Starting phenix.real_space_refine on Fri Sep 11 05:33:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q2z_13786/09_2026/7q2z_13786.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q2z_13786/09_2026/7q2z_13786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q2z_13786/09_2026/7q2z_13786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q2z_13786/09_2026/7q2z_13786.map" model { file = "/net/cci-nas-00/data/ceres_data/7q2z_13786/09_2026/7q2z_13786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q2z_13786/09_2026/7q2z_13786.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 32 5.16 5 C 5130 2.51 5 N 1403 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8258 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 6543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6543 Classifications: {'peptide': 812} Link IDs: {'PTRANS': 19, 'TRANS': 792} Chain breaks: 4 Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 772 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "F" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 460 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "G" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 483 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Time building chain proxies: 1.73, per 1000 atoms: 0.21 Number of scatterers: 8258 At special positions: 0 Unit cell: (85.32, 109.08, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 46 15.00 O 1647 8.00 N 1403 7.00 C 5130 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=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 288.6 milliseconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1754 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 77.3% alpha, 0.0% beta 19 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'E' and resid 8 through 25 Processing helix chain 'E' and resid 32 through 49 Processing helix chain 'E' and resid 50 through 64 removed outlier: 3.839A pdb=" N PHE E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS E 64 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 99 removed outlier: 3.547A pdb=" N ILE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU E 92 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 123 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 130 through 145 Processing helix chain 'E' and resid 152 through 167 Processing helix chain 'E' and resid 171 through 183 Processing helix chain 'E' and resid 206 through 217 removed outlier: 3.972A pdb=" N GLN E 215 " --> pdb=" O VAL E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 229 removed outlier: 3.548A pdb=" N ARG E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 242 Processing helix chain 'E' and resid 243 through 246 Processing helix chain 'E' and resid 248 through 258 removed outlier: 3.645A pdb=" N VAL E 255 " --> pdb=" O ASN E 251 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 264 Processing helix chain 'E' and resid 265 through 269 Processing helix chain 'E' and resid 272 through 284 Processing helix chain 'E' and resid 288 through 301 removed outlier: 3.589A pdb=" N ARG E 292 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 311 through 318 Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.994A pdb=" N GLU E 331 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA E 332 " --> pdb=" O LYS E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 355 through 372 removed outlier: 3.577A pdb=" N ASN E 372 " --> pdb=" O TYR E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 381 removed outlier: 3.607A pdb=" N LEU E 378 " --> pdb=" O ILE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.563A pdb=" N GLU E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR E 395 " --> pdb=" O HIS E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 431 removed outlier: 4.090A pdb=" N ARG E 431 " --> pdb=" O ILE E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 452 removed outlier: 3.634A pdb=" N ARG E 440 " --> pdb=" O ASP E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 474 through 503 removed outlier: 4.091A pdb=" N PHE E 478 " --> pdb=" O ASN E 474 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL E 479 " --> pdb=" O GLU E 475 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS E 502 " --> pdb=" O GLU E 498 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE E 503 " --> pdb=" O GLN E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 587 removed outlier: 3.767A pdb=" N