Starting phenix.real_space_refine on Thu Jul 2 08:52:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q2z_13786/07_2026/7q2z_13786.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q2z_13786/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7q2z_13786/07_2026/7q2z_13786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q2z_13786/07_2026/7q2z_13786.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q2z_13786/07_2026/7q2z_13786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q2z_13786/07_2026/7q2z_13786.map" } 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-dev-6108/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: 1.78, per 1000 atoms: 0.22 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: 0.68 Conformation dependent library (CDL) restraints added in 382.6 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: 0.92 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: 1.39 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: 11062 1.07 - 2.14: 413 2.14 - 3.21: 155 3.21 - 4.28: 19 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.090 ------------------------------------------------------------------------------- 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= 0.249 Angle : 0.530 5.347 11657 Z= 0.404 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 0.52991 / 0.40 (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 : 0.296 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: 0.6819 (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: 0.1208 time to fit residues: 27.6774 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 : 0.338 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.165474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.125437 restraints weight = 9485.515| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.36 r_work: 0.3100 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8488 Z= 0.160 Angle : 0.551 6.224 11657 Z= 0.307 Chirality : 0.039 0.256 1348 Planarity : 0.004 0.063 1325 Dihedral : 20.048 175.186 1516 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.70 % Favored : 97.18 % Rotamer: Outliers : 1.46 % Allowed : 7.05 % Favored : 91.49 % 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: -0.00 (0.28), residues: 888 helix: 0.93 (0.21), residues: 635 sheet: None (None), residues: 0 loop : -2.42 (0.34), residues: 253 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 0.007 0.001 TRP E 780 HIS 0.003 0.001 HIS E 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 8488) covalent geometry : angle 0.55132 / 0.31 (11657) hydrogen bonds : bond 0.04560 / 3.05 ( 468) hydrogen bonds : angle 3.41205 / 2.46 ( 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 112 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.307 Fit side-chains REVERT: E 23 LYS cc_start: 0.7166 (ttmm) cc_final: 0.6577 (mptt) REVERT: E 107 GLU cc_start: 0.7752 (mp0) cc_final: 0.7549 (mp0) REVERT: E 170 ARG cc_start: 0.8024 (ttm170) cc_final: 0.7366 (ttm170) REVERT: E 297 ARG cc_start: 0.8587 (tpt170) cc_final: 0.8223 (ttm-80) REVERT: E 312 ILE cc_start: 0.8854 (mm) cc_final: 0.8621 (mm) REVERT: E 466 ARG cc_start: 0.8390 (mtp85) cc_final: 0.7628 (mmm-85) REVERT: E 646 MET cc_start: 0.8098 (mmm) cc_final: 0.7829 (mmp) REVERT: E 894 ASP cc_start: 0.7262 (m-30) cc_final: 0.6850 (m-30) REVERT: C 482 LYS cc_start: 0.7501 (mtmm) cc_final: 0.6972 (ptpt) outliers start: 12 outliers final: 11 residues processed: 108 average time/residue: 0.1037 time to fit residues: 15.1270 Evaluate side-chains 100 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 0.9990 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.167892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.127332 restraints weight = 9454.771| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.34 r_work: 0.3077 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1925 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= 0.112 Angle : 0.461 5.678 11657 Z= 0.263 Chirality : 0.036 0.262 1348 Planarity : 0.003 0.057 1325 Dihedral : 19.998 176.163 1516 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.62 % Rotamer: Outliers : 1.34 % Allowed : 7.53 % 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: 0.76 (0.29), residues: 888 helix: 1.51 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.20 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 32 TYR 0.010 0.001 TYR E 657 PHE 0.012 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 0.00222 / 0.11 ( 8488) covalent geometry : angle 0.46104 / 0.26 (11657) hydrogen bonds : bond 0.03741 / 2.50 ( 468) hydrogen