_final: 0.7727 (p) REVERT: B 180 TRP cc_start: 0.4909 (OUTLIER) cc_final: 0.4452 (t60) REVERT: B 189 LYS cc_start: 0.6312 (mttt) cc_final: 0.5797 (mmtp) REVERT: B 215 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 280 HIS cc_start: 0.7462 (t-90) cc_final: 0.6801 (t70) REVERT: B 425 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8027 (tm-30) REVERT: B 587 ARG cc_start: 0.6244 (OUTLIER) cc_final: 0.5820 (mtt-85) REVERT: B 610 GLN cc_start: 0.8033 (mp10) cc_final: 0.7515 (pm20) REVERT: B 612 GLN cc_start: 0.7613 (mp-120) cc_final: 0.7259 (tm-30) REVERT: A 81 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8295 (mmm160) REVERT: A 180 TRP cc_start: 0.4885 (OUTLIER) cc_final: 0.4423 (t60) REVERT: A 189 LYS cc_start: 0.6337 (mttt) cc_final: 0.5820 (mmtp) REVERT: A 234 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: A 242 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6606 (ptt) REVERT: A 264 TRP cc_start: 0.6712 (t-100) cc_final: 0.6459 (t-100) REVERT: A 280 HIS cc_start: 0.7441 (t-90) cc_final: 0.6822 (t70) REVERT: A 425 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8034 (tm-30) REVERT: A 587 ARG cc_start: 0.6331 (OUTLIER) cc_final: 0.5588 (mpt-90) REVERT: A 612 GLN cc_start: 0.7679 (mp-120) cc_final: 0.7265 (tm-30) outliers start: 52 outliers final: 31 residues processed: 167 average time/residue: 0.3160 time to fit residues: 58.9273 Evaluate side-chains 170 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 587 ARG Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 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 = 0.4143 r_free = 0.4143 target = 0.183789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.149774 restraints weight = 12259.410| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.37 r_work: 0.3679 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10242 Z= 0.138 Angle : 0.774 28.157 14072 Z= 0.329 Chirality : 0.063 1.910 1622 Planarity : 0.004 0.042 1568 Dihedral : 15.044 175.943 2826 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.73 % Allowed : 21.74 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.25), residues: 1126 helix: 1.47 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -0.62 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.022 0.001 TYR B 249 PHE 0.018 0.001 PHE A 362 TRP 0.031 0.001 TRP A 585 HIS 0.002 0.000 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (10238) covalent geometry : angle 0.77395 / 0.33 (14072) hydrogen bonds : bond 0.05616 / 3.55 ( 584) hydrogen bonds : angle 5.00901 / 3.53 ( 1734) Misc. bond : bond 0.00376 / 0.18 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 168 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7569 (p) REVERT: B 180 TRP cc_start: 0.4757 (OUTLIER) cc_final: 0.4247 (t60) REVERT: B 215 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7699 (mt-10) REVERT: B 280 HIS cc_start: 0.7183 (t-90) cc_final: 0.6515 (t70) REVERT: B 425 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7797 (tm-30) REVERT: B 584 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7286 (tp) REVERT: B 587 ARG cc_start: 0.5886 (OUTLIER) cc_final: 0.5477 (mtt-85) REVERT: B 612 GLN cc_start: 0.7662 (mp-120) cc_final: 0.7140 (tm-30) REVERT: A 102 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7593 (tp) REVERT: A 180 TRP cc_start: 0.4749 (OUTLIER) cc_final: 0.4219 (t60) REVERT: A 189 LYS cc_start: 0.6278 (mttt) cc_final: 0.5703 (mmtp) REVERT: A 242 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6260 (ptt) REVERT: A 264 TRP cc_start: 0.6506 (t-100) cc_final: 0.6226 (t-100) REVERT: A 280 HIS cc_start: 0.7202 (t-90) cc_final: 0.6572 (t70) REVERT: A 425 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7802 (tm-30) REVERT: A 587 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5374 (mpt-90) REVERT: A 610 GLN cc_start: 0.7989 (mp10) cc_final: 0.7472 (pm20) REVERT: A 612 GLN cc_start: 0.7649 (mp-120) cc_final: 0.7148 (tm-30) outliers start: 45 outliers final: 28 residues processed: 168 average time/residue: 0.2874 time to fit residues: 54.1288 Evaluate side-chains 161 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 587 ARG Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 4.9990 chunk 17 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.6792 > 50:) chunk 20 optimal weight: 0.5980 chunk 69 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.184682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.150793 restraints weight = 12184.920| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.37 r_work: 0.3704 