TYR E 584 " --> pdb=" O THR E 580 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET E 585 " --> pdb=" O ARG E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 606 removed outlier: 3.614A pdb=" N ALA E 600 " --> pdb=" O ASN E 596 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP E 604 " --> pdb=" O ALA E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 612 removed outlier: 4.052A pdb=" N ARG E 612 " --> pdb=" O THR E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 631 Processing helix chain 'E' and resid 633 through 640 removed outlier: 3.623A pdb=" N ALA E 637 " --> pdb=" O ASP E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 650 Processing helix chain 'E' and resid 652 through 670 Processing helix chain 'E' and resid 671 through 675 removed outlier: 3.991A pdb=" N VAL E 674 " --> pdb=" O GLY E 671 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL E 675 " --> pdb=" O ASN E 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 671 through 675' Processing helix chain 'E' and resid 682 through 696 removed outlier: 4.023A pdb=" N LEU E 686 " --> pdb=" O ASP E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 716 removed outlier: 3.527A pdb=" N ALA E 716 " --> pdb=" O LYS E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 733 removed outlier: 3.995A pdb=" N PHE E 725 " --> pdb=" O ASP E 721 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 739 removed outlier: 3.613A pdb=" N SER E 738 " --> pdb=" O PRO E 735 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER E 739 " --> pdb=" O ILE E 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 735 through 739' Processing helix chain 'E' and resid 740 through 758 removed outlier: 3.576A pdb=" N VAL E 744 " --> pdb=" O ASN E 740 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE E 749 " --> pdb=" O GLN E 745 " (cutoff:3.500A) Proline residue: E 752 - end of helix removed outlier: 4.121A pdb=" N HIS E 758 " --> pdb=" O TYR E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 785 removed outlier: 3.736A pdb=" N THR E 768 " --> pdb=" O ARG E 764 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA E 770 " --> pdb=" O SER E 766 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ASP E 771 " --> pdb=" O ARG E 767 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL E 778 " --> pdb=" O LEU E 774 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU E 779 " --> pdb=" O ARG E 775 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP E 781 " --> pdb=" O CYS E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 810 Processing helix chain 'E' and resid 811 through 815 removed outlier: 3.855A pdb=" N LEU E 815 " --> pdb=" O PRO E 812 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 824 removed outlier: 4.244A pdb=" N LYS E 823 " --> pdb=" O GLY E 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 827 through 839 removed outlier: 3.738A pdb=" N PHE E 831 " --> pdb=" O VAL E 827 " (cutoff:3.500A) Processing helix chain 'E' and resid 840 through 842 No H-bonds generated for 'chain 'E' and resid 840 through 842' Processing helix chain 'E' and resid 844 through 854 removed outlier: 3.901A pdb=" N LYS E 848 " --> pdb=" O LYS E 844 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN E 854 " --> pdb=" O MET E 850 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 882 Processing helix chain 'E' and resid 887 through 909 Processing helix chain 'C' and resid 388 through 398 Processing helix chain 'C' and resid 468 through 475 removed outlier: 4.004A pdb=" N ASP C 472 " --> pdb=" O ASP C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 491 removed outlier: 4.247A pdb=" N LYS C 491 " --> pdb=" O LYS C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 511 430 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2310 1.34 - 1.45: 1458 1.45 - 1.57: 4579 1.57 - 1.69: 91 1.69 - 1.81: 50 Bond restraints: 8488 Sorted by residual: bond pdb=" C3' DT F 1 " pdb=" C2' DT F 1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT F 9 " pdb=" C2' DT F 9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA G 15 " pdb=" C2' DA G 15 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.04e+00 bond pdb=" C3' DT F 6 " pdb=" C2' DT F 6 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.66e+00 bond pdb=" C3' DT F 3 " pdb=" C2' DT F 3 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.64e+00 ... (remaining 8483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 