Starting phenix.real_space_refine on Wed May 14 04:36:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtj_36646/05_2025/8jtj_36646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtj_36646/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jtj_36646/05_2025/8jtj_36646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtj_36646/05_2025/8jtj_36646.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtj_36646/05_2025/8jtj_36646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtj_36646/05_2025/8jtj_36646.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.10, per 1000 atoms: 0.61 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: 3.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 4.13 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: 5.94 Time building geometry restraints manager: 3.56 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: 1.490 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.460 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP A 221 HIS 0.004 0.001 HIS A 702 PHE 0.009 0.001 PHE A 333 TYR 0.018 0.001 TYR A1013 ARG 0.006 0.001 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.18070 ( 412) hydrogen bonds : angle 6.02369 ( 1053) covalent geometry : bond 0.00281 (12163) covalent geometry : angle 0.65815 (17069) *********************** 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 : 1.027 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: 0.3180 time to fit residues: 49.2024 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 : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 0.0870 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.185809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.142399 restraints weight = 16686.431| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.98 r_work: 0.3530 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12163 Z= 0.221 Angle : 0.699 9.105 17069 Z= 0.369 Chirality : 0.043 0.207 1950 Planarity : 0.006 0.064 1668 Dihedral : 21.821 159.633 3234 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.38 % Favored : 90.14 % Rotamer: Outliers : 1.39 % Allowed : 6.65 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1024 helix: 0.01 (0.26), residues: 392 sheet: -1.23 (0.52), residues: 98 loop : -1.57 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 221 HIS 0.012 0.002 HIS A 816 PHE 0.018 0.002 PHE A1045 TYR 0.021 0.002 TYR A 981 ARG 0.005 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.05989 ( 412) hydrogen bonds : angle 4.50813 ( 1053) covalent geometry : bond 0.00491 (12163) covalent geometry : angle 0.69867 (17069) *********************** 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 119 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.154 Fit side-chains REVERT: A 1 MET cc_start: 0.8163 (mpp) cc_final: 0.7841 (mpp) REVERT: A 28 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6821 (m-30) REVERT: A 192 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7846 (mtm180) REVERT: A 337 ASP cc_start: 0.7990 (t70) cc_final: 0.7487 (t0) REVERT: A 550 PHE cc_start: 0.7806 (t80) cc_final: 0.7604 (t80) REVERT: A 726 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7624 (mp) REVERT: A 782 ILE cc_start: 0.5151 (mm) cc_final: 0.4942 (mm) REVERT: A 962 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8344 (mmtt) REVERT: A 1062 GLU cc_start: 0.6198 (mm-30) cc_final: 0.5994 (mm-30) outliers start: 13 outliers final: 8 residues processed: 116 average time/residue: 0.3630 time to fit residues: 55.2309 Evaluate side-chains 105 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 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 22 optimal weight: 0.3980 chunk 10 optimal weight: 0.4980 chunk 67 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4352 r_free = 0.4352 target = 0.187520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.145939 restraints weight = 16980.734| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 3.40 r_work: 0.3509 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2055 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= 0.145 Angle : 0.613 7.451 17069 Z= 0.323 Chirality : 0.039 0.197 1950 Planarity : 0.004 0.051 1668 Dihedral : 21.738 164.172 3234 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.71 % Favored : 91.89 % Rotamer: Outliers : 2.25 % Allowed : 8.57 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.26), residues: 1024 helix: 0.20 (0.26), residues: 394 sheet: -1.11 (0.52), residues: 98 loop : -1.54 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 763 HIS 0.008 0.001 HIS A 816 PHE 0.013 0.001 PHE A 333 TYR 0.012 0.001 TYR A 864 ARG 0.003 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04994 ( 412) hydrogen bonds : angle 4.23312 ( 1053) covalent