Starting phenix.real_space_refine on Fri Jul 3 01:27:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtj_36646/07_2026/8jtj_36646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtj_36646/07_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_36646/07_2026/8jtj_36646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtj_36646/07_2026/8jtj_36646.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jtj_36646/07_2026/8jtj_36646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtj_36646/07_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): 0.00s 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: 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: 2.12, per 1000 atoms: 0.18 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: 0.70 Conformation dependent library (CDL) restraints added in 375.7 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: 1.15 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: 2.45 Time building geometry restraints manager: 0.97 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: 16643 2.04 - 4.08: 385 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: 1518 0.043 - 0.086: 334 0.086 - 0.129: 88 0.129 - 0.172: 8 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 2.46 2.28 0.18 2.00e-01 2.50e+01 8.26e-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: 0.960 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 10.860 Find NCS groups from input model: 0.030 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.220 ------------------------------------------------------------------------------- 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= 0.246 Angle : 0.680 10.206 17069 Z= 0.464 Chirality : 0.040 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 0.00332 / 0.25 (12163) covalent geometry : angle 0.68026 / 0.46 (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 : 0.214 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: 0.6879 (mm-30) REVERT: A 829 ARG cc_start: 0.6912 (tmt-80) cc_final: 0.6687 (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: 0.1257 time to fit residues: 19.4763 Evaluate side-chains 91 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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: 10.0000 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: 4.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.183340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.141348 restraints weight = 16878.226| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 3.24 r_work: 0.3464 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 12163 Z= 0.297 Angle : 0.793 11.013 17069 Z= 0.440 Chirality : 0.051 0.345 1950 Planarity : 0.007 0.062 1668 Dihedral : 21.977 160.849 3234 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.77 % Favored : 89.75 % Rotamer: Outliers : 1.29 % Allowed : 7.18 % 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: -0.49 (0.25), residues: 395 sheet: -1.21 (0.54), residues: 90 loop : -1.72 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 870 TYR 0.030 0.003 TYR A 981 PHE 0.028 0.002 PHE A1045 TRP 0.019 0.003 TRP A 221 HIS 0.017 0.003 HIS A1072 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.30 (12163) covalent geometry : angle 0.79298 / 0.44 (17069) hydrogen bonds : bond 0.07737 / 5.43 ( 412) hydrogen bonds : angle 4.80563 / 3.39 ( 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 116 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8222 (mpp) cc_final: 0.7865 (mpp) REVERT: A 28 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6918 (m-30) REVERT: A 192 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7926 (mtm180) REVERT: A 654 GLU cc_start: 0.7019 (tp30) cc_final: 0.6755 (tp30) REVERT: A 782 ILE cc_start: 0.5233 (mm) cc_final: 0.5020 (mm) REVERT: A 962 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8420 (mmtt) REVERT: A 1017 ASP cc_start: 0.6958 (t0) cc_final: 0.6594 (p0) REVERT: A 1062 GLU cc_start: 0.6261 (mm-30) cc_final: 0.6052 (mm-30) outliers start: 12 outliers final: 7 residues processed: 113 average time/residue: 0.1323 time to fit residues: 19.7578 Evaluate side-chains 103 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 941 VAL 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: 0.9980 chunk 75 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 ASN A 955 ASN A 961 ASN ** A1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.186596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.143031 restraints weight = 16948.301| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.30 r_work: 0.3514 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12163 Z= 0.138 Angle : 0.606 8.444 17069 Z= 0.339 Chirality : 0.042 0.345 1950 Planarity : 0.004 0.057 1668 Dihedral : 21.934 165.685 3234 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.71 % Favored : 91.89 % Rotamer: Outliers : 2.25 % Allowed : 8.68 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.25), residues: 1024 helix: 0.08 (0.26), residues: 393 sheet: -1.35 (0.54), residues: 91 loop : -1.66 