11061 1.07 - 2.14: 413 2.14 - 3.21: 155 3.21 - 4.28: 20 4.28 - 5.35: 8 Bond angle restraints: 11657 Sorted by residual: angle pdb=" N3 DT F 14 " pdb=" C4 DT F 14 " pdb=" O4 DT F 14 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT F 5 " pdb=" C4 DT F 5 " pdb=" O4 DT F 5 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT F 10 " pdb=" C4 DT F 10 " pdb=" O4 DT F 10 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT F 19 " pdb=" C4 DT F 19 " pdb=" O4 DT F 19 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT F 7 " pdb=" C4 DT F 7 " pdb=" O4 DT F 7 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 ... (remaining 11652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 4817 34.83 - 69.66: 279 69.66 - 104.48: 11 104.48 - 139.31: 0 139.31 - 174.14: 1 Dihedral angle restraints: 5108 sinusoidal: 2435 harmonic: 2673 Sorted by residual: dihedral pdb=" C4' DT F 3 " pdb=" C3' DT F 3 " pdb=" O3' DT F 3 " pdb=" P DT F 4 " ideal model delta sinusoidal sigma weight residual 220.00 45.86 174.14 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASP E 302 " pdb=" CB ASP E 302 " pdb=" CG ASP E 302 " pdb=" OD1 ASP E 302 " ideal model delta sinusoidal sigma weight residual -30.00 -86.83 56.83 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP E 286 " pdb=" CB ASP E 286 " pdb=" CG ASP E 286 " pdb=" OD1 ASP E 286 " ideal model delta sinusoidal sigma weight residual -30.00 -82.99 52.99 1 2.00e+01 2.50e-03 9.55e+00 ... (remaining 5105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 868 0.030 - 0.061: 345 0.061 - 0.091: 103 0.091 - 0.121: 31 0.121 - 0.152: 1 Chirality restraints: 1348 Sorted by residual: chirality pdb=" C3' DT F 3 " pdb=" C4' DT F 3 " pdb=" O3' DT F 3 " pdb=" C2' DT F 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" C4' DT F 13 " pdb=" C5' DT F 13 " pdb=" O4' DT F 13 " pdb=" C3' DT F 13 " both_signs ideal model delta sigma weight residual False -2.53 -2.41 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA PRO E 799 " pdb=" N PRO E 799 " pdb=" C PRO E 799 " pdb=" CB PRO E 799 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 1345 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 591 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO E 592 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 592 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 592 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 272 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO E 273 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 273 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 273 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA G 13 " -0.022 2.00e-02 2.50e+03 1.03e-02 2.91e+00 pdb=" N9 DA G 13 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA G 13 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA G 13 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA G 13 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA G 13 " -0.009 2.00e-02 2.50e+03 pdb=" N6 DA G 13 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA G 13 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA G 13 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA G 13 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DA G 13 " 0.007 2.00e-02 2.50e+03 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1291 2.76 - 3.30: 7672 3.30 - 3.83: 13540 3.83 - 4.37: 15544 4.37 - 4.90: 26188 Nonbonded interactions: 64235 Sorted by model distance: nonbonded pdb=" O SER E 601 " pdb=" OG1 THR E 605 " model vdw 2.227 3.040 nonbonded pdb=" O PRO E 383 " pdb=" OH TYR E 432 " model vdw 2.231 3.040 nonbonded pdb=" O ASP E 782 " pdb=" OG SER E 786 " model vdw 2.251 3.040 nonbonded pdb=" O ASP E 319 " pdb=" N SER E 321 " model vdw 2.283 3.120 nonbonded pdb=" OE1 GLN E 22 " pdb=" NE2 GLN E 25 " model vdw 2.306 3.120 ... (remaining 64230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.003 0.084 8488 Z= 0.250 Angle : 0.532 5.347 11657 Z= 0.406 Chirality : 0.036 0.152 1348 Planarity : 0.004 0.083 1325 Dihedral : 18.984 174.140 3354 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.53 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -1.44 (0.26), residues: 888 helix: -0.12 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.95 (0.31), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 775 TYR 0.009 0.001 TYR E 168 PHE 0.009 0.001 PHE E 360 TRP 0.012 0.001 TRP E 57 HIS 0.003 0.001 HIS E 