geometry : bond 0.00316 (12163) covalent geometry : angle 0.61293 (17069) *********************** 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 118 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.999 Fit side-chains REVERT: A 1 MET cc_start: 0.8108 (mpp) cc_final: 0.7756 (mpp) REVERT: A 28 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6863 (m-30) REVERT: A 192 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7850 (mtm180) REVERT: A 337 ASP cc_start: 0.7950 (t70) cc_final: 0.7430 (t0) REVERT: A 491 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.5810 (p90) REVERT: A 654 GLU cc_start: 0.7093 (tp30) cc_final: 0.6849 (tp30) REVERT: A 726 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7517 (mp) REVERT: A 782 ILE cc_start: 0.5016 (mm) cc_final: 0.4811 (mm) REVERT: A 962 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8262 (mmtt) outliers start: 21 outliers final: 11 residues processed: 111 average time/residue: 0.3103 time to fit residues: 46.1719 Evaluate side-chains 106 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 864 TYR Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 950 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 39 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 40.0000 chunk 115 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.181453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.137306 restraints weight = 16822.916| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.22 r_work: 0.3430 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12163 Z= 0.223 Angle : 0.699 8.601 17069 Z= 0.367 Chirality : 0.043 0.190 1950 Planarity : 0.005 0.047 1668 Dihedral : 21.853 167.501 3234 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.28 % Favored : 90.43 % Rotamer: Outliers : 3.00 % Allowed : 9.97 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.25), residues: 1024 helix: 0.04 (0.26), residues: 389 sheet: -1.22 (0.51), residues: 99 loop : -1.57 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 221 HIS 0.011 0.002 HIS A 816 PHE 0.020 0.002 PHE A 333 TYR 0.020 0.002 TYR A 864 ARG 0.004 0.001 ARG A 427 Details of bonding type rmsd hydrogen bonds : bond 0.05884 ( 412) hydrogen bonds : angle 4.35435 ( 1053) covalent geometry : bond 0.00496 (12163) covalent geometry : angle 0.69892 (17069) *********************** 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 119 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.157 Fit side-chains REVERT: A 28 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6832 (m-30) REVERT: A 192 ARG cc_start: 0.8358 (mtp180) cc_final: 0.8030 (mtm180) REVERT: A 337 ASP cc_start: 0.7957 (t70) cc_final: 0.7419 (t0) REVERT: A 491 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.6313 (p90) REVERT: A 726 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7484 (mp) REVERT: A 782 ILE cc_start: 0.5300 (mm) cc_final: 0.5078 (mm) REVERT: A 962 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8412 (mmtt) REVERT: A 1072 HIS cc_start: 0.6281 (OUTLIER) cc_final: 0.5223 (t-90) outliers start: 28 outliers final: 17 residues processed: 114 average time/residue: 0.3237 time to fit residues: 49.2211 Evaluate side-chains 107 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 81 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 462 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 950 LYS 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 62 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.0570 chunk 89 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.182369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.140155 restraints weight = 16816.137| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 3.33 r_work: 0.3444 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12163 Z= 0.181 Angle : 0.640 8.805 17069 Z= 0.336 Chirality : 0.041 0.185 1950 Planarity : 0.004 0.047 1668 Dihedral : 21.786 168.522 3234 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.30 % Favored : 91.41 % Rotamer: Outliers : 2.36 % Allowed : 12.54 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.25), residues: 1024 helix: 0.14 (0.26), residues: 389 sheet: -1.18 (0.53), residues: 95 loop : -1.55 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 763 HIS 0.010 0.001 HIS A 816 PHE 0.017 0.001 PHE A 333 TYR 0.014 0.002 TYR A 864 ARG 0.004 0.000 ARG A 588 Details of bonding type rmsd hydrogen bonds : bond 0.05108 ( 412) hydrogen bonds : angle 4.21311 ( 1053) covalent geometry : bond 0.00401 (12163) covalent geometry : angle 0.63979 (17069) *********************** 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 112 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.099 Fit side-chains REVERT: A 28 