bonds : angle 3.17545 / 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 110 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.494 Fit side-chains REVERT: E 23 LYS cc_start: 0.7048 (ttmm) cc_final: 0.6464 (mptt) REVERT: E 170 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7383 (ttm170) REVERT: E 297 ARG cc_start: 0.8587 (tpt170) cc_final: 0.8305 (ttm-80) REVERT: E 312 ILE cc_start: 0.8885 (mm) cc_final: 0.8630 (mm) REVERT: E 466 ARG cc_start: 0.8429 (mtp85) cc_final: 0.7709 (mmm-85) REVERT: E 646 MET cc_start: 0.8151 (mmm) cc_final: 0.7907 (mmp) REVERT: E 688 LYS cc_start: 0.7772 (mtmt) cc_final: 0.7327 (mmtm) REVERT: E 691 TYR cc_start: 0.8558 (m-10) cc_final: 0.8290 (m-80) REVERT: E 894 ASP cc_start: 0.7223 (m-30) cc_final: 0.6939 (m-30) REVERT: C 482 LYS cc_start: 0.7534 (mtmm) cc_final: 0.7068 (ptpt) outliers start: 11 outliers final: 9 residues processed: 107 average time/residue: 0.1115 time to fit residues: 15.8983 Evaluate side-chains 102 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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: 0.9980 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 40.0000 chunk 92 optimal weight: 50.0000 chunk 89 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 49 optimal weight: 0.0470 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 overall best weight: 1.0880 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.164856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.124473 restraints weight = 9507.532| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.35 r_work: 0.3062 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8488 Z= 0.108 Angle : 0.454 6.407 11657 Z= 0.257 Chirality : 0.035 0.265 1348 Planarity : 0.003 0.053 1325 Dihedral : 19.949 176.578 1516 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.14 % Favored : 97.75 % Rotamer: Outliers : 1.70 % Allowed : 7.53 % Favored : 90.77 % 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: 1.18 (0.29), residues: 888 helix: 1.79 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.95 (0.36), 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 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 0.00215 / 0.11 ( 8488) covalent geometry : angle 0.45439 / 0.26 (11657) hydrogen bonds : bond 0.03517 / 2.35 ( 468) hydrogen bonds : angle 3.07370 / 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 116 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.228 Fit side-chains REVERT: E 23 LYS cc_start: 0.6839 (ttmm) cc_final: 0.6284 (mptt) REVERT: E 170 ARG cc_start: 0.8000 (ttm170) cc_final: 0.7367 (ttm170) REVERT: E 297 ARG cc_start: 0.8582 (tpt170) cc_final: 0.8331 (ttm-80) REVERT: E 312 ILE cc_start: 0.8912 (mm) cc_final: 0.8582 (mm) REVERT: E 344 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7317 (mt) REVERT: E 466 ARG cc_start: 0.8458 (mtp85) cc_final: 0.7723 (mmm-85) REVERT: E 641 MET cc_start: 0.8938 (mmt) cc_final: 0.8536 (mmt) REVERT: E 646 MET cc_start: 0.8235 (mmm) cc_final: 0.8017 (mmp) REVERT: E 691 TYR cc_start: 0.8606 (m-80) cc_final: 0.8375 (m-80) REVERT: E 823 LYS cc_start: 0.8316 (ptmt) cc_final: 0.8043 (ptmt) REVERT: E 894 ASP cc_start: 0.7440 (m-30) cc_final: 0.7232 (m-30) REVERT: C 482 LYS cc_start: 0.7567 (mtmm) cc_final: 0.7097 (ptpt) REVERT: C 510 THR cc_start: 0.8851 (m) cc_final: 0.8508 (m) outliers start: 14 outliers final: 11 residues processed: 110 average time/residue: 0.1098 time to fit residues: 16.0874 Evaluate side-chains 105 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 594 THR Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 838 ILE Chi-restraints excluded: chain C residue 494 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 77 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 91 optimal weight: 40.0000 chunk 86 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.164772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127149 restraints weight = 9451.890| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.33 r_work: 0.3154 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2307 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= 0.104 Angle : 0.449 5.668 11657 Z= 0.255 Chirality : 0.035 0.264 1348 Planarity : 0.003 0.053 1325 Dihedral : 19.884 176.825 1516 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.70 % Favored : 97.18 % Rotamer: Outliers : 1.58 % Allowed : 8.38 % Favored : 90.04 % 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: 1.45 (0.30), residues: 888 helix: 1.97 (0.21), residues: 639 sheet: None (None), residues: 0 loop : -1.85 