Starting phenix.real_space_refine on Tue May 13 03:46:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6r_29779/05_2025/8g6r_29779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6r_29779/05_2025/8g6r_29779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6r_29779/05_2025/8g6r_29779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6r_29779/05_2025/8g6r_29779.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6r_29779/05_2025/8g6r_29779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6r_29779/05_2025/8g6r_29779.cif" } resolution = 3.4 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= 0.016 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 40 5.49 5 S 71 5.16 5 C 5846 2.51 5 N 1565 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9406 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7198 Classifications: {'peptide': 899} Link IDs: {'PTRANS': 25, 'TRANS': 873} Chain breaks: 2 Chain: "B" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 878 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "C" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 477 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "I" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 428 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 7} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2370 SG CYS A 296 27.578 61.099 83.170 1.00104.05 S ATOM 2408 SG CYS A 301 28.842 64.368 84.713 1.00 97.50 S ATOM 2439 SG CYS A 305 30.494 60.986 85.568 1.00 91.72 S ATOM 3802 SG CYS A 482 18.288 63.589 63.785 1.00111.18 S ATOM 5042 SG CYS A 640 18.703 66.880 65.627 1.00110.13 S ATOM 5048 SG CYS A 641 17.625 63.682 67.468 1.00111.44 S Time building chain proxies: 5.84, per 1000 atoms: 0.62 Number of scatterers: 9406 At special positions: 0 Unit cell: (91.74, 97.578, 124.266, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 71 16.00 P 40 15.00 O 1882 8.00 N 1565 7.00 C 5846 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: 2.64 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 290 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 305 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 296 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 637 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 641 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 482 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 640 " Number of angles added : 6 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 11 sheets defined 54.7% alpha, 11.5% beta 14 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.889A pdb=" N ARG A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 73 through 86 removed outlier: 4.509A pdb=" N LYS A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.812A pdb=" N ASN A 153 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 194 removed outlier: 4.097A pdb=" N ARG A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.760A pdb=" N MET A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Proline residue: A 237 - end of helix Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 298 through 314 removed outlier: 4.074A pdb=" N THR A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.707A pdb=" N GLN A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 removed outlier: 4.342A pdb=" N LEU A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 422 Processing helix chain 'A' and resid 442 through 449 removed outlier: 3.721A pdb=" N LYS A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 460 through 474 removed outlier: 4.170A pdb=" N VAL A 466 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 498 through 503 removed outlier: 4.529A pdb=" N LYS A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 3.996A pdb=" N TYR A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 556 through 577 removed outlier: 3.684A pdb=" N THR A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS A 570 " --> pdb=" O TYR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 624 through 635 Processing helix chain 'A' and resid 642 through 658 Processing helix chain 'A' and resid 681 through 704 removed outlier: 