Starting phenix.real_space_refine on Sat Aug 23 10:11:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtj_36646/08_2025/8jtj_36646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtj_36646/08_2025/8jtj_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_2025/8jtj_36646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtj_36646/08_2025/8jtj_36646.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jtj_36646/08_2025/8jtj_36646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtj_36646/08_2025/8jtj_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-2.0-5787/lib/python3.9/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: 2.90, per 1000 atoms: 0.25 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: 1.05 Conformation dependent library (CDL) restraints added in 429.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.62 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: 2.85 Time building geometry restraints manager: 1.38 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=" C GLU A 756 " pdb=" O GLU A 756 " ideal model delta sigma weight residual 1.235 1.227 0.008 4.70e-03 4.53e+04 2.65e+00 bond pdb=" CA ASN A1020 " pdb=" CB ASN A1020 " ideal model delta sigma weight residual 1.532 1.556 -0.024 1.51e-02 4.39e+03 2.63e+00 bond pdb=" CB ILE A 468 " pdb=" CG2 ILE A 468 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.37e+00 bond pdb=" C VAL A 473 " pdb=" N MET A 474 " ideal model delta sigma weight residual 1.334 1.348 -0.014 1.20e-02 6.94e+03 1.33e+00 bond pdb=" C LEU A 430 " pdb=" N PRO A 431 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.31e+00 ... (remaining 12158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 16677 2.04 - 4.08: 351 4.08 - 6.12: 33 6.12 - 8.16: 5 8.16 - 10.21: 3 Bond angle restraints: 17069 Sorted by residual: angle pdb=" C ARG A 611 " pdb=" N ILE A 612 " pdb=" CA ILE A 612 " ideal model delta sigma weight residual 122.13 128.48 -6.35 1.85e+00 2.92e-01 1.18e+01 angle pdb=" CA ARG A 992 " pdb=" CB ARG A 992 " pdb=" CG ARG A 992 " ideal model delta sigma weight residual 114.10 120.76 -6.66 2.00e+00 2.50e-01 1.11e+01 angle pdb=" CA ASN A1020 " pdb=" CB ASN A1020 " pdb=" CG ASN A1020 " ideal model delta sigma weight residual 112.60 115.72 -3.12 1.00e+00 1.00e+00 9.76e+00 angle pdb=" N VAL A 727 " pdb=" CA VAL A 727 " pdb=" C VAL A 727 " ideal model delta sigma weight residual 112.35 107.98 4.37 1.41e+00 5.03e-01 9.60e+00 angle pdb=" C ALA A1019 " pdb=" N ASN A1020 " pdb=" CA ASN A1020 " ideal model delta sigma weight residual 122.61 127.43 -4.82 1.56e+00 4.11e-01 9.53e+00 ... (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: 1542 0.043 - 0.086: 320 0.086 - 0.129: 81 0.129 - 0.172: 5 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=" CA ASN A 786 " pdb=" N ASN A 786 " pdb=" C ASN A 786 " pdb=" CB ASN A 786 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.41e-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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.980 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 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 0.039 12163 Z= 0.134 Angle : 0.658 10.206 17069 Z= 0.342 Chirality : 0.038 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 aren 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 covalent geometry : bond 0.00281 (12163) covalent geometry : angle 0.65815 (17069) hydrogen bonds : bond 0.18070 ( 412) hydrogen bonds : angle 6.02369 ( 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 : 0.382 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: 0.6688 (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: 0.1613 time to fit residues: 24.8167 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 : 0.400 ------------------------------------------------------------------------------- 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: 5.9990 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... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 834 GLN A 955 ASN A 961 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.180842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.138011 restraints weight = 16861.862| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.35 r_work: 0.3439 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 12163 Z= 0.326 Angle : 0.828 9.933 17069 Z= 0.435 Chirality : 0.049 0.206 1950 Planarity : 0.007 0.064 1668 Dihedral : 22.054 165.697 3234 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.59 % Allowed : 9.47 % Favored : 89.94 % Rotamer: Outliers : 1.39 % Allowed : 7.72 % Favored : 90.89 % 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 aren not related in a simple way. whole: -1.73 (0.25), residues: 1024 helix: -0.39 (0.25), residues: 391 sheet: -1.22 (0.53), residues: 94 loop : -1.72 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 32 TYR 0.027 0.003 TYR A 864 PHE 0.025 0.002 PHE A 333 TRP 0.020 0.002 TRP A 221 HIS 0.014 0.003 HIS A1028 Details of bonding type rmsd covalent geometry : bond 0.00720 (12163) covalent geometry : angle 0.82813 (17069) hydrogen bonds : bond 0.07349 ( 412) hydrogen bonds : angle 4.80270 ( 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 122 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: A 192 ARG cc_start: 0.8314 (mtp180) cc_final: 0.8014 (mtm180) REVERT: A 232 ASP cc_start: 0.8213 (m-30) cc_final: 0.7996 (m-30) REVERT: A 337 ASP cc_start: 0.8028 (t70) cc_final: 0.7472 (t0) REVERT: A 726 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7607 (mp) REVERT: A 782 ILE cc_start: 0.5482 (mm) cc_final: 0.5262 (mm) REVERT: A 890 LYS cc_start: 0.6535 (mmtt) cc_final: 0.5914 (mmtt) REVERT: A 962 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8452 (mmtt) outliers start: 13 outliers final: 7 residues processed: 119 average time/residue: 0.1760 time to fit residues: 27.1134 Evaluate side-chains 106 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 726 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 Chi-restraints excluded: chain A residue 961 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 84 optimal weight: 0.0770 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.183947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.140605 restraints weight = 16906.861| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.91 r_work: 0.3494 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 12163 Z= 0.189 Angle : 0.663 7.685 17069 Z= 0.352 Chirality : 0.042 0.197 1950 Planarity : 0.005 0.052 1668 Dihedral : 21.872 166.635 3234 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.40 % Favored : 91.21 % Rotamer: Outliers : 3.11 % Allowed : 9.97 % Favored : 86.92 % 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 aren not related in a simple way. whole: -1.58 (0.25), residues: 1024 helix: -0.18 (0.26), residues: 391 sheet: -1.39 (0.52), residues: 98 loop : -1.65 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 870 TYR 0.016 0.002 TYR A 864 PHE 0.017 0.001 PHE A 333 TRP 0.012 0.001 TRP A 763 HIS 0.010 0.001 HIS A 816 Details of bonding type rmsd covalent geometry : bond 0.00423 (12163) covalent geometry : angle 0.66332 (17069) hydrogen bonds : bond 0.05511 ( 412) hydrogen bonds : angle 4.44118 ( 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 129 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.415 Fit side-chains REVERT: A 28 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: A 192 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7837 (mtm180) REVERT: A 337 ASP cc_start: 0.7986 (t70) cc_final: 0.7467 (t0) REVERT: A 491 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.6150 (p90) REVERT: A 726 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7631 (mp) REVERT: A 782 ILE cc_start: 0.5272 (mm) cc_final: 0.5034 (mm) REVERT: A 890 LYS cc_start: 0.6531 (mmtt) cc_final: 0.5918 (mmtt) REVERT: A 962 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8508 (mmtt) outliers start: 29 outliers final: 16 residues processed: 121 average time/residue: 0.1570 time to fit residues: 25.0246 Evaluate side-chains 110 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP 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 376 ASP 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 907 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 Chi-restraints excluded: chain A residue 965 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 385 ASN A 961 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.181077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.139907 restraints weight = 17130.841| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.18 r_work: 0.3442 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12163 Z= 0.222 Angle : 0.701 8.596 17069 Z= 0.368 Chirality : 0.043 0.197 1950 Planarity : 0.005 0.057 1668 Dihedral : 21.915 169.332 3234 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.86 % Favored : 89.84 % Rotamer: Outliers : 3.54 % Allowed : 11.90 % Favored : 84.57 % 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 aren not related in a simple way. whole: -1.54 (0.25), residues: 1024 helix: -0.13 (0.26), residues: 389 sheet: -1.44 (0.53), residues: 97 loop : -1.62 