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 870 TYR 0.011 0.001 TYR A 864 PHE 0.013 0.001 PHE A 333 TRP 0.011 0.001 TRP A 763 HIS 0.008 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (12163) covalent geometry : angle 0.60573 / 0.34 (17069) hydrogen bonds : bond 0.05743 / 4.06 ( 412) hydrogen bonds : angle 4.47024 / 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 125 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.360 Fit side-chains REVERT: A 1 MET cc_start: 0.8131 (mpp) cc_final: 0.7794 (mpp) REVERT: A 28 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6871 (m-30) REVERT: A 192 ARG cc_start: 0.8162 (mtp180) cc_final: 0.7842 (mtm180) REVERT: A 337 ASP cc_start: 0.7966 (t70) cc_final: 0.7494 (t0) REVERT: A 491 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.5822 (p90) REVERT: A 654 GLU cc_start: 0.7038 (tp30) cc_final: 0.6801 (tp30) REVERT: A 726 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7538 (mp) REVERT: A 782 ILE cc_start: 0.4992 (mm) cc_final: 0.4765 (mm) REVERT: A 962 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8303 (mmtt) REVERT: A 1062 GLU cc_start: 0.6139 (mm-30) cc_final: 0.5906 (mm-30) outliers start: 21 outliers final: 10 residues processed: 118 average time/residue: 0.1247 time to fit residues: 19.6527 Evaluate side-chains 106 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 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 791 ASP Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 949 MET 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: 2.9990 chunk 77 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 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: 0.8980 chunk 70 optimal weight: 0.0970 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.186640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.143141 restraints weight = 16905.886| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.08 r_work: 0.3514 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12163 Z= 0.147 Angle : 0.604 9.408 17069 Z= 0.334 Chirality : 0.042 0.347 1950 Planarity : 0.004 0.050 1668 Dihedral : 21.864 168.280 3234 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.59 % Favored : 91.02 % Rotamer: Outliers : 2.79 % Allowed : 10.08 % Favored : 87.14 % 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: -1.36 (0.25), residues: 1024 helix: 0.15 (0.26), residues: 394 sheet: -1.48 (0.51), residues: 100 loop : -1.62 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1035 TYR 0.014 0.001 TYR A 586 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 0.00304 / 0.15 (12163) covalent geometry : angle 0.60362 / 0.33 (17069) hydrogen bonds : bond 0.05514 / 3.91 ( 412) hydrogen bonds : angle 4.31992 / 3.06 ( 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 118 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.219 Fit side-chains REVERT: A 1 MET cc_start: 0.8103 (mpp) cc_final: 0.7784 (mpp) REVERT: A 28 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6883 (m-30) REVERT: A 192 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7850 (mtm180) REVERT: A 337 ASP cc_start: 0.7923 (t70) cc_final: 0.7489 (t0) REVERT: A 491 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.5826 (p90) REVERT: A 654 GLU cc_start: 0.7042 (tp30) cc_final: 0.6811 (tp30) REVERT: A 726 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7507 (mp) REVERT: A 782 ILE cc_start: 0.4996 (mm) cc_final: 0.4775 (mm) REVERT: A 962 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8287 (mmtt) outliers start: 26 outliers final: 13 residues processed: 111 average time/residue: 0.1018 time to fit residues: 15.3692 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 : 0.335 ------------------------------------------------------------------------------- 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 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 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 950 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 ASN A 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.183660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.139722 restraints weight = 16837.349| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 3.01 r_work: 0.3470 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12163 Z= 0.188 Angle : 0.640 8.553 17069 Z= 0.355 Chirality : 0.044 0.369 1950 Planarity : 0.005 0.047 1668 Dihedral : 21.885 170.247 3234 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.20 % Favored : 91.41 % Rotamer: Outliers : 3.22 % Allowed : 12.00 % Favored : 84.78 % 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: -1.47 (0.25), residues: 1024 helix: 0.02 (0.26), residues: 392 sheet: -1.53 (0.52), residues: 100 loop : -1.64 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1035 TYR 0.017 0.002 TYR A 864 PHE 0.016 0.001 PHE A 333 TRP 0.008 0.001 TRP A 763 HIS 0.011 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (12163) covalent geometry : angle 0.64022 / 0.36 (17069) hydrogen bonds : bond 0.05907 / 4.19 ( 412) hydrogen bonds : angle 