3.621A pdb=" N ASN A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 710 removed outlier: 5.805A pdb=" N ASN A 708 " --> pdb=" O VAL A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 727 Processing helix chain 'A' and resid 733 through 747 Processing helix chain 'A' and resid 763 through 768 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 799 through 803 Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 863 through 867 Processing helix chain 'A' and resid 869 through 890 removed outlier: 3.578A pdb=" N VAL A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 876 " --> pdb=" O TYR A 872 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 912 through 920 removed outlier: 4.280A pdb=" N TYR A 916 " --> pdb=" O ASP A 912 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET A 919 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 920 " --> pdb=" O TYR A 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 97 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.610A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 112 removed outlier: 5.825A pdb=" N ASP B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.697A pdb=" N VAL B 172 " --> pdb=" O HIS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'C' and resid 3 through 20 removed outlier: 4.052A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL C 12 " --> pdb=" O CYS C 8 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET C 20 " --> pdb=" O CYS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 42 removed outlier: 3.553A pdb=" N TRP C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 63 removed outlier: 3.597A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.838A pdb=" N PHE A 63 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.647A pdb=" N VAL A 29 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS A 48 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 198 removed outlier: 6.757A pdb=" N GLY A 197 " --> pdb=" O ILE A 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 350 removed outlier: 6.762A pdb=" N LEU A 324 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYR A 341 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY A 322 " --> pdb=" O TYR A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 382 through 385 removed outlier: 6.205A pdb=" N ALA A 382 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL B 131 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 384 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE B 156 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 395 removed outlier: 6.200A pdb=" N SER A 392 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 670 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA A 394 " --> pdb=" O PHE A 668 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 409 through 410 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AB1, first strand: chain 'A' and resid 748 through 753 removed outlier: 3.628A pdb=" N SER A 749 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP A 795 " --> pdb=" O GLY A 611 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 811 through 817 removed outlier: 3.674A pdb=" N HIS A 811 " --> pdb=" O TYR A 826 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 826 " --> pdb=" O HIS A 811 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2799 1.33 - 1.45: 1852 1.45 - 1.57: 4865 1.57 - 1.69: 78 1.69 - 1.81: 100 Bond restraints: 9694 Sorted by residual: bond pdb=" N ASP A 3 " pdb=" CA ASP A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LYS C 2 " pdb=" CA LYS C 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N ARG B 79 " pdb=" CA ARG B 79 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" CB CYS A 651 " pdb=" SG CYS A 651 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" CB ASN A 698 " pdb=" CG ASN A 698 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.22e+00 ... (remaining 9689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 12902 1.23 - 2.45: 345 2.45 - 3.68: 55 3.68 - 4.91: 14 4.91 - 6.14: 3 Bond angle restraints: 13319 Sorted by residual: angle pdb=" C TYR A 782 " pdb=" N TYR A 783 " pdb=" CA TYR A 783 " ideal model delta sigma weight residual 122.38 117.34 5.04 1.81e+00 3.05e-01 7.75e+00 angle pdb=" C GLU C 50 " pdb=" N MET C 51 " pdb=" CA MET C 51 " ideal model delta sigma weight residual 120.28 117.75 2.53 1.34e+00 5.57e-01 3.57e+00 angle pdb=" N TYR A 783 " pdb=" CA TYR A 783 " pdb=" CB TYR A 783 " ideal model delta sigma weight residual 110.44 113.18 -2.74 1.53e+00 4.27e-01 3.20e+00 angle pdb=" N MET C 51 " pdb=" CA MET C 51 " pdb=" CB MET C 51 " ideal model delta sigma weight residual 110.12 112.66 -2.54 1.47e+00 4.63e-01 2.98e+00 angle pdb=" N PRO C 45 " pdb=" CA PRO C 45 " pdb=" C PRO C 45 " ideal model delta sigma weight residual 112.47 115.99 -3.52 2.06e+00 2.36e-01 2.92e+00 ... (remaining 13314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 5248 17.57 - 35.14: 371 35.14 - 52.71: 91 52.71 - 70.28: 49 70.28 - 87.85: 15 Dihedral angle restraints: 5774 sinusoidal: 2611 harmonic: 3163 Sorted by residual: dihedral pdb=" CA GLN A 656 " pdb=" C GLN A 656 " pdb=" N VAL A 657 " pdb=" CA VAL A 657 " ideal model delta harmonic sigma weight residual 180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LEU A 125 " pdb=" C LEU A 125 " pdb=" N ARG A 126 " pdb=" CA ARG A 126 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" O4' G J 25 " pdb=" C1' G J 25 " pdb=" N9 G J 25 " pdb=" C4 G J 25 " ideal model delta sinusoidal sigma weight residual 70.00 6.87 63.13 1 2.00e+01 2.50e-03 1.32e+01 ... (remaining 5771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 931 0.028 - 0.056: 421 0.056 - 0.084: 89 0.084 - 0.112: 66 0.112 - 0.140: 9 Chirality restraints: 1516 Sorted by residual: chirality pdb=" CA PRO C 45 " pdb=" N PRO C 45 " pdb=" C PRO C 45 " pdb=" CB PRO C 45 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE B 159 " pdb=" N ILE B 159 " pdb=" C ILE B 159 " pdb=" CB ILE B 159 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA PRO A 863 " pdb=" N PRO A 863 " pdb=" C PRO A 863 " pdb=" CB PRO A 863 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1513 not shown) Planarity restraints: 1545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 531 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 532 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 380 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 381 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 158 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 159 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " 0.020 5.00e-02 4.00e+02 ... (remaining 1542 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 102 2.51 - 3.11: 8157 3.11 - 3.71: 14949 3.71 - 4.30: 21408 4.30 - 4.90: 33968 Nonbonded interactions: 78584 Sorted by model distance: nonbonded pdb=" OG SER A 809 " pdb=" OP1 A I 33 " model vdw 1.919 3.040 nonbonded pdb=" OG1 THR A 533 " pdb=" OE1 GLN A 656 " model vdw 1.967 3.040 nonbonded pdb=" OD1 ASP A 618 " pdb=" OG1 THR A 675 " model vdw 1.981 3.040 nonbonded pdb=" O LEU A 509 " pdb=" OG SER A 513 " model vdw 1.984 3.040 nonbonded pdb=" OH TYR A 289 " pdb=" OD1 ASN A 309 " model vdw 2.052 3.040 ... (remaining 78579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.100 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.005 0.042 9702 Z= 0.228 Angle : 0.514 6.136 13325 Z= 0.290 Chirality : 0.036 0.140 1516 Planarity : 0.003 0.041 1545 Dihedral : 14.608 87.846 3744 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % 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: -0.24 (0.26), residues: 1065 helix: 0.50 (0.24), residues: 478 sheet: -1.14 (0.46), residues: 116 loop : -0.45 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 911 HIS 0.010 0.001 HIS A 342 PHE 0.013 0.001 PHE A 648 TYR 0.016 0.002 TYR A 234 ARG 0.008 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.21461 ( 445) hydrogen bonds : angle 8.31244 ( 1195) metal coordination : bond 0.01920 ( 8) metal coordination : angle 2.00026 ( 6) covalent geometry : bond 0.00486 ( 9694) covalent geometry : angle 0.51215 (13319) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.7563 (mp0) cc_final: 0.7355 (mp0) REVERT: A 547 