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 131 TYR 0.017 0.002 TYR A 864 PHE 0.019 0.002 PHE A 333 TRP 0.010 0.001 TRP A 763 HIS 0.010 0.002 HIS A 816 Details of bonding type rmsd covalent geometry : bond 0.00492 (12163) covalent geometry : angle 0.70062 (17069) hydrogen bonds : bond 0.05816 ( 412) hydrogen bonds : angle 4.43835 ( 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 124 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.281 Fit side-chains REVERT: A 19 MET cc_start: 0.6331 (mmm) cc_final: 0.5995 (mmm) REVERT: A 28 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6612 (m-30) REVERT: A 192 ARG cc_start: 0.8255 (mtp180) cc_final: 0.7965 (mtm180) REVERT: A 337 ASP cc_start: 0.7989 (t70) cc_final: 0.7451 (t0) REVERT: A 491 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.6388 (p90) REVERT: A 726 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7557 (mp) REVERT: A 782 ILE cc_start: 0.5373 (mm) cc_final: 0.5163 (mm) REVERT: A 1023 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7595 (mt) REVERT: A 1072 HIS cc_start: 0.6408 (OUTLIER) cc_final: 0.5656 (t-90) outliers start: 33 outliers final: 19 residues processed: 118 average time/residue: 0.1321 time to fit residues: 20.8197 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 : 0.382 ------------------------------------------------------------------------------- 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 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 496 SER Chi-restraints excluded: chain A residue 515 THR 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 907 THR Chi-restraints excluded: chain A residue 908 LYS 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 1023 LEU Chi-restraints excluded: chain A residue 1072 HIS 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: 7.9990 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4329 r_free = 0.4329 target = 0.184542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.143608 restraints weight = 16998.143| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.23 r_work: 0.3507 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12163 Z= 0.132 Angle : 0.617 11.397 17069 Z= 0.324 Chirality : 0.039 0.197 1950 Planarity : 0.004 0.069 1668 Dihedral : 21.786 169.182 3234 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.91 % Favored : 91.80 % Rotamer: Outliers : 2.57 % Allowed : 13.72 % 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 aren not related in a simple way. whole: -1.24 (0.26), residues: 1024 helix: 0.21 (0.26), residues: 391 sheet: -1.30 (0.52), residues: 97 loop : -1.52 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 131 TYR 0.011 0.001 TYR A 864 PHE 0.012 0.001 PHE A 333 TRP 0.012 0.001 TRP A 763 HIS 0.005 0.001 HIS A 816 Details of bonding type rmsd covalent geometry : bond 0.00283 (12163) covalent geometry : angle 0.61667 (17069) hydrogen bonds : bond 0.04564 ( 412) hydrogen bonds : angle 4.20748 ( 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 114 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.356 Fit side-chains REVERT: A 28 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6446 (m-30) REVERT: A 77 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 192 ARG cc_start: 0.8156 (mtp180) cc_final: 0.7861 (mtm180) REVERT: A 337 ASP cc_start: 0.7949 (t70) cc_final: 0.7437 (t0) REVERT: A 491 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.6263 (p90) REVERT: A 534 MET cc_start: 0.2135 (mmm) cc_final: 0.0791 (mpp) REVERT: A 685 GLU cc_start: 0.8040 (pm20) cc_final: 0.7622 (pm20) REVERT: A 726 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7434 (mp) REVERT: A 782 ILE cc_start: 0.5234 (mm) cc_final: 0.5023 (mm) REVERT: A 890 LYS cc_start: 0.6593 (mmtm) cc_final: 0.5805 (mmtp) REVERT: A 1072 HIS cc_start: 0.6268 (OUTLIER) cc_final: 0.5472 (t-90) outliers start: 24 outliers final: 13 residues processed: 110 average time/residue: 0.1399 time to fit residues: 20.4835 Evaluate side-chains 107 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 461 LEU Chi-restraints excluded: chain A residue 491 TYR 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 871 LEU Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 907 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 16 optimal weight: 0.0030 chunk 22 optimal weight: 0.1980 chunk 82 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4320 r_free = 0.4320 target = 0.183521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.142487 restraints weight = 17022.059| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.23 r_work: 0.3473 