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.25 ( 8488) covalent geometry : angle 0.53172 / 0.41 (11657) hydrogen bonds : bond 0.13334 / 8.79 ( 468) hydrogen bonds : angle 4.53375 / 3.21 ( 1339) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.246 Fit side-chains REVERT: E 23 LYS cc_start: 0.7039 (ttmm) cc_final: 0.6708 (mptt) REVERT: E 69 LYS cc_start: 0.7788 (ttmm) cc_final: 0.7530 (tttm) REVERT: E 312 ILE cc_start: 0.8625 (mm) cc_final: 0.8186 (mm) REVERT: E 434 TYR cc_start: 0.8136 (m-80) cc_final: 0.7042 (m-10) REVERT: E 466 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7048 (mmm-85) REVERT: E 488 ASP cc_start: 0.6882 (m-30) cc_final: 0.6598 (m-30) REVERT: E 697 ASN cc_start: 0.7293 (t0) cc_final: 0.7078 (t0) REVERT: E 838 ILE cc_start: 0.8424 (mt) cc_final: 0.8173 (pt) REVERT: E 894 ASP cc_start: 0.7045 (m-30) cc_final: 0.6820 (m-30) REVERT: C 482 LYS cc_start: 0.7247 (mtmm) cc_final: 0.6784 (pttp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1135 time to fit residues: 26.1967 Evaluate side-chains 98 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 305 ASN E 381 ASN E 391 HIS E 737 ASN C 489 ASN C 492 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.165250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.125151 restraints weight = 9485.482| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.36 r_work: 0.3074 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8488 Z= 0.155 Angle : 0.554 6.344 11657 Z= 0.308 Chirality : 0.040 0.266 1348 Planarity : 0.004 0.065 1325 Dihedral : 20.029 174.473 1516 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.30 % Rotamer: Outliers : 1.46 % Allowed : 7.17 % Favored : 91.37 % 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: -0.05 (0.28), residues: 888 helix: 0.89 (0.21), residues: 639 sheet: None (None), residues: 0 loop : -2.48 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 208 TYR 0.011 0.001 TYR E 366 PHE 0.024 0.002 PHE E 733 TRP 0.008 0.001 TRP E 780 HIS 0.003 0.001 HIS E 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 8488) covalent geometry : angle 0.55364 / 0.31 (11657) hydrogen bonds : bond 0.04649 / 3.11 ( 468) hydrogen bonds : angle 3.41743 / 2.47 ( 1339) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: E 23 LYS cc_start: 0.7094 (ttmm) cc_final: 0.6536 (mptt) REVERT: E 170 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7346 (ttm170) REVERT: E 297 ARG cc_start: 0.8601 (tpt170) cc_final: 0.8263 (ttm-80) REVERT: E 312 ILE cc_start: 0.8841 (mm) cc_final: 0.8603 (mm) REVERT: E 466 ARG cc_start: 0.8378 (mtp85) cc_final: 0.7614 (mmm-85) REVERT: E 646 MET cc_start: 0.8094 (mmm) cc_final: 0.7829 (mmp) REVERT: E 894 ASP cc_start: 0.7276 (m-30) cc_final: 0.6865 (m-30) outliers start: 12 outliers final: 11 residues processed: 109 average time/residue: 0.0947 time to fit residues: 13.8121 Evaluate side-chains 99 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 604 ASP Chi-restraints excluded: chain C residue 494 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 73 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.167408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126724 restraints weight = 9445.064| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.34 r_work: 0.3069 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8488 Z= 0.112 Angle : 0.467 5.787 11657 Z= 0.265 Chirality : 0.036 0.284 1348 Planarity : 0.003 0.057 1325 Dihedral : 19.949 175.700 1516 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.28 % Rotamer: Outliers : 1.46 % Allowed : 7.41 % Favored : 91.13 % 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: 0.80 (0.29), residues: 888 helix: 1.53 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.17 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 32 TYR 0.010 0.001 TYR E 366 PHE 0.012 0.001 PHE C 523 TRP 0.007 0.001 TRP E 780 HIS 0.002 0.001 HIS E 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 8488) covalent geometry : angle 0.46739 / 0.27 (11657) hydrogen bonds : bond 0.03826 / 2.55 ( 468) hydrogen bonds : angle 3.16990 / 2.30 ( 1339) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: E 23 LYS cc_start: 0.7073 (ttmm) cc_final: 0.6482 (mptt) REVERT: E 170 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7384 (ttm170) REVERT: E 297 ARG cc_start: 0.8594 (tpt170) cc_final: 0.8324 (ttm-80) REVERT: E 312 ILE cc_start: 0.8912 (mm) cc_final: 0.8644 (mm) REVERT: E 344 