4.33951 / 3.08 ( 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 122 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.251 Fit side-chains REVERT: A 19 MET cc_start: 0.6373 (mmm) cc_final: 0.5991 (mmm) REVERT: A 28 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6786 (m-30) REVERT: A 192 ARG cc_start: 0.8323 (mtp180) cc_final: 0.8004 (mtm180) REVERT: A 337 ASP cc_start: 0.7957 (t70) cc_final: 0.7520 (t0) REVERT: A 491 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.6021 (p90) REVERT: A 654 GLU cc_start: 0.7015 (tp30) cc_final: 0.6765 (tp30) REVERT: A 726 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7544 (mp) REVERT: A 782 ILE cc_start: 0.5101 (mm) cc_final: 0.4872 (mm) REVERT: A 962 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8272 (mmtt) outliers start: 30 outliers final: 17 residues processed: 116 average time/residue: 0.1312 time to fit residues: 20.4320 Evaluate side-chains 106 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 334 LEU 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 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 965 SER 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: 0.7980 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 16 optimal weight: 0.0170 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.186651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.143496 restraints weight = 16810.701| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.13 r_work: 0.3516 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12163 Z= 0.123 Angle : 0.574 8.092 17069 Z= 0.320 Chirality : 0.040 0.362 1950 Planarity : 0.004 0.048 1668 Dihedral : 21.872 169.671 3234 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.81 % Favored : 91.80 % Rotamer: Outliers : 2.36 % Allowed : 13.40 % Favored : 84.24 % 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 (0.26), residues: 1024 helix: 0.37 (0.26), residues: 394 sheet: -1.45 (0.52), residues: 98 loop : -1.56 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.011 0.001 TYR A 864 PHE 0.011 0.001 PHE A 658 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 0.00239 / 0.12 (12163) covalent geometry : angle 0.57424 / 0.32 (17069) hydrogen bonds : bond 0.05044 / 3.57 ( 412) hydrogen bonds : angle 4.20145 / 2.98 ( 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 115 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.402 Fit side-chains REVERT: A 1 MET cc_start: 0.8050 (mpp) cc_final: 0.7850 (mpp) REVERT: A 19 MET cc_start: 0.6337 (mmm) cc_final: 0.6084 (mmm) REVERT: A 28 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6790 (m-30) REVERT: A 192 ARG cc_start: 0.8195 (mtp180) cc_final: 0.7894 (mtm180) REVERT: A 337 ASP cc_start: 0.7938 (t70) cc_final: 0.7499 (t0) REVERT: A 445 ARG cc_start: 0.7807 (ptp-170) cc_final: 0.7494 (ptp-170) REVERT: A 491 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.6032 (p90) REVERT: A 654 GLU cc_start: 0.6958 (tp30) cc_final: 0.6724 (tp30) REVERT: A 726 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7231 (mp) REVERT: A 782 ILE cc_start: 0.4983 (mm) cc_final: 0.4755 (mm) REVERT: A 962 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8181 (mmtt) REVERT: A 1072 HIS cc_start: 0.6238 (OUTLIER) cc_final: 0.5166 (t-90) outliers start: 22 outliers final: 12 residues processed: 108 average time/residue: 0.1300 time to fit residues: 18.9037 Evaluate side-chains 105 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 438 VAL 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 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 1072 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.0030 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 10.9990 chunk 59 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 0.0570 overall best weight: 1.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.186134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.144208 restraints weight = 16866.614| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 3.30 r_work: 0.3497 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12163 Z= 0.130 Angle : 0.574 8.650 17069 Z= 0.318 Chirality : 0.040 0.358 1950 Planarity : 0.004 0.047 1668 Dihedral : 21.830 171.109 3234 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.01 % Favored : 91.70 % Rotamer: Outliers : 3.11 % Allowed : 14.04 % Favored : 82.85 % 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: -1.04 (0.26), residues: 1024 helix: 0.53 (0.26), residues: 391 sheet: -1.42 (0.51), residues: 100 loop : -1.49 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 131 TYR 0.012 0.001 TYR A 668 PHE 0.011 0.001 PHE A 333 TRP 0.009 0.001 TRP A 763 HIS 0.007 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (12163) covalent geometry : angle 0.57367 / 0.32 (17069) hydrogen bonds : bond 0.04987 / 3.56 ( 412) hydrogen bonds : angle 4.13317 / 2.93 ( 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 121 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8060 (mpp) cc_final: 0.7555 (mpp) REVERT: A 28 