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7725 (mp0) REVERT: A 660 GLU cc_start: 0.7104 (pm20) cc_final: 0.6883 (pm20) REVERT: A 698 ASN cc_start: 0.8392 (m110) cc_final: 0.8160 (m110) REVERT: B 137 SER cc_start: 0.9516 (m) cc_final: 0.8964 (p) REVERT: B 159 ILE cc_start: 0.9303 (mp) cc_final: 0.9056 (mt) REVERT: B 160 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8334 (mmmt) REVERT: C 8 CYS cc_start: 0.8537 (p) cc_final: 0.8191 (p) REVERT: C 37 ASN cc_start: 0.9373 (m-40) cc_final: 0.8932 (m-40) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1956 time to fit residues: 49.3061 Evaluate side-chains 147 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A 403 GLN A 421 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.110821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075776 restraints weight = 22865.585| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.57 r_work: 0.3134 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9702 Z= 0.129 Angle : 0.583 10.404 13325 Z= 0.304 Chirality : 0.040 0.172 1516 Planarity : 0.004 0.032 1545 Dihedral : 12.649 79.535 1759 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.43 % Allowed : 7.81 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.27), residues: 1065 helix: 0.99 (0.23), residues: 500 sheet: -0.74 (0.51), residues: 110 loop : 0.14 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 182 HIS 0.003 0.001 HIS A 342 PHE 0.010 0.001 PHE C 58 TYR 0.024 0.002 TYR A 211 ARG 0.003 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 445) hydrogen bonds : angle 5.06758 ( 1195) metal coordination : bond 0.00983 ( 8) metal coordination : angle 1.37484 ( 6) covalent geometry : bond 0.00275 ( 9694) covalent geometry : angle 0.58193 (13319) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9076 (mmm) cc_final: 0.8867 (mmp) REVERT: A 119 MET cc_start: 0.9087 (tpt) cc_final: 0.8462 (tpp) REVERT: A 248 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8621 (mp0) REVERT: A 267 GLU cc_start: 0.8298 (mp0) cc_final: 0.8090 (mp0) REVERT: A 415 TYR cc_start: 0.8307 (t80) cc_final: 0.8080 (t80) REVERT: A 419 LEU cc_start: 0.9288 (mm) cc_final: 0.8876 (mm) REVERT: A 450 TYR cc_start: 0.8956 (m-80) cc_final: 0.8634 (m-80) REVERT: A 534 MET cc_start: 0.8766 (mpp) cc_final: 0.8513 (mpp) REVERT: A 660 GLU cc_start: 0.8020 (pm20) cc_final: 0.7627 (pm20) REVERT: A 887 TYR cc_start: 0.9225 (t80) cc_final: 0.8630 (t80) REVERT: A 912 ASP cc_start: 0.8737 (t0) cc_final: 0.8294 (p0) REVERT: A 919 MET cc_start: 0.8987 (mmt) cc_final: 0.8714 (mmt) REVERT: B 137 SER cc_start: 0.9635 (m) cc_final: 0.9274 (p) REVERT: B 159 ILE cc_start: 0.9245 (mp) cc_final: 0.8962 (mp) REVERT: B 160 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8595 (mmmt) REVERT: B 165 LYS cc_start: 0.9402 (ptmm) cc_final: 0.9000 (ptmm) REVERT: B 189 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8398 (tm-30) REVERT: C 8 CYS cc_start: 0.8813 (p) cc_final: 0.8429 (p) REVERT: C 20 MET cc_start: 0.8402 (mtm) cc_final: 0.8151 (ptt) REVERT: C 35 LEU cc_start: 0.9182 (tp) cc_final: 0.8900 (tp) REVERT: C 38 LYS cc_start: 0.8675 (ptmm) cc_final: 0.8311 (ptmm) REVERT: C 46 GLU cc_start: 0.9182 (pm20) cc_final: 0.8971 (pm20) REVERT: C 51 MET cc_start: 0.9511 (mpp) cc_final: 0.9160 (mpp) outliers start: 23 outliers final: 12 residues processed: 187 average time/residue: 0.2009 time to fit residues: 54.0600 Evaluate side-chains 161 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 6 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 48 optimal weight: 4.9990 chunk 43 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A 364 ASN A 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.109772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075575 restraints weight = 22275.198| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.57 r_work: 0.3064 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9702 Z= 0.121 Angle : 0.560 13.279 13325 Z= 0.282 Chirality : 0.040 0.215 1516 Planarity : 0.004 0.038 1545 Dihedral : 12.531 79.641 1759 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.74 % Allowed : 11.81 % Favored : 85.44 % 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: 0.71 (0.27), residues: 1065 helix: 1.13 (0.24), residues: 496 sheet: -0.62 (0.52), residues: 108 loop : 0.18 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 98 HIS 0.004 0.001 HIS B 148 PHE 0.017 0.001 PHE C 58 TYR 0.024 0.001 TYR A 211 ARG 0.003 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 445) hydrogen bonds : angle 4.64399 ( 1195) metal coordination : bond 0.01028 ( 8) metal coordination : angle 1.28838 ( 6) covalent geometry : bond 0.00266 ( 9694) covalent geometry : angle 0.55954 (13319) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9168 (tt0) cc_final: 0.8782 (tp30) REVERT: A 119 MET cc_start: 0.9061 (tpt) cc_final: 0.8461 (tpp) REVERT: A 223 MET cc_start: 0.9163 (mmm) cc_final: 0.8742 (ptp) REVERT: A 248 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8587 (mp0) REVERT: A 267 GLU cc_start: 0.8278 (mp0) cc_final: 0.7959 (mp0) REVERT: A 403 GLN cc_start: 0.8743 (tt0) cc_final: 0.7845 (pm20) REVERT: A 415 TYR cc_start: 0.8433 (t80) cc_final: 0.8201 (t80) REVERT: A 419 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8928 (mm) REVERT: A 450 TYR cc_start: 0.8907 (m-80) cc_final: 0.8664 (m-80) REVERT: A 660 GLU cc_start: 0.8109 (pm20) cc_final: 0.7650 (pm20) REVERT: A 887 TYR cc_start: 0.9343 (t80) cc_final: 0.9092 (t80) REVERT: A 911 TRP cc_start: 0.7810 (t-100) cc_final: 0.7328 (m100) REVERT: A 912 ASP cc_start: 0.8765 (t0) cc_final: 0.8329 (p0) REVERT: A 919 MET cc_start: 0.8895 (mmt) cc_final: 0.8638 (mmt) REVERT: B 91 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.7057 (tt) REVERT: B 137 SER cc_start: 0.9631 (m) cc_final: 0.9350 (p) REVERT: B 140 ARG cc_start: 0.9009 (mtm-85) cc_final: 0.8781 (mtm-85) REVERT: B 158 ASP cc_start: 0.8998 (t0) cc_final: 0.8716 (t0) REVERT: B 159 ILE cc_start: 0.9211 (mp) cc_final: 0.8756 (mp) REVERT: B 160 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8612 (mmmt) REVERT: B 165 LYS cc_start: 0.9439 (ptmm) cc_final: 0.9088 (ptmm) REVERT: C 8 CYS cc_start: 0.8898 (p) cc_final: 0.8497 (p) REVERT: C 20 MET cc_start: 0.8438 (mtm) cc_final: 0.8126 (ptt) REVERT: C 35 LEU cc_start: 0.9243 (tp) cc_final: 0.8967 (tp) REVERT: C 38 LYS cc_start: 0.8676 (ptmm) cc_final: 0.8178 (ptmm) REVERT: C 51 MET cc_start: 0.9530 (mpp) cc_final: 0.8738 (ptp) outliers start: 26 outliers final: 15 residues processed: 173 average time/residue: 0.2046 time to fit residues: 50.3243 Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 27 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 89 optimal weight: 0.0980 chunk 57 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A 698 ASN B 148 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.110692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.076663 restraints weight = 22171.892| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.52 r_work: 0.3091 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9702 Z= 0.112 Angle : 0.562 13.052 13325 Z= 0.276 Chirality : 0.039 0.176 1516 Planarity : 0.003 0.033 1545 Dihedral : 12.446 79.330 1759 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.38 % Allowed : 13.50 % Favored : 83.12 % 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: 0.80 (0.27), residues: 1065 helix: 1.19 (0.24), residues: 497 sheet: -0.55 (0.52), residues: 108 loop : 0.25 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 182 HIS 0.002 0.001 HIS B 148 PHE 0.011 0.001 PHE A 736 TYR 0.024 0.001 TYR A 211 ARG 0.005 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 445) hydrogen bonds : angle 4.42693 ( 1195) metal coordination : bond 0.01002 ( 8) metal coordination : angle 1.35072 ( 6) covalent geometry : bond 0.00247 ( 9694) covalent geometry : angle 0.56157 (13319) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9161 (mmm) cc_final: 0.8901 (mmp) REVERT: A 115 GLU cc_start: 0.9136 (tt0) cc_final: 0.8722 (tp30) REVERT: A 119 MET cc_start: 0.9044 (tpt) cc_final: 0.8438 (tpp) REVERT: A 248 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8593 (mp0) REVERT: A 263 TYR cc_start: 0.7769 (p90) cc_final: 0.7547 (p90) REVERT: A 267 