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 322 TYR 0.010 0.001 TYR E 657 PHE 0.016 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 0.00202 / 0.10 ( 8488) covalent geometry : angle 0.44890 / 0.25 (11657) hydrogen bonds : bond 0.03371 / 2.24 ( 468) hydrogen bonds : angle 3.03802 / 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 105 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.194 Fit side-chains REVERT: E 23 LYS cc_start: 0.6737 (ttmm) cc_final: 0.6286 (mptt) REVERT: E 170 ARG cc_start: 0.7973 (ttm170) cc_final: 0.7360 (ttm170) REVERT: E 297 ARG cc_start: 0.8572 (tpt170) cc_final: 0.8326 (ttm-80) REVERT: E 322 ARG cc_start: 0.8078 (ptp-170) cc_final: 0.7686 (ptp90) REVERT: E 344 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7358 (mt) REVERT: E 466 ARG cc_start: 0.8458 (mtp85) cc_final: 0.7674 (mtm-85) REVERT: E 646 MET cc_start: 0.8182 (mmm) cc_final: 0.7976 (mmp) REVERT: E 691 TYR cc_start: 0.8618 (m-80) cc_final: 0.8394 (m-80) REVERT: E 823 LYS cc_start: 0.8322 (ptmt) cc_final: 0.8066 (ptmt) REVERT: E 879 ILE cc_start: 0.7816 (mm) cc_final: 0.7437 (mm) REVERT: E 894 ASP cc_start: 0.7065 (m-30) cc_final: 0.6786 (m-30) REVERT: C 482 LYS cc_start: 0.7616 (mtmm) cc_final: 0.7145 (ptpt) REVERT: C 510 THR cc_start: 0.8875 (m) cc_final: 0.8569 (m) outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.1058 time to fit residues: 14.4460 Evaluate side-chains 101 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 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 = 0.3834 r_free = 0.3834 target = 0.162737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124662 restraints weight = 9356.990| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.29 r_work: 0.3109 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2508 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= 0.118 Angle : 0.465 6.069 11657 Z= 0.261 Chirality : 0.036 0.266 1348 Planarity : 0.003 0.054 1325 Dihedral : 19.834 177.021 1516 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.25 % Favored : 97.64 % Rotamer: Outliers : 1.82 % Allowed : 9.36 % 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: 1.56 (0.30), residues: 888 helix: 2.03 (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 0.005 0.000 ARG E 32 TYR 0.010 0.001 TYR E 366 PHE 0.016 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 0.00251 / 0.12 ( 8488) covalent geometry : angle 0.46536 / 0.26 (11657) hydrogen bonds : bond 0.03727 / 2.50 ( 468) hydrogen bonds : angle 3.04917 / 2.21 ( 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 106 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.288 Fit side-chains REVERT: E 23 LYS cc_start: 0.6704 (ttmm) cc_final: 0.6231 (mptt) REVERT: E 170 ARG cc_start: 0.8040 (ttm170) cc_final: 0.7377 (ttm170) REVERT: E 297 ARG cc_start: 0.8553 (tpt170) cc_final: 0.8306 (ttm-80) REVERT: E 322 ARG cc_start: 0.8119 (ptp-170) cc_final: 0.7909 (ptp-170) REVERT: E 344 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7424 (mt) REVERT: E 379 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: E 466 ARG cc_start: 0.8432 (mtp85) cc_final: 0.7659 (mtm-85) REVERT: E 646 MET cc_start: 0.8163 (mmm) cc_final: 0.7961 (mmp) REVERT: E 823 LYS cc_start: 0.8298 (ptmt) cc_final: 0.8011 (ptmt) REVERT: E 894 ASP cc_start: 0.7065 (m-30) cc_final: 0.6764 (m-30) REVERT: C 397 ASN cc_start: 0.8326 (m110) cc_final: 0.8025 (m-40) REVERT: C 482 LYS cc_start: 0.7585 (mtmm) cc_final: 0.7086 (ptpt) outliers start: 15 outliers final: 11 residues processed: 103 average time/residue: 0.0925 time to fit residues: 12.8653 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 : 0.318 ------------------------------------------------------------------------------- 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 C residue 494 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 93 optimal weight: 40.0000 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.162282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.120695 restraints weight = 9470.645| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.34 r_work: 0.3032 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2774 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= 0.144 Angle : 0.503 6.162 11657 Z= 0.278 Chirality : 0.038 0.271 1348 Planarity : 0.004 0.051 1325 Dihedral : 19.803 177.603 1516 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.70 % Favored : 97.18 % Rotamer: Outliers : 1.70 % Allowed : 9.72 % Favored : 88.58 % 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: 1.50 (0.29), residues: 888 helix: 1.99 