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7403 (mt) REVERT: E 466 ARG cc_start: 0.8420 (mtp85) cc_final: 0.7700 (mmm-85) REVERT: E 646 MET cc_start: 0.8201 (mmm) cc_final: 0.7963 (mmp) REVERT: E 688 LYS cc_start: 0.7772 (mtmt) cc_final: 0.7311 (mmtm) REVERT: E 691 TYR cc_start: 0.8598 (m-10) cc_final: 0.8359 (m-80) REVERT: E 823 LYS cc_start: 0.8321 (ptmt) cc_final: 0.8048 (ptmt) REVERT: E 894 ASP cc_start: 0.7343 (m-30) cc_final: 0.7073 (m-30) outliers start: 12 outliers final: 8 residues processed: 112 average time/residue: 0.1085 time to fit residues: 16.0650 Evaluate side-chains 105 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 838 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 8.9990 chunk 84 optimal weight: 0.3980 chunk 36 optimal weight: 0.0470 chunk 90 optimal weight: 40.0000 chunk 92 optimal weight: 50.0000 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 overall best weight: 1.2280 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.164043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126106 restraints weight = 9496.585| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.35 r_work: 0.3143 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8488 Z= 0.111 Angle : 0.468 7.521 11657 Z= 0.262 Chirality : 0.036 0.286 1348 Planarity : 0.003 0.054 1325 Dihedral : 19.905 175.835 1516 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % Rotamer: Outliers : 1.46 % Allowed : 8.38 % Favored : 90.16 % 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: 1.20 (0.29), residues: 888 helix: 1.81 (0.21), residues: 639 sheet: None (None), residues: 0 loop : -1.99 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 32 TYR 0.010 0.001 TYR E 366 PHE 0.019 0.001 PHE C 523 TRP 0.007 0.001 TRP E 780 HIS 0.003 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 8488) covalent geometry : angle 0.46758 / 0.26 (11657) hydrogen bonds : bond 0.03591 / 2.40 ( 468) hydrogen bonds : angle 3.06658 / 2.23 ( 1339) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.182 Fit side-chains REVERT: E 23 LYS cc_start: 0.6688 (ttmm) cc_final: 0.6223 (mptt) REVERT: E 170 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7398 (ttm170) REVERT: E 297 ARG cc_start: 0.8575 (tpt170) cc_final: 0.8322 (ttm-80) REVERT: E 312 ILE cc_start: 0.8960 (mm) cc_final: 0.8398 (mm) REVERT: E 322 ARG cc_start: 0.8089 (ptm160) cc_final: 0.7566 (ptp90) REVERT: E 344 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7343 (mt) REVERT: E 466 ARG cc_start: 0.8462 (mtp85) cc_final: 0.7683 (mtm-85) REVERT: E 641 MET cc_start: 0.8930 (mmt) cc_final: 0.8605 (mmt) REVERT: E 646 MET cc_start: 0.8141 (mmm) cc_final: 0.7940 (mmp) REVERT: E 691 TYR cc_start: 0.8624 (m-80) cc_final: 0.8402 (m-80) REVERT: E 823 LYS cc_start: 0.8327 (ptmt) cc_final: 0.8071 (ptmt) REVERT: E 894 ASP cc_start: 0.7490 (m-30) cc_final: 0.7273 (m-30) REVERT: C 482 LYS cc_start: 0.7613 (mtmm) cc_final: 0.7109 (ptpt) REVERT: C 510 THR cc_start: 0.8876 (m) cc_final: 0.8535 (m) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.0981 time to fit residues: 13.8463 Evaluate side-chains 100 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 838 ILE Chi-restraints excluded: chain E residue 909 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 77 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 91 optimal weight: 40.0000 chunk 86 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.163620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126309 restraints weight = 9428.162| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.30 r_work: 0.3117 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8488 Z= 0.109 Angle : 0.455 5.813 11657 Z= 0.257 Chirality : 0.036 0.287 1348 Planarity : 0.003 0.053 1325 Dihedral : 19.836 176.616 1516 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.30 % Rotamer: Outliers : 1.70 % Allowed : 9.48 % Favored : 88.82 % 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: 1.42 (0.29), residues: 888 helix: 1.95 (0.21), residues: 639 sheet: None (None), residues: 0 loop : -1.86 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 897 TYR 0.010 0.001 TYR E 657 PHE 0.015 0.001 PHE C 523 TRP 0.006 0.001 TRP E 780 HIS 0.003 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 8488) covalent geometry : angle 0.45478 / 0.26 (11657) hydrogen bonds : bond 0.03515 / 2.35 ( 468) hydrogen bonds : angle 3.05257 / 2.20 ( 1339) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.329 