Starting phenix.real_space_refine on Wed Aug 5 19:20:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtj_36646/08_2026/8jtj_36646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtj_36646/08_2026/8jtj_36646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jtj_36646/08_2026/8jtj_36646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtj_36646/08_2026/8jtj_36646.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jtj_36646/08_2026/8jtj_36646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtj_36646/08_2026/8jtj_36646.map" } resolution = 3.08 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= 0.001 sd= 0.028 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 144 5.49 5 S 20 5.16 5 C 6812 2.51 5 N 2106 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11637 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8576 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 45, 'TRANS': 996} Chain breaks: 8 Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 2292 Classifications: {'RNA': 107} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 53, 'rna3p_pyr': 42} Link IDs: {'rna2p': 12, 'rna3p': 94} Chain: "C" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 579 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 1.92, per 1000 atoms: 0.16 Number of scatterers: 11637 At special positions: 0 Unit cell: (98.6, 116.45, 136, 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 20 16.00 P 144 15.00 O 2555 8.00 N 2106 7.00 C 6812 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: 0.80 Conformation dependent library (CDL) restraints added in 430.7 milliseconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1986 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 43.1% alpha, 10.4% beta 43 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 48 through 76 removed outlier: 3.975A pdb=" N ARG A 54 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 70 " --> pdb=" O ARG A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.735A pdb=" N ASP A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.211A pdb=" N GLU A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 112 through 124 removed outlier: 3.524A pdb=" N LEU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 124 " --> pdb=" O HIS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 Processing helix chain 'A' and resid 159 through 167 removed outlier: 3.610A pdb=" N VAL A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 205 removed outlier: 3.703A pdb=" N LEU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.677A pdb=" N ASN A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 removed outlier: 3.812A pdb=" N LYS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 removed outlier: 3.981A pdb=" N GLU A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASN A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.621A pdb=" N PHE A 292 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 336 through 351 removed outlier: 3.836A pdb=" N ILE A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 373 removed outlier: 3.879A pdb=" N PHE A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.803A pdb=" N HIS A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 423 through 434 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.633A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 removed outlier: 4.047A pdb=" N SER A 506 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 537 removed outlier: 3.877A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.748A pdb=" N GLN A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 4.369A pdb=" N LEU A 573 " --> pdb=" O GLU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 604 No H-bonds generated for 'chain 'A' and resid 604 through 604' Processing helix chain 'A' and resid 606 through 609 removed outlier: 4.310A pdb=" N GLY A 609 " --> pdb=" O ARG A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 609' Processing helix chain 'A' and resid 639 through 646 Processing helix chain 'A' and resid 651 through 664 Processing helix chain 'A' and resid 667 through 679 Processing helix chain 'A' and resid 696 through 707 removed outlier: 4.084A pdb=" N THR A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 718 No H-bonds generated for 'chain 'A' and resid 716 through 718' Processing helix chain 'A' and resid 719 through 729 Processing helix chain 'A' and resid 731 through 736 removed outlier: 3.918A pdb=" N ALA A 736 " --> pdb=" O PRO A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.513A pdb=" N GLN A 743 " --> pdb=" O ALA A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 removed outlier: 4.217A pdb=" N LYS A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 774 removed outlier: 3.505A pdb=" N ARG A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.573A pdb=" N SER