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12163 Z= 0.161 Angle : 0.630 8.848 17069 Z= 0.329 Chirality : 0.040 0.186 1950 Planarity : 0.005 0.075 1668 Dihedral : 21.763 169.794 3234 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.08 % Favored : 90.62 % Rotamer: Outliers : 2.89 % Allowed : 15.11 % Favored : 81.99 % 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 aren not related in a simple way. whole: -1.18 (0.26), residues: 1024 helix: 0.29 (0.26), residues: 391 sheet: -1.29 (0.53), residues: 96 loop : -1.51 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 588 TYR 0.011 0.001 TYR A 864 PHE 0.014 0.001 PHE A 333 TRP 0.010 0.001 TRP A 763 HIS 0.006 0.001 HIS A 816 Details of bonding type rmsd covalent geometry : bond 0.00356 (12163) covalent geometry : angle 0.63007 (17069) hydrogen bonds : bond 0.04834 ( 412) hydrogen bonds : angle 4.14791 ( 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 117 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.289 Fit side-chains REVERT: A 19 MET cc_start: 0.6228 (mmm) cc_final: 0.5687 (mmm) REVERT: A 28 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6513 (m-30) REVERT: A 192 ARG cc_start: 0.8222 (mtp180) cc_final: 0.7924 (mtm180) REVERT: A 337 ASP cc_start: 0.7979 (t70) cc_final: 0.7474 (t0) REVERT: A 491 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.6378 (p90) REVERT: A 534 MET cc_start: 0.2227 (mmm) cc_final: 0.0846 (mpp) REVERT: A 726 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7223 (mp) REVERT: A 782 ILE cc_start: 0.5247 (mm) cc_final: 0.5036 (mm) REVERT: A 890 LYS cc_start: 0.6714 (mmtm) cc_final: 0.6026 (mmtp) REVERT: A 1023 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7580 (mt) REVERT: A 1072 HIS cc_start: 0.6302 (OUTLIER) cc_final: 0.5493 (t-90) outliers start: 27 outliers final: 14 residues processed: 110 average time/residue: 0.1441 time to fit residues: 21.0002 Evaluate side-chains 108 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 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 907 THR Chi-restraints excluded: chain A residue 927 VAL 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 1023 LEU 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: 0.8980 chunk 29 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4327 r_free = 0.4327 target = 0.184230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.143182 restraints weight = 17045.922| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 3.17 r_work: 0.3492 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12163 Z= 0.149 Angle : 0.618 9.468 17069 Z= 0.323 Chirality : 0.039 0.230 1950 Planarity : 0.004 0.073 1668 Dihedral : 21.709 170.192 3234 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.59 % Favored : 91.11 % Rotamer: Outliers : 3.00 % Allowed : 15.33 % Favored : 81.67 % 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 aren not related in a simple way. whole: -1.07 (0.26), residues: 1024 helix: 0.40 (0.26), residues: 392 sheet: -1.05 (0.57), residues: 88 loop : -1.50 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 588 TYR 0.010 0.001 TYR A 864 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 covalent geometry : bond 0.00329 (12163) covalent geometry : angle 0.61780 (17069) hydrogen bonds : bond 0.04589 ( 412) hydrogen bonds : angle 4.11194 ( 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: 28 poor density : 93 time to evaluate : 0.359 Fit side-chains REVERT: A 19 MET cc_start: 0.6336 (mmm) cc_final: 0.6024 (mmm) REVERT: A 28 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6505 (m-30) REVERT: A 77 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7391 (tm-30) REVERT: A 192 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7905 (mtm180) REVERT: A 337 ASP cc_start: 0.7989 (t70) cc_final: 0.7485 (t0) REVERT: A 491 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.6346 (p90) REVERT: A 534 MET cc_start: 0.2216 (mmm) cc_final: 0.0862 (mpp) REVERT: A 726 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7050 (mp) REVERT: A 782 ILE cc_start: 0.5274 (mm) cc_final: 0.5070 (mm) REVERT: A 1023 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7513 (mt) REVERT: A 1064 ARG cc_start: 0.7954 (ptp-170) cc_final: 0.7670 (ptm160) REVERT: A 1072 HIS cc_start: 0.6122 (OUTLIER) cc_final: 0.5368 (t-90) outliers start: 28 outliers final: 15 residues processed: 116 average time/residue: 0.1500 time to fit residues: 22.9645 Evaluate side-chains 111 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 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 515 THR 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 