Fit side-chains REVERT: E 23 LYS cc_start: 0.6718 (ttmm) cc_final: 0.6259 (mptt) REVERT: E 170 ARG cc_start: 0.8025 (ttm170) cc_final: 0.7374 (ttm170) REVERT: E 297 ARG cc_start: 0.8560 (tpt170) cc_final: 0.8315 (ttm-80) REVERT: E 322 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7661 (ptp90) REVERT: E 344 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7384 (mt) REVERT: E 379 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: E 466 ARG cc_start: 0.8472 (mtp85) cc_final: 0.7701 (mtm-85) REVERT: E 646 MET cc_start: 0.8161 (mmm) cc_final: 0.7958 (mmp) REVERT: E 691 TYR cc_start: 0.8642 (m-80) cc_final: 0.8415 (m-80) REVERT: E 823 LYS cc_start: 0.8306 (ptmt) cc_final: 0.8025 (ptmt) REVERT: E 879 ILE cc_start: 0.7800 (mm) cc_final: 0.7428 (mm) REVERT: E 894 ASP cc_start: 0.7123 (m-30) cc_final: 0.6832 (m-30) REVERT: C 482 LYS cc_start: 0.7598 (mtmm) cc_final: 0.7078 (ptpt) REVERT: C 510 THR cc_start: 0.8919 (m) cc_final: 0.8644 (m) outliers start: 14 outliers final: 11 residues processed: 101 average time/residue: 0.0994 time to fit residues: 13.5439 Evaluate side-chains 98 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 838 ILE Chi-restraints excluded: chain E residue 909 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 44 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.161347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123457 restraints weight = 9337.861| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.31 r_work: 0.3086 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8488 Z= 0.127 Angle : 0.480 5.967 11657 Z= 0.268 Chirality : 0.037 0.291 1348 Planarity : 0.004 0.054 1325 Dihedral : 19.795 176.724 1516 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.14 % Favored : 97.75 % Rotamer: Outliers : 1.58 % Allowed : 9.72 % Favored : 88.70 % 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: 1.49 (0.29), residues: 888 helix: 1.97 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.72 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 32 TYR 0.011 0.001 TYR E 366 PHE 0.017 0.001 PHE C 523 TRP 0.005 0.001 TRP E 780 HIS 0.003 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8488) covalent geometry : angle 0.47984 / 0.27 (11657) hydrogen bonds : bond 0.03959 / 2.66 ( 468) hydrogen bonds : angle 3.08114 / 2.23 ( 1339) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.226 Fit side-chains REVERT: E 23 LYS cc_start: 0.6748 (ttmm) cc_final: 0.6204 (mptt) REVERT: E 170 ARG cc_start: 0.8100 (ttm170) cc_final: 0.7430 (ttm170) REVERT: E 297 ARG cc_start: 0.8592 (tpt170) cc_final: 0.8338 (ttm-80) REVERT: E 322 ARG cc_start: 0.8285 (ptm160) cc_final: 0.7924 (ptp-170) REVERT: E 379 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: E 466 ARG cc_start: 0.8480 (mtp85) cc_final: 0.7725 (mtm-85) REVERT: E 823 LYS cc_start: 0.8349 (ptmt) cc_final: 0.8137 (ptmt) REVERT: E 894 ASP cc_start: 0.7281 (m-30) cc_final: 0.6970 (m-30) REVERT: C 482 LYS cc_start: 0.7629 (mtmm) cc_final: 0.7102 (ptpt) outliers start: 13 outliers final: 9 residues processed: 99 average time/residue: 0.0982 time to fit residues: 13.2274 Evaluate side-chains 96 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 838 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 93 optimal weight: 50.0000 chunk 23 optimal weight: 0.1980 chunk 78 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.162457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120527 restraints weight = 9455.242| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.36 r_work: 0.3033 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8488 Z= 0.134 Angle : 0.491 8.236 11657 Z= 0.272 Chirality : 0.037 0.296 1348 Planarity : 0.004 0.049 1325 Dihedral : 19.772 177.675 1516 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.93 % Favored : 96.96 % Rotamer: Outliers : 1.70 % Allowed : 9.84 % Favored : 88.46 % 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: 1.53 (0.29), residues: 888 helix: 2.01 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -1.67 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 32 TYR 0.012 0.001 TYR E 366 PHE 0.015 0.001 PHE C 523 TRP 0.005 0.001 TRP E 780 HIS 0.003 0.001 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8488) covalent geometry : angle 0.49127 / 0.27 (11657) hydrogen bonds : bond 0.04118 / 2.77 ( 468) hydrogen bonds : angle 3.11404 / 2.26 ( 1339) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.287 