A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 Processing helix chain 'A' and resid 845 through 849 Processing helix chain 'A' and resid 862 through 871 removed outlier: 3.732A pdb=" N ARG A 868 " --> pdb=" O TYR A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 882 removed outlier: 3.918A pdb=" N PHE A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 878 through 882' Processing helix chain 'A' and resid 945 through 950 removed outlier: 3.526A pdb=" N LYS A 950 " --> pdb=" O MET A 946 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 692 through 694 removed outlier: 6.789A pdb=" N ILE A 497 " --> pdb=" O TYR A 693 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 496 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 28 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASN A 20 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE A 26 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N SER A 804 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 31 " --> pdb=" O SER A 804 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 250 removed outlier: 5.848A pdb=" N LEU A 421 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 582 removed outlier: 4.635A pdb=" N ASP A 581 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 598 " --> pdb=" O ASP A 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 825 through 826 removed outlier: 3.685A pdb=" N LYS A 908 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 912 through 914 removed outlier: 4.021A pdb=" N THR A 919 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 937 through 944 removed outlier: 4.209A pdb=" N PHE A 978 " --> pdb=" O VAL A 931 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU A 933 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N PHE A 976 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1033 through 1038 removed outlier: 4.652A pdb=" N LEU A1023 " --> pdb=" O GLY A1036 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY A1022 " --> pdb=" O ILE A1016 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A1016 " --> pdb=" O GLY A1022 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU A1024 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 988 " --> pdb=" O VAL A1009 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A1011 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 985 " --> pdb=" O TYR A1048 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 995 through 998 306 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.17 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: 3057 1.34 - 1.45: 2873 1.45 - 1.57: 5912 1.57 - 1.69: 286 1.69 - 1.81: 35 Bond restraints: 12163 Sorted by residual: bond pdb=" C3' DC C 26 " pdb=" C2' DC C 26 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.35e+01 bond pdb=" C1' DT C 22 " pdb=" N1 DT C 22 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.16e+01 bond pdb=" C3' DT C 15 " pdb=" C2' DT C 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.64e+00 bond pdb=" C3' DG C 12 " pdb=" C2' DG C 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.74e+00 bond pdb=" C3' DC C 9 " pdb=" C2' DC C 9 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.68e+00 ... (remaining 12158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 16388 2.04 - 4.08: 640 4.08 - 6.12: 33 6.12 - 8.16: 5 8.16 - 10.21: 3 Bond angle restraints: 17069 Sorted by residual: angle pdb=" C1' C B 89 " pdb=" N1 C B 89 " pdb=" C2 C B 89 " ideal model delta sigma weight residual 118.80 125.16 -6.36 1.10e+00 8.26e-01 3.34e+01 angle pdb=" O4' DC C 14 " pdb=" C4' DC C 14 " pdb=" C3' DC C 14 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.51e+01 angle pdb=" O2 U B 101 " pdb=" C2 U B 101 " pdb=" N3 U B 101 " ideal model delta sigma weight residual 122.20 118.70 3.50 7.00e-01 2.04e+00 2.51e+01 angle pdb=" N1 U B 101 " pdb=" C2 U B 101 " pdb=" O2 U B 101 " ideal model delta sigma weight residual 122.80 126.20 -3.40 7.00e-01 2.04e+00 2.36e+01 angle pdb=" C1' U B 101 " pdb=" N1 U B 101 " pdb=" C2 U B 101 " ideal model delta sigma weight residual 117.70 123.09 -5.39 1.20e+00 6.94e-01 2.02e+01 ... (remaining 17064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 6971 35.32 - 70.64: 441 70.64 - 105.96: 51 105.96 - 141.28: 3 141.28 - 176.59: 2 Dihedral angle restraints: 7468 sinusoidal: 4405 harmonic: 3063 Sorted by residual: dihedral pdb=" O4' C B 89 " pdb=" C1' C B 89 " pdb=" N1 C B 89 " pdb=" C2 C B 89 " ideal model delta sinusoidal sigma weight residual -160.00 16.59 -176.59 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C B 92 " pdb=" C1' C B 92 " pdb=" N1 C B 92 " pdb=" C2 C B 92 " ideal model delta sinusoidal sigma weight residual -160.00 -45.13 -114.87 1 1.50e+01 4.44e-03 6.06e+01 dihedral pdb=" O4' U B 101 " pdb=" C1' U B 101 " pdb=" N1 U B 101 " pdb=" C2 U B 101 " ideal