871 LEU Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 927 VAL 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 1023 LEU 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: 5.9990 chunk 4 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 385 ASN A 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.178969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136432 restraints weight = 17121.670| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.40 r_work: 0.3409 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12163 Z= 0.256 Angle : 0.728 9.354 17069 Z= 0.379 Chirality : 0.045 0.300 1950 Planarity : 0.005 0.070 1668 Dihedral : 21.900 170.292 3234 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.06 % Favored : 89.65 % Rotamer: Outliers : 3.00 % Allowed : 15.76 % Favored : 81.24 % 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 aren not related in a simple way. whole: -1.40 (0.26), residues: 1024 helix: 0.02 (0.26), residues: 386 sheet: -1.23 (0.53), residues: 99 loop : -1.59 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 25 TYR 0.015 0.002 TYR A 864 PHE 0.019 0.002 PHE A 333 TRP 0.009 0.001 TRP A 262 HIS 0.013 0.002 HIS A 816 Details of bonding type rmsd covalent geometry : bond 0.00575 (12163) covalent geometry : angle 0.72783 (17069) hydrogen bonds : bond 0.06006 ( 412) hydrogen bonds : angle 4.45141 ( 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 119 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6593 (m-30) REVERT: A 192 ARG cc_start: 0.8368 (mtp180) cc_final: 0.8052 (mtm180) REVERT: A 337 ASP cc_start: 0.8151 (t70) cc_final: 0.7753 (t0) REVERT: A 491 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.6435 (p90) REVERT: A 534 MET cc_start: 0.2117 (mmm) cc_final: 0.0777 (mpp) REVERT: A 726 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7171 (mp) REVERT: A 782 ILE cc_start: 0.5271 (mm) cc_final: 0.5041 (mm) REVERT: A 1023 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7605 (mt) REVERT: A 1064 ARG cc_start: 0.8143 (ptp-170) cc_final: 0.7828 (ptm160) REVERT: A 1072 HIS cc_start: 0.6502 (OUTLIER) cc_final: 0.5858 (t-90) outliers start: 28 outliers final: 20 residues processed: 114 average time/residue: 0.1566 time to fit residues: 23.3795 Evaluate side-chains 113 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 496 SER Chi-restraints excluded: chain A residue 515 THR 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 871 LEU Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 927 VAL 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 1023 LEU 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: 0.7980 chunk 111 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4309 r_free = 0.4309 target = 0.182652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141943 restraints weight = 16894.137| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.08 r_work: 0.3477 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12163 Z= 0.158 Angle : 0.646 10.887 17069 Z= 0.336 Chirality : 0.040 0.270 1950 Planarity : 0.004 0.070 1668 Dihedral : 21.785 171.022 3234 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.59 % Favored : 91.11 % Rotamer: Outliers : 3.00 % Allowed : 15.97 % Favored : 81.03 % 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 aren not related in a simple way. whole: -1.18 (0.26), residues: 1024 helix: 0.28 (0.26), residues: 387 sheet: -1.01 (0.58), residues: 87 loop : -1.55 (0.26), residues: 550 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 0.012 0.001 PHE A 333 TRP 0.012 0.001 TRP A 763 HIS 0.006 0.001 HIS A 816 Details of bonding type rmsd covalent geometry : bond 0.00351 (12163) covalent geometry : angle 0.64621 (17069) hydrogen bonds : bond 0.04731 ( 412) hydrogen bonds : angle 4.23584 ( 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 117 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6533 (m-30) REVERT: A 77 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 192 ARG cc_start: 0.8192 (mtp180) cc_final: 0.7907 (mtm180) REVERT: A 337 ASP cc_start: 0.8044 (t70) cc_final: 0.7591 (t0) REVERT: A 491 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.6368 (p90) REVERT: A 534 MET cc_start: 0.2284 (mmm) cc_final: 0.0870 (mpp) REVERT: A 726 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7154 (mp) REVERT: A 782 ILE cc_start: 0.5253 (mm) cc_final: 0.5033 (mm) REVERT: A 1023 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7515 (mt) REVERT: A 1064 ARG cc_start: 0.8133 (ptp-170) cc_final: 0.7782 (ptm160) REVERT: A 1072 HIS cc_start: 0.6143 (OUTLIER) cc_final: 0.5580 (t-90) outliers