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -1.68 (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 0.004 0.001 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 8488) covalent geometry : angle 0.50320 / 0.28 (11657) hydrogen bonds : bond 0.04317 / 2.91 ( 468) hydrogen bonds : angle 3.11408 / 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 103 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.309 Fit side-chains REVERT: E 23 LYS cc_start: 0.6743 (ttmm) cc_final: 0.6175 (mptt) REVERT: E 170 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7492 (ttm170) REVERT: E 297 ARG cc_start: 0.8644 (tpt170) cc_final: 0.8380 (ttm-80) REVERT: E 344 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7420 (mt) REVERT: E 379 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: E 466 ARG cc_start: 0.8519 (mtp85) cc_final: 0.7752 (mtm-85) REVERT: E 823 LYS cc_start: 0.8380 (ptmt) cc_final: 0.8179 (ptmt) REVERT: E 879 ILE cc_start: 0.7786 (mm) cc_final: 0.7304 (mm) REVERT: E 894 ASP cc_start: 0.7148 (m-30) cc_final: 0.6840 (m-30) REVERT: C 397 ASN cc_start: 0.8427 (m110) cc_final: 0.8179 (m-40) REVERT: C 482 LYS cc_start: 0.7659 (mtmm) cc_final: 0.7133 (ptpt) outliers start: 14 outliers final: 10 residues processed: 100 average time/residue: 0.1040 time to fit residues: 13.9955 Evaluate side-chains 96 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 30 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.161788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120080 restraints weight = 9345.539| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.31 r_work: 0.3026 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8488 Z= 0.151 Angle : 0.504 6.182 11657 Z= 0.280 Chirality : 0.038 0.276 1348 Planarity : 0.004 0.051 1325 Dihedral : 19.836 177.765 1516 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.48 % Favored : 97.41 % Rotamer: Outliers : 1.58 % Allowed : 10.45 % Favored : 87.97 % 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: 1.43 (0.29), residues: 888 helix: 1.91 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -1.65 (0.37), residues: 251 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 0.016 0.001 PHE C 523 TRP 0.006 0.001 TRP E 351 HIS 0.003 0.001 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8488) covalent geometry : angle 0.50448 / 0.28 (11657) hydrogen bonds : bond 0.04402 / 2.96 ( 468) hydrogen bonds : angle 3.14196 / 2.28 ( 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 99 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.252 Fit side-chains REVERT: E 23 LYS cc_start: 0.6669 (ttmm) cc_final: 0.6114 (mptt) REVERT: E 170 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7537 (ttm170) REVERT: E 297 ARG cc_start: 0.8635 (tpt170) cc_final: 0.8360 (ttm-80) REVERT: E 344 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7459 (mt) REVERT: E 379 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: E 466 ARG cc_start: 0.8516 (mtp85) cc_final: 0.7753 (mtm-85) REVERT: E 879 ILE cc_start: 0.7902 (mm) cc_final: 0.7289 (mm) REVERT: E 894 ASP cc_start: 0.7383 (m-30) cc_final: 0.7043 (m-30) REVERT: C 397 ASN cc_start: 0.8421 (m110) cc_final: 0.8173 (m-40) REVERT: C 482 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7109 (ptpt) outliers start: 13 outliers final: 10 residues processed: 96 average time/residue: 0.1113 time to fit residues: 14.3056 Evaluate side-chains 96 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 614 THR Chi-restraints excluded: chain E residue 838 ILE Chi-restraints excluded: chain E residue 909 GLU Chi-restraints excluded: chain C residue 494 THR 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: 10.0000 chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.162517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120903 restraints weight = 9368.353| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.34 r_work: 0.3035 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8488 Z= 0.125 Angle : 0.477 6.102 11657 Z= 0.267 Chirality : 0.037 0.275 1348 Planarity : 0.003 0.051 1325 Dihedral : 19.835 178.239 1516 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.07 % Rotamer: Outliers : 1.58 % Allowed : 10.33 % Favored : 88.09 % 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: 1.60 (0.29), residues: 888 helix: 2.02 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -1.58 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 32 TYR 0.010 0.001 TYR E 657 PHE 0.016 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 0.00272 / 0.12 ( 8488) covalent geometry : angle 0.47704 / 