Fit side-chains REVERT: E 23 LYS cc_start: 0.6702 (ttmm) cc_final: 0.6143 (mptt) REVERT: E 44 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7312 (mmtm) REVERT: E 170 ARG cc_start: 0.8179 (ttm170) cc_final: 0.7512 (ttm170) REVERT: E 297 ARG cc_start: 0.8647 (tpt170) cc_final: 0.8384 (ttm-80) REVERT: E 322 ARG cc_start: 0.8337 (ptm160) cc_final: 0.8071 (ptp-170) REVERT: E 379 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: E 466 ARG cc_start: 0.8531 (mtp85) cc_final: 0.7759 (mtm-85) REVERT: E 823 LYS cc_start: 0.8383 (ptmt) cc_final: 0.8179 (ptmt) REVERT: E 894 ASP cc_start: 0.7411 (m-30) cc_final: 0.7109 (m-30) REVERT: C 397 ASN cc_start: 0.8404 (m110) cc_final: 0.8144 (m-40) REVERT: C 482 LYS cc_start: 0.7726 (mtmm) cc_final: 0.7087 (ptpt) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.1063 time to fit residues: 14.4482 Evaluate side-chains 95 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 838 ILE Chi-restraints excluded: chain C residue 494 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.157901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116448 restraints weight = 9356.590| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.30 r_work: 0.2978 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8488 Z= 0.239 Angle : 0.607 6.745 11657 Z= 0.327 Chirality : 0.042 0.306 1348 Planarity : 0.005 0.051 1325 Dihedral : 19.947 177.606 1516 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 1.46 % Allowed : 11.06 % Favored : 87.48 % 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: 1.03 (0.29), residues: 888 helix: 1.60 (0.21), residues: 639 sheet: None (None), residues: 0 loop : -1.80 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 252 TYR 0.015 0.002 TYR E 366 PHE 0.018 0.002 PHE E 382 TRP 0.012 0.002 TRP E 351 HIS 0.006 0.001 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.24 ( 8488) covalent geometry : angle 0.60720 / 0.33 (11657) hydrogen bonds : bond 0.05734 / 3.87 ( 468) hydrogen bonds : angle 3.33761 / 2.42 ( 1339) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.216 Fit side-chains REVERT: E 23 LYS cc_start: 0.6927 (ttmm) cc_final: 0.6334 (mptt) REVERT: E 170 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7691 (ttm170) REVERT: E 297 ARG cc_start: 0.8665 (tpt170) cc_final: 0.8349 (ttm-80) REVERT: E 322 ARG cc_start: 0.8380 (ptm160) cc_final: 0.8143 (ptp-170) REVERT: E 379 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: E 466 ARG cc_start: 0.8506 (mtp85) cc_final: 0.7778 (mtm-85) REVERT: E 468 MET cc_start: 0.9003 (ttt) cc_final: 0.8771 (ttp) REVERT: E 894 ASP cc_start: 0.7432 (m-30) cc_final: 0.7100 (m-30) REVERT: C 397 ASN cc_start: 0.8439 (m110) cc_final: 0.8180 (m-40) REVERT: C 482 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7116 (ptpt) outliers start: 12 outliers final: 11 residues processed: 96 average time/residue: 0.0902 time to fit residues: 11.7455 Evaluate side-chains 97 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 381 ASN Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 838 ILE Chi-restraints excluded: chain C residue 509 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 90 optimal weight: 40.0000 chunk 8 optimal weight: 4.9990 chunk 83 optimal weight: 0.0270 chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7840 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.161870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120443 restraints weight = 9349.666| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.32 r_work: 0.3031 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8488 Z= 0.109 Angle : 0.476 6.183 11657 Z= 0.268 Chirality : 0.036 0.293 1348 Planarity : 0.004 0.049 1325 Dihedral : 19.843 177.717 1516 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 1.22 % Allowed : 11.06 % Favored : 87.73 % 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: 1.53 (0.29), residues: 888 helix: 1.97 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -1.61 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 32 TYR 0.010 0.001 TYR E 657 PHE 0.034 0.001 PHE E 382 TRP 0.007 0.001 TRP E 780 HIS 0.003 0.000 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.11 ( 8488) covalent geometry : angle 0.47631 / 0.27 (11657) hydrogen bonds : bond 0.03902 / 2.62 ( 468) hydrogen bonds : angle 3.13287 / 2.28 ( 1339) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.298 Fit side-chains REVERT: E 23 LYS cc_start: 