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6790 (m-30) REVERT: A 192 ARG cc_start: 0.8191 (mtp180) cc_final: 0.7897 (mtm180) REVERT: A 337 ASP cc_start: 0.7952 (t70) cc_final: 0.7518 (t0) REVERT: A 491 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.5899 (p90) REVERT: A 654 GLU cc_start: 0.7009 (tp30) cc_final: 0.6749 (tp30) REVERT: A 726 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7139 (mp) REVERT: A 782 ILE cc_start: 0.4953 (mm) cc_final: 0.4726 (mm) REVERT: A 818 GLU cc_start: 0.7922 (mp0) cc_final: 0.7718 (mp0) REVERT: A 962 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8245 (mmtt) REVERT: A 1072 HIS cc_start: 0.6320 (OUTLIER) cc_final: 0.5275 (t-90) outliers start: 29 outliers final: 17 residues processed: 114 average time/residue: 0.1348 time to fit residues: 20.9463 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 : 0.371 ------------------------------------------------------------------------------- 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 185 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 438 VAL 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 726 ILE Chi-restraints excluded: chain A residue 733 SER 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 949 MET 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: 6.9990 chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 103 optimal weight: 0.0770 chunk 65 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 HIS A 385 ASN A 389 GLN ** A1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.181956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.141366 restraints weight = 17032.140| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.20 r_work: 0.3469 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12163 Z= 0.200 Angle : 0.653 9.449 17069 Z= 0.359 Chirality : 0.044 0.375 1950 Planarity : 0.005 0.047 1668 Dihedral : 21.857 172.404 3234 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.98 % Favored : 90.72 % Rotamer: Outliers : 3.11 % Allowed : 14.36 % 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: -1.28 (0.25), residues: 1024 helix: 0.21 (0.26), residues: 390 sheet: -1.44 (0.53), residues: 95 loop : -1.55 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 588 TYR 0.021 0.002 TYR A1012 PHE 0.017 0.002 PHE A 333 TRP 0.007 0.001 TRP A 967 HIS 0.010 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (12163) covalent geometry : angle 0.65295 / 0.36 (17069) hydrogen bonds : bond 0.05870 / 4.14 ( 412) hydrogen bonds : angle 4.28529 / 3.05 ( 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 120 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.392 Fit side-chains REVERT: A 28 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6759 (m-30) REVERT: A 192 ARG cc_start: 0.8230 (mtp180) cc_final: 0.7961 (mtm180) REVERT: A 337 ASP cc_start: 0.7896 (t70) cc_final: 0.7495 (t0) REVERT: A 445 ARG cc_start: 0.7886 (ptp-170) cc_final: 0.7454 (ptp-170) REVERT: A 491 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.6195 (p90) REVERT: A 726 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7256 (mp) REVERT: A 782 ILE cc_start: 0.5173 (mm) cc_final: 0.4931 (mm) REVERT: A 1072 HIS cc_start: 0.6421 (OUTLIER) cc_final: 0.5389 (t-90) outliers start: 29 outliers final: 20 residues processed: 113 average time/residue: 0.1447 time to fit residues: 21.8830 Evaluate side-chains 110 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 162 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 438 VAL 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 496 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 733 SER 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 941 VAL Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 965 SER 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: 7.9990 chunk 111 optimal weight: 40.0000 chunk 23 optimal weight: 0.0050 chunk 13 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 overall best weight: 2.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 HIS A 385 ASN ** A1020 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 = 0.4299 r_free = 0.4299 target = 0.181562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140753 restraints weight = 16819.157| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.08 r_work: 0.3474 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12163 Z= 0.198 Angle : 0.672 12.153 17069 Z= 0.366 Chirality : 0.044 0.379 1950 Planarity : 0.005 0.068 1668 Dihedral : 21.897 172.771 3234 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.69 % Favored : 91.02 % Rotamer: Outliers : 2.68 % Allowed : 14.79 % 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: -1.33 (0.25), residues: 1024 helix: 0.16 (0.26), residues: 388 sheet: -1.36 (0.54), residues: 94 loop : -1.59 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 588 TYR 0.016 0.002 TYR A 974 PHE 0.014 0.001 PHE A 333 TRP 0.008 0.001 TRP A 262 HIS 0.010 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (12163) covalent geometry : angle 0.67167 / 0.37 (17069) hydrogen bonds : bond 0.05715 / 4.04 ( 412) hydrogen bonds : angle 4.35251 / 3.09 ( 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 112 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.380 Fit side-chains REVERT: A 19 MET cc_start: 0.6240 (mmm) cc_final: 0.5783 (mmm) REVERT: A 28 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6723 (m-30) REVERT: A 192 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7950 (mtm180) REVERT: A 491 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.6315 (p90) REVERT: A 726 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7164 (mp) REVERT: A 782 ILE cc_start: 0.5253 (mm) cc_final: 0.5003 (mm) REVERT: A 1072 HIS cc_start: 0.6259 (OUTLIER) cc_final: 0.5412 (t-90) outliers start: 25 outliers final: 19 residues processed: 105 average time/residue: 0.1413 time to fit residues: 19.9626 Evaluate side-chains 107 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 162 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 438 VAL 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 496 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 733 SER 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 941 VAL Chi-restraints excluded: chain A residue 949 MET 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: 5.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 HIS A 385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.182605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.141619 restraints weight = 17114.099| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 3.20 r_work: 0.3468 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12163 Z= 0.185 Angle : 0.665 10.805 17069 Z= 0.361 Chirality : 0.044 0.374 1950 Planarity : 0.005 0.067 1668 Dihedral : 21.898 173.479 3234 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.47 % Favored : 90.23 % Rotamer: Outliers : 2.68 % Allowed : 15.11 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.26), residues: 1024 helix: 0.16 (0.26), residues: 389 sheet: -1.34 (0.54), residues: 94 loop : -1.54 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 588 TYR 0.015 0.002 TYR A 864 PHE 0.016 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 0.00403 / 0.19 (12163) covalent geometry : angle 0.66507 / 0.36 (17069) hydrogen bonds : bond 0.05651 / 3.99 ( 412) hydrogen bonds : angle 4.35253 / 3.09 ( 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 110 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.375 Fit side-chains REVERT: A 19 MET cc_start: 0.6281 (mmm) cc_final: 0.5797 (mmm) REVERT: A 28 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6706 (m-30) REVERT: A 192 ARG cc_start: 0.8218 (mtp180) cc_final: 0.7947 (mtm180) REVERT: A 491 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.6327 (p90) REVERT: A 726 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.7149 (mp) REVERT: A 782 ILE cc_start: 0.5272 (mm) cc_final: 0.5023 (mm) REVERT: A 1072 HIS cc_start: 0.6402 (OUTLIER) cc_final: 0.5563 (t-90) outliers start: 25 outliers final: 19 residues processed: 103 average time/residue: 0.1548 time to fit residues: 21.0391 Evaluate side-chains 108 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 185 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 438 VAL 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 496 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 733 SER 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 941 VAL Chi-restraints excluded: chain A residue 949 MET 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 55 optimal weight: 20.0000 chunk 111 optimal weight: 40.0000 chunk 13 optimal weight: 9.9990 chunk 104 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 71 optimal weight: 0.3980 chunk 110 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 chunk 4 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS A 385 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.177190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.135739 restraints weight = 17164.438| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.48 r_work: 0.3377 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 12163 Z= 0.353 Angle : 0.853 12.223 17069 Z= 0.461 Chirality : 0.054 0.391 1950 Planarity : 0.007 0.066 1668 Dihedral : 22.085 174.741 3234 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.35 % Favored : 89.36 % Rotamer: Outliers : 2.68 % Allowed : 15.43 % Favored : 81.89 % 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: -1.89 (0.25), residues: 1024 helix: -0.50 (0.25), residues: 389 sheet: -1.46 (0.50), residues: 108 loop : -1.79 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 588 TYR 0.023 0.003 TYR A1012 PHE 0.027 0.003 PHE A 333 TRP 0.011 0.002 TRP A 221 HIS 0.016 0.003 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00790 / 0.35 (12163) covalent geometry : angle 0.85293 / 0.46 (17069) hydrogen bonds : bond 0.07819 / 5.49 ( 412) hydrogen bonds : angle 4.84494 / 3.44 ( 1053) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2816.01 seconds wall clock time: 48 minutes 56.41 seconds (2936.41 seconds total)