model delta sinusoidal sigma weight residual 232.00 157.37 74.63 1 1.70e+01 3.46e-03 2.44e+01 ... (remaining 7465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1404 0.043 - 0.086: 348 0.086 - 0.129: 107 0.129 - 0.172: 89 0.172 - 0.215: 2 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CA ASN A1020 " pdb=" N ASN A1020 " pdb=" C ASN A1020 " pdb=" CB ASN A1020 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C1' G B 69 " pdb=" O4' G B 69 " pdb=" C2' G B 69 " pdb=" N9 G B 69 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" C3' DG D 3 " pdb=" C4' DG D 3 " pdb=" O3' DG D 3 " pdb=" C2' DG D 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 1947 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 466 " 0.057 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO A 467 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 23 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO A 24 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 24 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 24 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 860 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO A 861 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 861 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 861 " -0.033 5.00e-02 4.00e+02 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 337 2.67 - 3.23: 10772 3.23 - 3.78: 18353 3.78 - 4.34: 24491 4.34 - 4.90: 37654 Nonbonded interactions: 91607 Sorted by model distance: nonbonded pdb=" OG SER A1018 " pdb=" OP2 DG D 5 " model vdw 2.112 3.040 nonbonded pdb=" O2' U B 68 " pdb=" N2 G B 69 " model vdw 2.178 3.120 nonbonded pdb=" OE2 GLU A 437 " pdb=" OG SER A 441 " model vdw 2.198 3.040 nonbonded pdb=" OG SER A 272 " pdb=" O TYR A 313 " model vdw 2.202 3.040 nonbonded pdb=" NH1 ARG A 59 " pdb=" OP2 G B 19 " model vdw 2.203 3.120 ... (remaining 91602 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: 1.450 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.400 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 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 0.048 12163 Z= 0.251 Angle : 0.753 10.206 17069 Z= 0.532 Chirality : 0.050 0.215 1950 Planarity : 0.005 0.087 1668 Dihedral : 20.096 176.595 5482 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.62 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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 (0.25), residues: 1024 helix: -0.16 (0.26), residues: 391 sheet: -0.70 (0.60), residues: 76 loop : -1.61 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 384 TYR 0.018 0.001 TYR A1013 PHE 0.009 0.001 PHE A 333 TRP 0.016 0.002 TRP A 221 HIS 0.004 0.001 HIS A 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.25 (12163) covalent geometry : angle 0.75263 / 0.53 (17069) hydrogen bonds : bond 0.18070 / 12.77 ( 412) hydrogen bonds : angle 6.02369 / 4.38 ( 1053) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.319 Fit side-chains REVERT: A 1 MET cc_start: 0.6965 (mpp) cc_final: 0.6672 (mpp) REVERT: A 148 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6880 (mm-30) REVERT: A 822 ARG cc_start: 0.7117 (tpt170) cc_final: 0.6773 (tpt170) REVERT: A 829 ARG cc_start: 0.6912 (tmt-80) cc_final: 0.6689 (tpt170) REVERT: A 890 LYS cc_start: 0.5843 (mmtt) cc_final: 0.4994 (mmmt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1172 time to fit residues: 18.1684 Evaluate side-chains 92 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN A 507 GLN A 834 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.183219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.139890 restraints weight = 16844.114| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.07 r_work: 0.3488 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 12163 Z= 0.314 Angle : 0.826 10.839 17069 Z= 0.446 Chirality : 0.054 0.360 1950 Planarity : 0.007 0.063 1668 Dihedral : 21.933 159.808 3234 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.59 % Allowed : 9.67 % Favored : 89.75 % Rotamer: Outliers : 1.18 % Allowed : 7.29 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.24), residues: 1024 helix: -0.50 (0.25), residues: 395 sheet: -1.25 (0.53), residues: 90 loop : -1.71 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 870 TYR 0.028 0.003 TYR A 981 PHE 0.026 0.002 PHE A1045 TRP 0.019 0.002 TRP A 221 HIS 0.018 0.003 HIS A1072 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.31 (12163) covalent geometry : angle 0.82570 / 0.45 (17069) hydrogen bonds : bond 0.07908 / 5.55 ( 412) hydrogen bonds : angle 4.84930 / 3.43 ( 1053) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8244 (mpp) cc_final: 0.7881 (mpp) REVERT: A 28 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6906 (m-30) REVERT: A 192 ARG cc_start: 0.8237 (mtp180) cc_final: 0.7928 (mtm180) REVERT: A 782 ILE cc_start: 0.5230 (mm) cc_final: 0.5017 (mm) REVERT: A 962 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8417 (mmtt) REVERT: A 1017 ASP cc_start: 0.6959 (t0) cc_final: 0.6559 (p0) REVERT: A 1062 GLU cc_start: 0.6272 (mm-30) cc_final: 0.6061 (mm-30) outliers start: 11 outliers final: 6 residues processed: 110 average time/residue: 0.1373 time to fit residues: 19.9989 Evaluate side-chains 102 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 950 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 84 optimal weight: 0.0970 chunk 100 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 ASN A 507 GLN A 955 ASN A 961 ASN ** A1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.187957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.144607 restraints weight = 16942.604| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.31 r_work: 0.3534 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12163 Z= 0.129 Angle : 0.608 7.722 17069 Z= 0.338 Chirality : 0.041 0.364 1950 Planarity : 0.004 0.055 1668 Dihedral : 21.860 163.166 3234 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.52 % Favored : 92.09 % Rotamer: Outliers : 2.14 % Allowed : 8.47 % Favored : 89.39 % 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: -1.39 (0.25), residues: 1024 helix: 0.11 (0.26), residues: 392 sheet: -1.33 (0.53), residues: 91 loop : -1.64 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 870 TYR 0.011 0.001 TYR A 491 PHE 0.012 0.001 PHE A 333 TRP 0.011 0.001 TRP A 763 HIS 0.007 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (12163) covalent geometry : angle 0.60833 / 0.34 (17069) hydrogen bonds : bond 0.05780 / 4.08 ( 412) hydrogen bonds : angle 4.47673 / 3.16 ( 1053) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8102 (mpp) cc_final: 0.7716 (mpp) REVERT: A 28 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6836 (m-30) REVERT: A 192 ARG cc_start: 0.8114 (mtp180) cc_final: 0.7781 (mtm180) REVERT: A 337 ASP cc_start: 0.7985 (t70) cc_final: 0.7509 (t0) REVERT: A 654 GLU cc_start: 0.7070 (tp30) cc_final: 0.6808 (tp30) REVERT: A 726 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7554 (mp) REVERT: A 870 ARG cc_start: 0.7588 (mmt180) cc_final: 0.7376 (mmt180) REVERT: A 962 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8243 (mmtt) REVERT: A 1062 GLU cc_start: 0.6107 (mm-30) cc_final: 0.5900 (mm-30) outliers start: 20 outliers final: 10 residues processed: 116 average time/residue: 0.1080 time to fit residues: 17.0047 Evaluate side-chains 111 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 961 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 74 optimal weight: 0.0870 chunk 25 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 ASN A 961 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.185969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.142612 restraints weight = 16884.293| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 3.22 r_work: 0.3508 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12163 Z= 0.155 Angle : 0.624 9.169 17069 Z= 0.340 Chirality : 0.043 0.375 1950 Planarity : 0.004 0.049 1668 Dihedral : 21.783 166.806 3234 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.08 % Favored : 90.53 % Rotamer: Outliers : 2.47 % Allowed : 10.29 % Favored : 87.25 % 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: -1.31 (0.25), residues: 1024 helix: 0.16 (0.26), residues: 394 sheet: -1.37 (0.53), residues: 93 loop : -1.58 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.014 0.001 TYR A 864 PHE 0.013 0.001 PHE A 333 TRP 0.009 0.001 TRP A 763 HIS 0.009 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (12163) covalent geometry : angle 0.62423 / 0.34 (17069) hydrogen bonds : bond 0.05728 / 4.07 ( 412) hydrogen bonds : angle 4.28755 / 3.02 ( 1053) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.353 Fit side-chains REVERT: A 1 MET cc_start: 0.8090 (mpp) cc_final: 0.7771 (mpp) REVERT: A 28 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6878 (m-30) REVERT: A 192 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7857 (mtm180) REVERT: A 337 ASP cc_start: 0.7911 (t70) cc_final: 0.7440 (t0) REVERT: A 491 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.5868 (p90) REVERT: A 654 GLU cc_start: 0.7042 (tp30) cc_final: 0.6795 (tp30) REVERT: A 685 GLU cc_start: 0.7916 (pm20) cc_final: 0.7394 (pm20) REVERT: A 726 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7511 (mp) REVERT: A 782 ILE cc_start: 0.4951 (mm) cc_final: 0.4733 (mm) REVERT: A 962 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8272 (mmtt) REVERT: A 1062 GLU cc_start: 0.6204 (mm-30) cc_final: 0.5996 (mm-30) outliers start: 23 outliers final: 13 residues processed: 111 average time/residue: 0.1169 time to fit residues: 17.7083 Evaluate side-chains 107 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 