GLU cc_start: 0.8355 (mp0) cc_final: 0.7996 (mp0) REVERT: A 419 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8912 (mm) REVERT: A 450 TYR cc_start: 0.8897 (m-80) cc_final: 0.8680 (m-80) REVERT: A 660 GLU cc_start: 0.8092 (pm20) cc_final: 0.7666 (pm20) REVERT: A 887 TYR cc_start: 0.9256 (t80) cc_final: 0.8917 (t80) REVERT: A 912 ASP cc_start: 0.8731 (t0) cc_final: 0.8363 (p0) REVERT: A 919 MET cc_start: 0.8879 (mmt) cc_final: 0.8614 (mmt) REVERT: B 137 SER cc_start: 0.9619 (m) cc_final: 0.9271 (p) REVERT: B 140 ARG cc_start: 0.9018 (mtm-85) cc_final: 0.8772 (mtm-85) REVERT: B 158 ASP cc_start: 0.8981 (t0) cc_final: 0.8563 (t0) REVERT: B 159 ILE cc_start: 0.9149 (mp) cc_final: 0.8674 (mp) REVERT: B 160 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8602 (mmmt) REVERT: B 165 LYS cc_start: 0.9457 (ptmm) cc_final: 0.9166 (ptmm) REVERT: C 8 CYS cc_start: 0.8863 (p) cc_final: 0.8401 (p) REVERT: C 35 LEU cc_start: 0.9273 (tp) cc_final: 0.9015 (tp) REVERT: C 38 LYS cc_start: 0.8662 (ptmm) cc_final: 0.8256 (ptmm) outliers start: 32 outliers final: 22 residues processed: 180 average time/residue: 0.1955 time to fit residues: 51.1353 Evaluate side-chains 178 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.0050 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS B 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.112658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.079140 restraints weight = 22141.428| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.43 r_work: 0.3192 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9702 Z= 0.105 Angle : 0.555 13.007 13325 Z= 0.271 Chirality : 0.039 0.257 1516 Planarity : 0.003 0.032 1545 Dihedral : 12.364 79.444 1759 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.38 % Allowed : 14.24 % Favored : 82.38 % 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: 0.89 (0.27), residues: 1065 helix: 1.22 (0.23), residues: 504 sheet: -0.61 (0.54), residues: 99 loop : 0.32 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 182 HIS 0.003 0.001 HIS B 148 PHE 0.011 0.001 PHE A 736 TYR 0.025 0.001 TYR A 415 ARG 0.006 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 445) hydrogen bonds : angle 4.29420 ( 1195) metal coordination : bond 0.00771 ( 8) metal coordination : angle 1.39868 ( 6) covalent geometry : bond 0.00228 ( 9694) covalent geometry : angle 0.55436 (13319) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9062 (tt0) cc_final: 0.8688 (tp30) REVERT: A 119 MET cc_start: 0.9003 (tpt) cc_final: 0.8357 (tpp) REVERT: A 236 MET cc_start: 0.8897 (mmm) cc_final: 0.8552 (mmm) REVERT: A 239 MET cc_start: 0.9028 (ttm) cc_final: 0.8807 (ttm) REVERT: A 248 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8646 (mp0) REVERT: A 263 TYR cc_start: 0.7741 (p90) cc_final: 0.7501 (p90) REVERT: A 267 GLU cc_start: 0.8365 (mp0) cc_final: 0.7981 (mp0) REVERT: A 403 GLN cc_start: 0.8776 (tt0) cc_final: 0.8423 (mm110) REVERT: A 419 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9037 (mm) REVERT: A 660 GLU cc_start: 0.8074 (pm20) cc_final: 0.7611 (pm20) REVERT: A 887 TYR cc_start: 0.9289 (t80) cc_final: 0.9056 (t80) REVERT: A 912 ASP cc_start: 0.8703 (t0) cc_final: 0.8401 (p0) REVERT: A 919 MET cc_start: 0.8923 (mmt) cc_final: 0.8653 (mmt) REVERT: B 137 SER cc_start: 0.9603 (m) cc_final: 0.9142 (p) REVERT: B 140 ARG cc_start: 0.9058 (mtm-85) cc_final: 0.8760 (mtm-85) REVERT: B 158 ASP cc_start: 0.8955 (t0) cc_final: 0.8404 (t0) REVERT: B 159 ILE cc_start: 0.9095 (mp) cc_final: 0.8601 (mp) REVERT: B 160 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8543 (mmmt) REVERT: B 165 LYS cc_start: 0.9395 (ptmm) cc_final: 0.9186 (ptmm) REVERT: C 8 CYS cc_start: 0.8851 (p) cc_final: 0.8580 (p) REVERT: C 35 LEU cc_start: 0.9254 (tp) cc_final: 0.8983 (tp) REVERT: C 38 LYS cc_start: 0.8664 (ptmm) cc_final: 0.8234 (ptmm) outliers start: 32 outliers final: 22 residues processed: 181 average time/residue: 0.1965 time to fit residues: 51.0184 Evaluate side-chains 179 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN A 568 GLN B 148 