0.6768 (ttmm) cc_final: 0.6229 (mptt) REVERT: E 170 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7644 (ttm-80) REVERT: E 297 ARG cc_start: 0.8626 (tpt170) cc_final: 0.8332 (ttm-80) REVERT: E 322 ARG cc_start: 0.8319 (ptm160) cc_final: 0.8091 (ptp-170) REVERT: E 377 MET cc_start: 0.8202 (ttm) cc_final: 0.7917 (ttt) REVERT: E 379 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: E 466 ARG cc_start: 0.8472 (mtp85) cc_final: 0.7734 (mtm-85) REVERT: E 879 ILE cc_start: 0.7817 (mm) cc_final: 0.7320 (mm) REVERT: E 894 ASP cc_start: 0.7390 (m-30) cc_final: 0.7072 (m-30) REVERT: C 482 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7101 (ptpt) outliers start: 10 outliers final: 9 residues processed: 95 average time/residue: 0.0960 time to fit residues: 12.5767 Evaluate side-chains 94 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 381 ASN Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 838 ILE Chi-restraints excluded: chain C residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 0.0270 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.2644 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.162256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120656 restraints weight = 9387.586| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.34 r_work: 0.3038 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8488 Z= 0.112 Angle : 0.464 5.971 11657 Z= 0.261 Chirality : 0.036 0.292 1348 Planarity : 0.003 0.049 1325 Dihedral : 19.847 177.626 1516 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.25 % Favored : 97.64 % Rotamer: Outliers : 0.97 % Allowed : 11.54 % Favored : 87.48 % 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: 1.72 (0.29), residues: 888 helix: 2.10 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -1.50 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 32 TYR 0.011 0.001 TYR E 657 PHE 0.017 0.001 PHE C 523 TRP 0.007 0.001 TRP E 780 HIS 0.003 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 8488) covalent geometry : angle 0.46421 / 0.26 (11657) hydrogen bonds : bond 0.03746 / 2.50 ( 468) hydrogen bonds : angle 3.07295 / 2.23 ( 1339) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.289 Fit side-chains REVERT: E 23 LYS cc_start: 0.6771 (ttmm) cc_final: 0.6199 (mptt) REVERT: E 170 ARG cc_start: 0.8208 (ttm170) cc_final: 0.7636 (ttm-80) REVERT: E 297 ARG cc_start: 0.8576 (tpt170) cc_final: 0.8304 (ttm-80) REVERT: E 322 ARG cc_start: 0.8364 (ptm160) cc_final: 0.8139 (ptp-170) REVERT: E 379 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: E 466 ARG cc_start: 0.8494 (mtp85) cc_final: 0.7764 (mtm-85) REVERT: E 879 ILE cc_start: 0.7779 (mm) cc_final: 0.7290 (mm) REVERT: E 894 ASP cc_start: 0.7214 (m-30) cc_final: 0.6901 (m-30) REVERT: C 397 ASN cc_start: 0.8378 (m110) cc_final: 0.8157 (m-40) REVERT: C 482 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7113 (ptpt) outliers start: 8 outliers final: 6 residues processed: 92 average time/residue: 0.0942 time to fit residues: 11.7660 Evaluate side-chains 90 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain C residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 90 optimal weight: 40.0000 chunk 15 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 9 optimal weight: 0.2980 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.159200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117777 restraints weight = 9419.732| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.32 r_work: 0.2999 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8488 Z= 0.170 Angle : 0.536 7.215 11657 Z= 0.292 Chirality : 0.039 0.299 1348 Planarity : 0.004 0.050 1325 Dihedral : 19.911 177.636 1516 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Rotamer: Outliers : 0.73 % Allowed : 11.66 % Favored : 87.61 % 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: 1.42 (0.29), residues: 888 helix: 1.86 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.59 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 32 TYR 0.014 0.002 TYR E 366 PHE 0.016 0.002 PHE C 523 TRP 0.008 0.001 TRP E 351 HIS 0.004 0.001 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 8488) covalent geometry : angle 0.53644 / 0.29 (11657) hydrogen bonds : bond 0.04820 / 3.25 ( 468) hydrogen bonds : angle 3.20127 / 2.33 ( 1339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2008.76 seconds wall clock time: 34 minutes 59.11 seconds (2099.11 seconds total)