950 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.182791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.138852 restraints weight = 16839.044| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.07 r_work: 0.3456 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12163 Z= 0.209 Angle : 0.685 8.742 17069 Z= 0.371 Chirality : 0.047 0.401 1950 Planarity : 0.005 0.048 1668 Dihedral : 21.832 168.787 3234 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.69 % Favored : 91.02 % Rotamer: Outliers : 2.89 % Allowed : 12.65 % Favored : 84.46 % 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: -1.57 (0.25), residues: 1024 helix: -0.11 (0.25), residues: 393 sheet: -1.55 (0.52), residues: 100 loop : -1.66 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 868 TYR 0.015 0.002 TYR A 981 PHE 0.019 0.002 PHE A 333 TRP 0.008 0.002 TRP A 262 HIS 0.012 0.002 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 (12163) covalent geometry : angle 0.68494 / 0.37 (17069) hydrogen bonds : bond 0.06295 / 4.42 ( 412) hydrogen bonds : angle 4.45152 / 3.16 ( 1053) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.352 Fit side-chains REVERT: A 19 MET cc_start: 0.6397 (mmm) cc_final: 0.5944 (mmm) REVERT: A 28 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: A 192 ARG cc_start: 0.8343 (mtp180) cc_final: 0.8016 (mtm180) REVERT: A 337 ASP cc_start: 0.7969 (t70) cc_final: 0.7531 (t0) REVERT: A 491 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.6012 (p90) REVERT: A 654 GLU cc_start: 0.7023 (tp30) cc_final: 0.6792 (tp30) REVERT: A 726 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7522 (mp) REVERT: A 782 ILE cc_start: 0.5113 (mm) cc_final: 0.4875 (mm) REVERT: A 962 LYS cc_start: 0.8635 (mmtt) cc_final: 0.8294 (mmtt) outliers start: 27 outliers final: 16 residues processed: 113 average time/residue: 0.1193 time to fit residues: 18.3109 Evaluate side-chains 107 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 986 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 55 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 113 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.186891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.145292 restraints weight = 16792.514| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.27 r_work: 0.3490 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12163 Z= 0.123 Angle : 0.589 8.358 17069 Z= 0.325 Chirality : 0.041 0.393 1950 Planarity : 0.004 0.048 1668 Dihedral : 21.799 168.094 3234 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.62 % Favored : 91.99 % Rotamer: Outliers : 2.68 % Allowed : 13.61 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.26), residues: 1024 helix: 0.33 (0.26), residues: 392 sheet: -1.40 (0.53), residues: 93 loop : -1.54 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 512 TYR 0.011 0.001 TYR A 368 PHE 0.013 0.001 PHE A 658 TRP 0.012 0.001 TRP A 763 HIS 0.006 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (12163) covalent geometry : angle 0.58906 / 0.33 (17069) hydrogen bonds : bond 0.05195 / 3.66 ( 412) hydrogen bonds : angle 4.24504 / 3.00 ( 1053) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.216 Fit side-chains REVERT: A 19 MET cc_start: 0.6289 (mmm) cc_final: 0.6028 (mmm) REVERT: A 28 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6721 (m-30) REVERT: A 192 ARG cc_start: 0.8235 (mtp180) cc_final: 0.7931 (mtm180) REVERT: A 337 ASP cc_start: 0.7929 (t70) cc_final: 0.7492 (t0) REVERT: A 491 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.6108 (p90) REVERT: A 654 GLU cc_start: 0.6966 (tp30) cc_final: 0.6740 (tp30) REVERT: A 718 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8233 (tt) REVERT: A 726 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7411 (mp) REVERT: A 782 ILE cc_start: 0.5013 (mm) cc_final: 0.4786 (mm) REVERT: A 962 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8193 (mmtt) outliers start: 25 outliers final: 15 residues processed: 111 average time/residue: 0.1009 time to fit residues: 15.3311 Evaluate side-chains 107 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 950 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.184479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.141943 restraints weight = 16803.830| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.29 r_work: 0.3468 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12163 Z= 0.139 Angle : 0.604 8.915 17069 Z= 0.329 Chirality : 0.042 0.390 1950 Planarity : 0.004 0.047 1668 Dihedral : 21.751 169.853 3234 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.69 % Favored : 91.02 % Rotamer: Outliers : 2.68 % Allowed : 13.72 % Favored : 83.60 % 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: -1.11 (0.26), residues: 1024 helix: 0.40 (0.26), residues: 391 sheet: -1.38 (0.54), residues: 