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6813 (m-30) REVERT: A 77 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 192 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7950 (mtm180) REVERT: A 337 ASP cc_start: 0.7962 (t70) cc_final: 0.7438 (t0) REVERT: A 491 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.6375 (p90) REVERT: A 726 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7300 (mp) REVERT: A 782 ILE cc_start: 0.5362 (mm) cc_final: 0.5135 (mm) outliers start: 22 outliers final: 13 residues processed: 107 average time/residue: 0.3162 time to fit residues: 45.4297 Evaluate side-chains 103 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.182416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.139023 restraints weight = 17085.301| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.94 r_work: 0.3477 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3326 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= 0.183 Angle : 0.647 8.870 17069 Z= 0.338 Chirality : 0.041 0.179 1950 Planarity : 0.005 0.048 1668 Dihedral : 21.763 169.311 3234 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.28 % Favored : 90.43 % Rotamer: Outliers : 2.79 % Allowed : 14.26 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 1024 helix: 0.22 (0.26), residues: 389 sheet: -1.15 (0.49), residues: 111 loop : -1.58 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 763 HIS 0.009 0.001 HIS A 816 PHE 0.016 0.001 PHE A 333 TYR 0.014 0.001 TYR A 864 ARG 0.005 0.000 ARG A 588 Details of bonding type rmsd hydrogen bonds : bond 0.05142 ( 412) hydrogen bonds : angle 4.22842 ( 1053) covalent geometry : bond 0.00406 (12163) covalent geometry : angle 0.64657 (17069) *********************** 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 114 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 1.094 Fit side-chains REVERT: A 19 MET cc_start: 0.6311 (mmm) cc_final: 0.5722 (mmm) REVERT: A 28 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6800 (m-30) REVERT: A 77 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 192 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7912 (mtm180) REVERT: A 337 ASP cc_start: 0.7962 (t70) cc_final: 0.7458 (t0) REVERT: A 491 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.6198 (p90) REVERT: A 726 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.7111 (mp) REVERT: A 782 ILE cc_start: 0.5311 (mm) cc_final: 0.5089 (mm) REVERT: A 890 LYS cc_start: 0.6676 (mmtm) cc_final: 0.6033 (mmtp) REVERT: A 1023 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7513 (mt) REVERT: A 1072 HIS cc_start: 0.6183 (OUTLIER) cc_final: 0.5349 (t-90) outliers start: 26 outliers final: 14 residues processed: 109 average time/residue: 0.3367 time to fit residues: 48.5251 Evaluate side-chains 107 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 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 871 LEU Chi-restraints excluded: chain A residue 901 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 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 55 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.178784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.135417 restraints weight = 17114.441| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.94 r_work: 0.3442 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3674 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= 0.240 Angle : 0.711 12.146 17069 Z= 0.369 Chirality : 0.043 0.195 1950 Planarity : 0.005 0.076 1668 Dihedral : 21.866 169.667 3234 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.86 % Favored : 89.84 % Rotamer: Outliers : 3.22 % Allowed : 14.68 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.26), residues: 1024 helix: 0.05 (0.26), residues: 388 sheet: -1.28 (0.50), residues: 111 loop : -1.64 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 763 HIS 0.011 0.002 HIS A 816 PHE 0.019 0.002 PHE A 333 TYR 0.016 0.002 TYR A 864 ARG 0.004 0.001 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.05740 ( 412) hydrogen bonds : angle 4.39851 ( 1053) covalent geometry : bond 0.00536 (12163) covalent geometry : angle 0.71079 (17069) *********************** 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 123 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6855 (m-30) REVERT: A 77 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7405 (tm-30) REVERT: A 192 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7996 (mtm180) REVERT: A 337 ASP cc_start: 0.7994 (t70) cc_final: 0.7466 (t0) REVERT: A 491 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.6397 (p90) REVERT: A 726 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7111 (mp) REVERT: A 782 ILE cc_start: 0.5468 (mm) cc_final: 0.5253 (mm) REVERT: A 890 LYS cc_start: 0.6664 (mmtm) cc_final: 0.6026 (mmtp) REVERT: A 1023 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7596 (mt) REVERT: A 1064 ARG cc_start: 0.8136 (ptp-170) cc_final: 0.7789 (ptm160) REVERT: A 1072 HIS cc_start: 0.6322 (OUTLIER) cc_final: 0.5622 (t-90) outliers start: 30 outliers final: 18 residues processed: 119 average time/residue: 0.3279 time to fit residues: 51.9178 Evaluate side-chains 113 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 871 LEU Chi-restraints excluded: chain A residue 901 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 34 optimal weight: 0.0470 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- 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 = 0.182607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.139828 restraints weight = 16982.622| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.98 r_work: 0.3480 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3664 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= 0.153 Angle : 0.645 10.368 17069 Z= 0.334 Chirality : 0.040 0.191 1950 Planarity : 0.004 0.076 1668 Dihedral : 21.758 169.951 3234 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.89 % Favored : 90.82 % Rotamer: Outliers : 2.68 % Allowed : 15.54 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.26), residues: 1024 helix: 0.29 (0.26), residues: 390 sheet: -1.14 (0.53), residues: 99 loop : -1.59 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 763 HIS 0.007 0.001 HIS A 816 PHE 0.014 0.001 PHE A 333 TYR 0.012 0.001 TYR A 864 ARG 0.005 0.000 ARG A 588 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 412) hydrogen bonds : angle 4.19340 ( 1053) covalent geometry : bond 0.00336 (12163) covalent geometry : angle 0.64476 (17069) *********************** 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 113 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.038 Fit side-chains REVERT: A 19 MET cc_start: 0.6279 (mmm) cc_final: 0.5858 (mmm) REVERT: A 28 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6813 (m-30) REVERT: A 77 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 192 ARG cc_start: 0.8204 (mtp180) cc_final: 0.7919 (mtm180) REVERT: A 337 ASP cc_start: 0.7982 (t70) cc_final: 0.7472 (t0) REVERT: A 491 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.6360 (p90) REVERT: A 726 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7111 (mp) REVERT: A 782 ILE cc_start: 0.5374 (mm) cc_final: 0.5144 (mm) REVERT: A 890 LYS cc_start: 0.6601 (mmtm) cc_final: 0.5974 (mmtp) REVERT: A 1064 ARG cc_start: 0.8118 (ptp-170) cc_final: 0.7784 (ptm160) REVERT: A 1072 HIS cc_start: 0.6015 (OUTLIER) cc_final: 0.5348 (t-90) outliers start: 25 outliers final: 17 residues processed: 108 average time/residue: 0.3345 time to fit residues: 47.4724 Evaluate side-chains 107 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 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 871 LEU Chi-restraints excluded: chain A residue 901 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 1065 VAL 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 50 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.177716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.135321 restraints weight = 17055.226| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.39 r_work: 0.3391 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12163 Z= 0.273 Angle : 0.762 9.632 17069 Z= 0.395 Chirality : 0.045 0.220 1950 Planarity : 0.005 0.073 1668 Dihedral : 21.959 169.894 3234 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.06 % Favored : 89.65 % Rotamer: Outliers : 3.54 % Allowed : 15.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.26), residues: 1024 helix: -0.11 (0.25), residues: 391 sheet: -1.38 (0.49), residues: 111 loop : -1.67 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 221 HIS 0.014 0.002 HIS A 816 PHE 0.020 0.002 PHE A 333 TYR 0.016 0.002 TYR A 864 ARG 0.005 0.001 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.06291 ( 412) hydrogen bonds : angle 4.55976 ( 1053) covalent geometry : bond 0.00611 (12163) covalent geometry : angle 0.76229 (17069) *********************** 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 120 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 19 MET cc_start: 0.6390 (mmm) cc_final: 0.5929 (mmm) REVERT: A 28 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6826 (m-30) REVERT: A 77 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7419 (tm-30) REVERT: A 192 ARG cc_start: 0.8373 (mtp180) cc_final: 0.8084 (mtm180) REVERT: A 337 ASP cc_start: 0.8014 (t70) cc_final: 0.7497 (t0) REVERT: A 491 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.6466 (p90) REVERT: A 588 ARG cc_start: 0.7173 (mtp-110) cc_final: 0.6868 (mtp-110) REVERT: A 726 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7280 (mp) REVERT: A 782 ILE cc_start: 0.5538 (mm) cc_final: 0.5321 (mm) REVERT: A 890 LYS cc_start: 0.6726 (mmtm) cc_final: 0.6093 (mmtp) REVERT: A 1023 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7715 (mt) REVERT: A 1064 ARG cc_start: 0.8167 (ptp-170) cc_final: 0.7811 (ptm160) REVERT: A 1072 HIS cc_start: 0.6171 (OUTLIER) cc_final: 0.5614 (t-90) outliers start: 33 outliers final: 22 residues processed: 111 average time/residue: 0.3261 time to fit residues: 48.2366 Evaluate side-chains 111 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 472 VAL Chi-restraints excluded: chain A residue 474 MET 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 871 LEU Chi-restraints excluded: chain A residue 901 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 986 ILE 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 19 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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 ** 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 = 0.4320 r_free = 0.4320 target = 0.183640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.141142 restraints weight = 17000.311| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.01 r_work: 0.3503 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12163 Z= 0.128 Angle : 0.624 9.955 17069 Z= 0.324 Chirality : 0.039 0.227 1950 Planarity : 0.004 0.072 1668 Dihedral : 21.764 170.340 3234 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.71 % Favored : 91.89 % Rotamer: Outliers : 2.04 % Allowed : 16.51 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.26), residues: 1024 helix: 0.34 (0.26), residues: 389 sheet: -1.19 (0.50), residues: 111 loop : -1.55 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 763 HIS 0.005 0.001 HIS A 816 PHE 0.012 0.001 PHE A 333 TYR 0.011 0.001 TYR A 288 ARG 0.004 0.000 ARG A 588 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 412) hydrogen bonds : angle 4.19393 ( 1053) covalent geometry : bond 0.00274 (12163) covalent geometry : angle 0.62440 (17069) ********************** 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 105 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 1.183 Fit side-chains REVERT: A 19 MET cc_start: 0.6324 (mmm) cc_final: 0.5859 (mmm) REVERT: A 28 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6795 (m-30) REVERT: A 77 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 192 ARG cc_start: 0.8171 (mtp180) cc_final: 0.7883 (mtm180) REVERT: A 491 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.6285 (p90) REVERT: A 588 ARG cc_start: 0.6974 (mtp-110) cc_final: 0.6736 (mtp-110) REVERT: A 726 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7068 (mp) REVERT: A 782 ILE cc_start: 0.5308 (mm) cc_final: 0.5073 (mm) REVERT: A 890 LYS cc_start: 0.6561 (mmtm) cc_final: 0.5969 (mmtp) REVERT: A 1023 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7530 (mt) REVERT: A 1064 ARG cc_start: 0.8129 (ptp-170) cc_final: 0.7670 (ptm160) REVERT: A 1072 HIS cc_start: 0.5938 (OUTLIER) cc_final: 0.5366 (t-90) outliers start: 19 outliers final: 12 residues processed: 100 average time/residue: 0.3318 time to fit residues: 44.5048 Evaluate side-chains 100 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 474 MET 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 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 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 14 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 56 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.179648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137688 restraints weight = 16975.134| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.35 r_work: 0.3423 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12163 Z= 0.213 Angle : 0.684 9.755 17069 Z= 0.356 Chirality : 0.042 0.218 1950 Planarity : 0.005 0.070 1668 Dihedral : 21.805 170.690 3234 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.67 % Favored : 89.94 % Rotamer: Outliers : 2.36 % Allowed : 16.51 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.26), residues: 1024 helix: 0.22 (0.26), residues: 387 sheet: -1.23 (0.50), residues: 111 loop : -1.59 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 763 HIS 0.011 0.001 HIS A 816 PHE 0.015 0.001 PHE A 333 TYR 0.012 0.002 TYR A 288 ARG 0.004 0.000 ARG A 445 Details of bonding type rmsd hydrogen bonds : bond 0.05347 ( 412) hydrogen bonds : angle 4.31332 ( 1053) covalent geometry : bond 0.00476 (12163) covalent geometry : angle 0.68442 (17069) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6046.84 seconds wall clock time: 105 minutes 19.72 seconds (6319.72 seconds total)