0.27 (11657) hydrogen bonds : bond 0.03980 / 2.67 ( 468) hydrogen bonds : angle 3.09808 / 2.25 ( 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 99 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.248 Fit side-chains REVERT: E 23 LYS cc_start: 0.6787 (ttmm) cc_final: 0.6231 (mptt) REVERT: E 170 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7543 (ttm170) REVERT: E 297 ARG cc_start: 0.8622 (tpt170) cc_final: 0.8332 (ttm-80) REVERT: E 344 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7480 (mt) REVERT: E 379 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: E 466 ARG cc_start: 0.8481 (mtp85) cc_final: 0.7738 (mtm-85) REVERT: E 879 ILE cc_start: 0.7792 (mm) cc_final: 0.7342 (mm) REVERT: E 894 ASP cc_start: 0.7210 (m-30) cc_final: 0.6892 (m-30) REVERT: C 397 ASN cc_start: 0.8417 (m110) cc_final: 0.8165 (m-40) REVERT: C 482 LYS cc_start: 0.7712 (mtmm) cc_final: 0.7130 (ptpt) outliers start: 13 outliers final: 10 residues processed: 96 average time/residue: 0.0911 time to fit residues: 11.9394 Evaluate side-chains 96 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 335 GLN E 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.161752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120087 restraints weight = 9377.493| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.34 r_work: 0.3026 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3020 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= 0.138 Angle : 0.496 6.111 11657 Z= 0.276 Chirality : 0.037 0.276 1348 Planarity : 0.004 0.050 1325 Dihedral : 19.863 178.101 1516 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.48 % Favored : 97.41 % Rotamer: Outliers : 1.70 % Allowed : 10.45 % Favored : 87.85 % 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: 1.54 (0.29), residues: 888 helix: 1.97 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -1.61 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 32 TYR 0.011 0.001 TYR E 366 PHE 0.016 0.001 PHE C 523 TRP 0.006 0.001 TRP E 351 HIS 0.003 0.001 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8488) covalent geometry : angle 0.49614 / 0.28 (11657) hydrogen bonds : bond 0.04212 / 2.83 ( 468) hydrogen bonds : angle 3.11851 / 2.26 ( 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 98 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.298 Fit side-chains REVERT: E 23 LYS cc_start: 0.6798 (ttmm) cc_final: 0.6236 (mptt) REVERT: E 170 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7579 (ttm170) REVERT: E 297 ARG cc_start: 0.8635 (tpt170) cc_final: 0.8345 (ttm-80) REVERT: E 344 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7516 (mt) REVERT: E 379 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: E 466 ARG cc_start: 0.8504 (mtp85) cc_final: 0.7766 (mtm-85) REVERT: E 879 ILE cc_start: 0.7805 (mm) cc_final: 0.7203 (mm) REVERT: E 894 ASP cc_start: 0.7363 (m-30) cc_final: 0.7049 (m-30) REVERT: C 397 ASN cc_start: 0.8449 (m110) cc_final: 0.8201 (m-40) REVERT: C 482 LYS cc_start: 0.7724 (mtmm) cc_final: 0.7134 (ptpt) outliers start: 14 outliers final: 11 residues processed: 95 average time/residue: 0.0881 time to fit residues: 11.5532 Evaluate side-chains 97 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 344 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 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: 2.9990 chunk 75 optimal weight: 0.5980 chunk 57 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 40.0000 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.162209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120536 restraints weight = 9410.395| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.34 r_work: 0.3038 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8488 Z= 0.121 Angle : 0.475 6.064 11657 Z= 0.266 Chirality : 0.037 0.276 1348 Planarity : 0.003 0.050 1325 Dihedral : 19.862 178.384 1516 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.30 % Rotamer: Outliers : 1.58 % Allowed : 10.69 % 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: 1.69 (0.29), residues: 888 helix: 2.09 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -1.53 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 32 TYR 0.011 0.001 TYR E 657 PHE 0.016 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 0.00261 / 0.12 ( 8488) covalent geometry : angle 0.47453 / 0.27 (11657) hydrogen bonds : bond 0.03862 / 2.58 ( 468) hydrogen bonds : angle 3.08850 / 2.24 ( 1339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2107.19 seconds wall clock time: 36 minutes 40.68 seconds (2200.68 seconds total)