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.106807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.072320 restraints weight = 22615.857| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.57 r_work: 0.2987 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 9702 Z= 0.276 Angle : 0.663 16.484 13325 Z= 0.330 Chirality : 0.042 0.200 1516 Planarity : 0.004 0.038 1545 Dihedral : 12.507 81.687 1759 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.27 % Allowed : 15.82 % Favored : 80.91 % 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: 0.59 (0.27), residues: 1065 helix: 0.92 (0.23), residues: 509 sheet: -0.71 (0.52), residues: 108 loop : 0.26 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 182 HIS 0.011 0.002 HIS B 168 PHE 0.015 0.002 PHE A 692 TYR 0.025 0.002 TYR A 211 ARG 0.005 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 445) hydrogen bonds : angle 4.76359 ( 1195) metal coordination : bond 0.02894 ( 8) metal coordination : angle 1.76859 ( 6) covalent geometry : bond 0.00624 ( 9694) covalent geometry : angle 0.66227 (13319) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9149 (mmm) cc_final: 0.8937 (mmm) REVERT: A 115 GLU cc_start: 0.9141 (tt0) cc_final: 0.8674 (tp30) REVERT: A 248 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8726 (mp0) REVERT: A 263 TYR cc_start: 0.7874 (p90) cc_final: 0.7651 (p90) REVERT: A 267 GLU cc_start: 0.8475 (mp0) cc_final: 0.8086 (mp0) REVERT: A 403 GLN cc_start: 0.8737 (tt0) cc_final: 0.7905 (pm20) REVERT: A 419 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9063 (mm) REVERT: A 536 GLN cc_start: 0.8143 (tt0) cc_final: 0.7876 (tt0) REVERT: A 660 GLU cc_start: 0.8173 (pm20) cc_final: 0.7739 (pm20) REVERT: A 887 TYR cc_start: 0.9391 (t80) cc_final: 0.9169 (t80) REVERT: A 919 MET cc_start: 0.8963 (mmt) cc_final: 0.8750 (mmt) REVERT: B 140 ARG cc_start: 0.9099 (mtm-85) cc_final: 0.8670 (mtm-85) REVERT: B 158 ASP cc_start: 0.9061 (t0) cc_final: 0.8713 (t0) REVERT: B 160 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8552 (mmmt) REVERT: B 165 LYS cc_start: 0.9415 (ptmm) cc_final: 0.9175 (ptmm) REVERT: C 8 CYS cc_start: 0.8971 (p) cc_final: 0.8650 (p) REVERT: C 35 LEU cc_start: 0.9306 (tp) cc_final: 0.9089 (tp) REVERT: C 38 LYS cc_start: 0.8654 (ptmm) cc_final: 0.8214 (ptmm) REVERT: C 51 MET cc_start: 0.9582 (OUTLIER) cc_final: 0.8780 (mtt) REVERT: C 55 LEU cc_start: 0.9523 (mt) cc_final: 0.9317 (mt) outliers start: 31 outliers final: 23 residues processed: 173 average time/residue: 0.1911 time to fit residues: 47.1503 Evaluate side-chains 177 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 chunk 47 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.112238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.077545 restraints weight = 23041.261| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.61 r_work: 0.3149 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9702 Z= 0.116 Angle : 0.603 16.866 13325 Z= 0.291 Chirality : 0.039 0.338 1516 Planarity : 0.003 0.034 1545 Dihedral : 12.407 81.711 1759 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.95 % Allowed : 16.98 % Favored : 80.06 % 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: 0.82 (0.27), residues: 1065 helix: 1.13 (0.24), residues: 509 sheet: -0.58 (0.55), residues: 94 loop : 0.29 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 182 HIS 0.002 0.001 HIS A 342 PHE 0.011 0.001 PHE A 736 TYR 0.023 0.001 TYR A 211 ARG 0.006 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 445) hydrogen bonds : angle 4.39951 ( 1195) metal coordination : bond 0.00992 ( 8) metal coordination : angle 1.34690 ( 6) covalent geometry : bond 0.00261 ( 9694) covalent geometry : angle 0.60207 (13319) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9160 (mmm) cc_final: 0.8905 (mmp) REVERT: A 115 GLU cc_start: 0.9068 (tt0) cc_final: 0.8653 (tp30) REVERT: A 248 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8646 (mp0) REVERT: A 263 TYR cc_start: 0.7756 (p90) cc_final: 0.7516 (p90) REVERT: A 267 GLU cc_start: 0.8383 (mp0) cc_final: 0.7974 (mp0) REVERT: A 403 GLN cc_start: 0.8727 (tt0) cc_final: 0.8397 (mm110) REVERT: A 412 LYS