93 loop : -1.49 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.014 0.001 TYR A 864 PHE 0.012 0.001 PHE A 333 TRP 0.010 0.001 TRP A 763 HIS 0.007 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (12163) covalent geometry : angle 0.60432 / 0.33 (17069) hydrogen bonds : bond 0.05250 / 3.73 ( 412) hydrogen bonds : angle 4.21980 / 2.98 ( 1053) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.277 Fit side-chains REVERT: A 19 MET cc_start: 0.6460 (mmm) cc_final: 0.6255 (mmm) REVERT: A 28 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6746 (m-30) REVERT: A 192 ARG cc_start: 0.8211 (mtp180) cc_final: 0.7913 (mtm180) REVERT: A 337 ASP cc_start: 0.7945 (t70) cc_final: 0.7518 (t0) REVERT: A 491 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.6158 (p90) REVERT: A 654 GLU cc_start: 0.7010 (tp30) cc_final: 0.6766 (tp30) REVERT: A 718 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8215 (tt) REVERT: A 726 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7256 (mp) REVERT: A 782 ILE cc_start: 0.4988 (mm) cc_final: 0.4756 (mm) REVERT: A 818 GLU cc_start: 0.7955 (mp0) cc_final: 0.7755 (mp0) REVERT: A 962 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8257 (mmtt) REVERT: A 1072 HIS cc_start: 0.6350 (OUTLIER) cc_final: 0.5315 (t-90) outliers start: 25 outliers final: 16 residues processed: 110 average time/residue: 0.1129 time to fit residues: 16.6774 Evaluate side-chains 110 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1072 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 0.0060 chunk 92 optimal weight: 0.0970 chunk 46 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.187222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.145773 restraints weight = 16904.958| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.30 r_work: 0.3497 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12163 Z= 0.121 Angle : 0.581 9.585 17069 Z= 0.317 Chirality : 0.040 0.393 1950 Planarity : 0.004 0.048 1668 Dihedral : 21.739 169.693 3234 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.62 % Favored : 92.09 % Rotamer: Outliers : 2.57 % Allowed : 14.47 % Favored : 82.96 % 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: -0.98 (0.26), residues: 1024 helix: 0.57 (0.26), residues: 392 sheet: -1.35 (0.54), residues: 93 loop : -1.47 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 588 TYR 0.012 0.001 TYR A 864 PHE 0.010 0.001 PHE A 333 TRP 0.011 0.001 TRP A 763 HIS 0.006 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (12163) covalent geometry : angle 0.58147 / 0.32 (17069) hydrogen bonds : bond 0.04890 / 3.47 ( 412) hydrogen bonds : angle 4.11330 / 2.91 ( 1053) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.292 Fit side-chains REVERT: A 28 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6738 (m-30) REVERT: A 192 ARG cc_start: 0.8171 (mtp180) cc_final: 0.7877 (mtm180) REVERT: A 337 ASP cc_start: 0.7930 (t70) cc_final: 0.7501 (t0) REVERT: A 445 ARG cc_start: 0.7831 (ptp-170) cc_final: 0.7411 (ptp-170) REVERT: A 491 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.6135 (p90) REVERT: A 718 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8203 (tt) REVERT: A 726 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7080 (mp) REVERT: A 782 ILE cc_start: 0.4843 (mm) cc_final: 0.4624 (mm) REVERT: A 962 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8287 (mmtt) REVERT: A 1072 HIS cc_start: 0.6328 (OUTLIER) cc_final: 0.5256 (t-90) outliers start: 24 outliers final: 14 residues processed: 109 average time/residue: 0.1170 time to fit residues: 17.0619 Evaluate side-chains 104 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1072 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 90 optimal weight: 4.9990 chunk 111 optimal weight: 50.0000 chunk 23 optimal weight: 0.0670 chunk 13 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN A 834 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.185455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.143794 restraints weight = 16704.134| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 3.29 r_work: 0.3485 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12163 Z= 0.144 Angle : 0.612 10.261 17069 Z= 0.330 Chirality : 0.042 0.395 1950 Planarity : 0.004 0.047 1668 Dihedral : 21.714 171.135 3234 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.40 % Favored : 91.31 % Rotamer: Outliers : 2.36 % Allowed : 15.01 % Favored : 82.64 % 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: -0.99 (0.26), residues: 1024 helix: 0.56 (0.26), residues: 391 sheet: -1.36 (0.53), residues: 96 loop : -1.46 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 588 TYR 0.016 0.001 TYR A 974 PHE 0.012 0.001 PHE A 333 TRP 0.010 0.001 TRP A 763 HIS 0.007 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (12163) covalent geometry : angle 0.61220 / 0.33 (17069) hydrogen bonds : bond 0.05103 / 3.62 ( 412) hydrogen bonds : angle 4.11797 / 2.92 ( 1053) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.214 Fit side-chains REVERT: A 19 MET cc_start: 0.6195 (mmm) cc_final: 0.5769 (mmm) REVERT: A 28 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6757 (m-30) REVERT: A 192 ARG cc_start: 0.8214 (mtp180) cc_final: 0.7913 (mtm180) REVERT: A 337 ASP cc_start: 0.7929 (t70) cc_final: 0.7519 (t0) REVERT: A 491 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.6012 (p90) REVERT: A 718 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8211 (tt) REVERT: A 726 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.7048 (mp) REVERT: A 782 ILE cc_start: 0.4919 (mm) cc_final: 0.4706 (mm) REVERT: A 962 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8349 (mptt) REVERT: A 1072 HIS cc_start: 0.6403 (OUTLIER) cc_final: 0.5334 (t-90) outliers start: 22 outliers final: 15 residues processed: 102 average time/residue: 0.1128 time to fit residues: 15.3580 Evaluate side-chains 104 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 1072 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 HIS A 385 ASN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.186205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.143046 restraints weight = 16891.568| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.16 r_work: 0.3491 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12163 Z= 0.129 Angle : 0.602 9.808 17069 Z= 0.324 Chirality : 0.041 0.399 1950 Planarity : 0.004 0.047 1668 Dihedral : 21.724 171.077 3234 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.71 % Favored : 91.99 % Rotamer: Outliers : 2.47 % Allowed : 14.90 % Favored : 82.64 % 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: -0.95 (0.26), residues: 1024 helix: 0.60 (0.26), residues: 392 sheet: -1.34 (0.53), residues: 96 loop : -1.45 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 588 TYR 0.012 0.001 TYR A 864 PHE 0.011 0.001 PHE A 333 TRP 0.011 0.001 TRP A 763 HIS 0.006 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (12163) covalent geometry : angle 0.60222 / 0.32 (17069) hydrogen bonds : bond 0.04941 / 3.50 ( 412) hydrogen bonds : angle 4.09286 / 2.90 ( 1053) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.294 Fit side-chains REVERT: A 19 MET cc_start: 0.6209 (mmm) cc_final: 0.5787 (mmm) REVERT: A 28 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: A 192 ARG cc_start: 0.8192 (mtp180) cc_final: 0.7886 (mtm180) REVERT: A 337 ASP cc_start: 0.7919 (t70) cc_final: 0.7503 (t0) REVERT: A 491 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.5999 (p90) REVERT: A 726 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.6986 (mp) REVERT: A 782 ILE cc_start: 0.4834 (mm) cc_final: 0.4614 (mm) REVERT: A 802 PHE cc_start: 0.7277 (t80) cc_final: 0.7068 (t80) REVERT: A 962 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8332 (mptt) REVERT: A 1072 HIS cc_start: 0.6315 (OUTLIER) cc_final: 0.5318 (t-90) outliers start: 23 outliers final: 16 residues processed: 104 average time/residue: 0.1126 time to fit residues: 15.9057 Evaluate side-chains 104 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1072 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 55 optimal weight: 20.0000 chunk 111 optimal weight: 50.0000 chunk 13 optimal weight: 10.0000 chunk 104 optimal weight: 40.0000 chunk 58 optimal weight: 20.0000 chunk 71 optimal weight: 0.0170 chunk 110 optimal weight: 9.9990 chunk 114 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 5.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN A 389 GLN A 834 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.178977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.137985 restraints weight = 17079.467| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.26 r_work: 0.3407 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 12163 Z= 0.320 Angle : 0.840 10.719 17069 Z= 0.444 Chirality : 0.055 0.425 1950 Planarity : 0.007 0.052 1668 Dihedral : 21.908 172.387 3234 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.25 % Favored : 89.45 % Rotamer: Outliers : 2.47 % Allowed : 15.01 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.25), residues: 1024 helix: -0.29 (0.25), residues: 389 sheet: -1.24 (0.54), residues: 96 loop : -1.67 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 124 TYR 0.026 0.003 TYR A1012 PHE 0.027 0.002 PHE A 333 TRP 0.011 0.002 TRP A 221 HIS 0.015 0.002 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.32 (12163) covalent geometry : angle 0.84026 / 0.44 (17069) hydrogen bonds : bond 0.07547 / 5.28 ( 412) hydrogen bonds : angle 4.65657 / 3.31 ( 1053) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2494.88 seconds wall clock time: 43 minutes 16.48 seconds (2596.48 seconds total)