start: 28 outliers final: 22 residues processed: 111 average time/residue: 0.1546 time to fit residues: 22.8728 Evaluate side-chains 113 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 185 ILE Chi-restraints excluded: chain A residue 318 VAL 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 496 SER Chi-restraints excluded: chain A residue 515 THR 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 871 LEU Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 908 LYS Chi-restraints excluded: chain A residue 927 VAL 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 1023 LEU Chi-restraints excluded: chain A residue 1065 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 36 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4317 r_free = 0.4317 target = 0.183404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140977 restraints weight = 17152.633| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.11 r_work: 0.3489 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12163 Z= 0.148 Angle : 0.635 10.735 17069 Z= 0.330 Chirality : 0.039 0.239 1950 Planarity : 0.004 0.071 1668 Dihedral : 21.733 171.444 3234 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.98 % Favored : 90.72 % Rotamer: Outliers : 3.00 % Allowed : 16.40 % Favored : 80.60 % 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 aren not related in a simple way. whole: -1.07 (0.26), residues: 1024 helix: 0.36 (0.26), residues: 394 sheet: -1.00 (0.57), residues: 87 loop : -1.49 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.012 0.001 TYR A 288 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 covalent geometry : bond 0.00327 (12163) covalent geometry : angle 0.63499 (17069) hydrogen bonds : bond 0.04546 ( 412) hydrogen bonds : angle 4.14297 ( 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 117 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6548 (m-30) REVERT: A 192 ARG cc_start: 0.8199 (mtp180) cc_final: 0.7914 (mtm180) REVERT: A 337 ASP cc_start: 0.8039 (t70) cc_final: 0.7576 (t0) REVERT: A 491 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.6306 (p90) REVERT: A 534 MET cc_start: 0.2172 (mmm) cc_final: 0.0846 (mpp) REVERT: A 726 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.7088 (mp) REVERT: A 782 ILE cc_start: 0.5201 (mm) cc_final: 0.4992 (mm) REVERT: A 1023 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7491 (mt) REVERT: A 1064 ARG cc_start: 0.8216 (ptp-170) cc_final: 0.7827 (ptm160) REVERT: A 1072 HIS cc_start: 0.6043 (OUTLIER) cc_final: 0.5499 (t-90) outliers start: 28 outliers final: 20 residues processed: 112 average time/residue: 0.1382 time to fit residues: 20.8766 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 : 0.239 ------------------------------------------------------------------------------- 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 185 ILE Chi-restraints excluded: chain A residue 318 VAL 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 496 SER Chi-restraints excluded: chain A residue 515 THR 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 871 LEU Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 927 VAL 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 1023 LEU Chi-restraints excluded: chain A residue 1065 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: 0.0370 chunk 111 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 385 ASN A 610 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.182164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.141090 restraints weight = 17116.841| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.25 r_work: 0.3461 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12163 Z= 0.165 Angle : 0.651 10.509 17069 Z= 0.338 Chirality : 0.040 0.224 1950 Planarity : 0.004 0.071 1668 Dihedral : 21.747 171.566 3234 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.38 % Favored : 90.33 % Rotamer: Outliers : 3.00 % Allowed : 16.83 % Favored : 80.17 % 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 aren not related in a simple way. whole: -1.11 (0.26), residues: 1024 helix: 0.34 (0.26), residues: 394 sheet: -1.19 (0.52), residues: 99 loop : -1.49 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 829 TYR 0.014 0.001 TYR A 288 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 covalent geometry : bond 0.00367 (12163) covalent geometry : angle 0.65097 (17069) hydrogen bonds : bond 0.04767 ( 412) hydrogen bonds : angle 4.17414 ( 1053) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2998.17 seconds wall clock time: 51 minutes 59.35 seconds (3119.35 seconds total)