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10242 Z= 0.134 Angle : 0.782 28.165 14072 Z= 0.329 Chirality : 0.063 1.905 1622 Planarity : 0.004 0.042 1568 Dihedral : 14.914 176.525 2826 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.41 % Allowed : 22.06 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.25), residues: 1126 helix: 1.54 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.57 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 56 TYR 0.016 0.001 TYR B 249 PHE 0.015 0.001 PHE A 362 TRP 0.032 0.001 TRP A 585 HIS 0.002 0.000 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (10238) covalent geometry : angle 0.78200 / 0.33 (14072) hydrogen bonds : bond 0.05430 / 3.44 ( 584) hydrogen bonds : angle 4.96927 / 3.50 ( 1734) Misc. bond : bond 0.00368 / 0.18 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7887 (mmm160) REVERT: B 168 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7464 (p) REVERT: B 180 TRP cc_start: 0.4702 (OUTLIER) cc_final: 0.4167 (t60) REVERT: B 215 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 242 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6259 (ptt) REVERT: B 280 HIS cc_start: 0.7151 (t-90) cc_final: 0.6487 (t70) REVERT: B 425 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7715 (tm-30) REVERT: B 587 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.5467 (mtt-85) REVERT: B 610 GLN cc_start: 0.7953 (mp10) cc_final: 0.7423 (pm20) REVERT: B 612 GLN cc_start: 0.7669 (mp-120) cc_final: 0.7104 (tm-30) REVERT: A 102 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7546 (tp) REVERT: A 180 TRP cc_start: 0.4720 (OUTLIER) cc_final: 0.4153 (t60) REVERT: A 242 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6178 (ptt) REVERT: A 264 TRP cc_start: 0.6396 (t-100) cc_final: 0.6113 (t-100) REVERT: A 280 HIS cc_start: 0.7100 (t-90) cc_final: 0.6441 (t70) REVERT: A 349 ILE cc_start: 0.7945 (mt) cc_final: 0.7694 (mm) REVERT: A 425 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 587 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.5360 (mpt-90) REVERT: A 610 GLN cc_start: 0.8035 (mp10) cc_final: 0.7510 (pm20) REVERT: A 612 GLN cc_start: 0.7686 (mp-120) cc_final: 0.7191 (tm-30) outliers start: 42 outliers final: 22 residues processed: 160 average time/residue: 0.2882 time to fit residues: 52.2480 Evaluate side-chains 158 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 587 ARG Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.179910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145210 restraints weight = 12183.605| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.40 r_work: 0.3618 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10242 Z= 0.164 Angle : 0.820 28.008 14072 Z= 0.348 Chirality : 0.064 1.906 1622 Planarity : 0.005 0.066 1568 Dihedral : 14.894 177.274 2824 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.20 % Allowed : 22.90 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.25), residues: 1126 helix: 1.33 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -0.61 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.021 0.002 TYR B 249 PHE 0.018 0.002 PHE B 362 TRP 0.037 0.002 TRP A 585 HIS 0.003 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (10238) covalent geometry : angle 0.81981 / 0.35 (14072) hydrogen bonds : bond 0.06090 / 3.86 ( 584) hydrogen bonds : angle 5.10136 / 3.59 ( 1734) Misc. bond : bond 0.00414 / 0.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8065 (tp) REVERT: B 168 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7757 (p) REVERT: B 180 TRP cc_start: 0.4835 (OUTLIER) cc_final: 0.4348 (t60) REVERT: B 264 TRP cc_start: 0.7026 (t-100) cc_final: 0.6580 (m100) REVERT: B 280 HIS cc_start: 0.7470 (t-90) cc_final: 0.6802 (t70) REVERT: B 425 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8037 (tm-30) REVERT: B 587 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5872 (mtt-85) REVERT: B 610 GLN cc_start: 0.8136 (mp10) cc_final: 0.7608 (pm20) REVERT: B 612 GLN cc_start: 0.7741 (mp-120) cc_final: 0.7255 (tm-30) REVERT: A 102 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8083 (tp) REVERT: A 180 TRP cc_start: 0.4802 (OUTLIER) cc_final: 0.4294 (t60) REVERT: A 242 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6637 (ptt) REVERT: A 264 TRP cc_start: 0.6728 (t-100) cc_final: 0.6457 (t-100) REVERT: A 280 HIS cc_start: 0.7430 (t-90) cc_final: 0.6835 (t70) REVERT: A 349 ILE cc_start: 0.8375 (mt) cc_final: 0.8135 (mm) REVERT: A 425 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8021 (tm-30) REVERT: A 556 TRP cc_start: 0.5541 (m100) cc_final: 0.5155 (t-100) REVERT: A 587 ARG cc_start: 0.6320 (OUTLIER) cc_final: 0.5626 (mpt-90) REVERT: A 610 GLN cc_start: 0.8154 (mp10) cc_final: 0.7687 (pm20) REVERT: A 612 GLN cc_start: 0.7772 (mp-120) cc_final: 0.7314 (tm-30) outliers start: 40 outliers final: 24 residues processed: 160 average time/residue: 0.2915 time to fit residues: 52.3376 Evaluate side-chains 158 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 587 ARG Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.176671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141839 restraints weight = 12065.810| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.38 r_work: 0.3575 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10242 Z= 0.177 Angle : 0.826 28.041 14072 Z= 0.356 Chirality : 0.065 1.909 1622 Planarity : 0.005 0.059 1568 Dihedral : 14.905 177.066 2824 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.10 % Allowed : 22.69 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.25), residues: 1126 helix: 1.20 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -0.72 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.023 0.002 TYR B 367 PHE 0.019 0.002 PHE A 362 TRP 0.040 0.002 TRP A 585 HIS 0.003 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (10238) covalent geometry : angle 0.82575 / 0.36 (14072) hydrogen bonds : bond 0.06440 / 4.08 ( 584) hydrogen bonds : angle 5.19047 / 3.65 ( 1734) Misc. bond : bond 0.00436 / 0.20 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: B 102 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8193 (tp) REVERT: B 180 TRP cc_start: 0.4869 (OUTLIER) cc_final: 0.4351 (t60) REVERT: B 189 LYS cc_start: 0.6447 (mttt) cc_final: 0.5824 (mmtp) REVERT: B 215 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7708 (mp0) REVERT: B 236 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: B 264 TRP cc_start: 0.7098 (t-100) cc_final: 0.6638 (m100) REVERT: B 280 HIS cc_start: 0.7503 (t-90) cc_final: 0.6814 (t70) REVERT: B 382 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: B 425 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 519 LEU cc_start: 0.8738 (mt) cc_final: 0.8525 (mm) REVERT: B 587 ARG cc_start: 0.6328 (OUTLIER) cc_final: 0.5708 (mpt-90) REVERT: B 610 GLN cc_start: 0.8063 (mp10) cc_final: 0.7633 (pm20) REVERT: B 612 GLN cc_start: 0.7742 (mp-120) cc_final: 0.7270 (tm-30) REVERT: A 102 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8172 (tp) REVERT: A 180 TRP cc_start: 0.4841 (OUTLIER) cc_final: 0.4333 (t60) REVERT: A 189 LYS cc_start: 0.6467 (mttt) cc_final: 0.5836 (mmtp) REVERT: A 234 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: A 264 TRP cc_start: 0.6756 (t-100) cc_final: 0.6483 (t-100) REVERT: A 280 HIS cc_start: 0.7446 (t-90) cc_final: 0.6826 (t70) REVERT: A 382 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: A 425 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8026 (tm-30) REVERT: A 556 TRP cc_start: 0.5537 (m100) cc_final: 0.5139 (t-100) REVERT: A 566 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.5557 (mpp) REVERT: A 587 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5582 (mpt-90) REVERT: A 612 GLN cc_start: 0.7857 (mp-120) cc_final: 0.7374 (tm-30) outliers start: 39 outliers final: 24 residues processed: 156 average time/residue: 0.2703 time to fit residues: 47.3597 Evaluate side-chains 160 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 587 ARG Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.180816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.146400 restraints weight = 12179.369| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.40 r_work: 0.3628 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10242 Z= 0.142 Angle : 0.799 28.161 14072 Z= 0.339 Chirality : 0.063 1.901 1622 Planarity : 0.005 0.052 1568 Dihedral : 14.610 177.977 2824 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.78 % Allowed : 22.58 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.25), residues: 1126 helix: 1.41 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.74 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.019 0.002 TYR A 572 PHE 0.017 0.001 PHE B 362 TRP 0.039 0.001 TRP A 585 HIS 0.001 0.000 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (10238) covalent geometry : angle 0.79933 / 0.34 (14072) hydrogen bonds : bond 0.05739 / 3.64 ( 584) hydrogen bonds : angle 5.07046 / 3.57 ( 1734) Misc. bond : bond 0.00378 / 0.18 ( 4) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2215.64 seconds wall clock time: 38 minutes 22.02 seconds (2302.02 seconds total)