cc_start: 0.9428 (tttp) cc_final: 0.9015 (tppt) REVERT: A 419 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9040 (mm) REVERT: A 660 GLU cc_start: 0.8097 (pm20) cc_final: 0.7725 (pm20) REVERT: A 887 TYR cc_start: 0.9280 (t80) cc_final: 0.8209 (t80) REVERT: A 912 ASP cc_start: 0.8690 (t0) cc_final: 0.8424 (p0) REVERT: A 919 MET cc_start: 0.8967 (mmt) cc_final: 0.8674 (mmt) REVERT: B 140 ARG cc_start: 0.9081 (mtm-85) cc_final: 0.8689 (mtm-85) REVERT: B 158 ASP cc_start: 0.9018 (t0) cc_final: 0.8644 (t0) REVERT: B 159 ILE cc_start: 0.9005 (mp) cc_final: 0.8767 (mp) REVERT: B 160 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8599 (mmmt) REVERT: C 8 CYS cc_start: 0.8878 (p) cc_final: 0.8618 (p) REVERT: C 38 LYS cc_start: 0.8607 (ptmm) cc_final: 0.8173 (ptmm) REVERT: C 51 MET cc_start: 0.9547 (OUTLIER) cc_final: 0.9143 (mpp) outliers start: 28 outliers final: 24 residues processed: 171 average time/residue: 0.2031 time to fit residues: 49.5398 Evaluate side-chains 179 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 106 optimal weight: 40.0000 chunk 93 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.110543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.075191 restraints weight = 23114.092| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.63 r_work: 0.3114 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9702 Z= 0.151 Angle : 0.620 17.162 13325 Z= 0.300 Chirality : 0.040 0.306 1516 Planarity : 0.003 0.035 1545 Dihedral : 12.351 82.372 1759 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.48 % Allowed : 16.67 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.27), residues: 1065 helix: 1.08 (0.24), residues: 508 sheet: -0.85 (0.54), residues: 98 loop : 0.32 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 182 HIS 0.003 0.001 HIS A 342 PHE 0.011 0.001 PHE A 736 TYR 0.023 0.001 TYR A 211 ARG 0.007 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 445) hydrogen bonds : angle 4.44354 ( 1195) metal coordination : bond 0.01462 ( 8) metal coordination : angle 1.44487 ( 6) covalent geometry : bond 0.00347 ( 9694) covalent geometry : angle 0.61949 (13319) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9103 (tt0) cc_final: 0.8665 (tp30) REVERT: A 248 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8701 (mp0) REVERT: A 263 TYR cc_start: 0.7786 (p90) cc_final: 0.7534 (p90) REVERT: A 267 GLU cc_start: 0.8443 (mp0) cc_final: 0.8017 (mp0) REVERT: A 403 GLN cc_start: 0.8704 (tt0) cc_final: 0.8382 (mm110) REVERT: A 412 LYS cc_start: 0.9442 (tttp) cc_final: 0.9030 (tppt) REVERT: A 419 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9055 (mm) REVERT: A 536 GLN cc_start: 0.8208 (tt0) cc_final: 0.7957 (tt0) REVERT: A 614 TYR cc_start: 0.8893 (m-10) cc_final: 0.8615 (m-10) REVERT: A 660 GLU cc_start: 0.8081 (pm20) cc_final: 0.7721 (pm20) REVERT: B 142 GLN cc_start: 0.8829 (pp30) cc_final: 0.8234 (pp30) REVERT: B 158 ASP cc_start: 0.9042 (t0) cc_final: 0.8611 (t0) REVERT: B 159 ILE cc_start: 0.9043 (mp) cc_final: 0.8442 (mp) REVERT: B 160 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8590 (mmmt) REVERT: B 189 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8465 (tm-30) REVERT: C 8 CYS cc_start: 0.8869 (p) cc_final: 0.8600 (p) REVERT: C 38 LYS cc_start: 0.8596 (ptmm) cc_final: 0.8174 (ptmm) REVERT: C 55 LEU cc_start: 0.9513 (mt) cc_final: 0.9311 (mt) outliers start: 33 outliers final: 28 residues processed: 175 average time/residue: 0.1906 time to fit residues: 47.7531 Evaluate side-chains 183 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 36 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.112261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.077107 restraints weight = 22807.170| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.68 r_work: 0.3155 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9702 Z= 0.121 Angle : 0.621 17.658 13325 Z= 0.298 Chirality : 0.039 0.342 1516 Planarity : 0.003 0.034 1545 Dihedral : 12.315 82.225 1759 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.16 % Allowed : 16.98 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.83 (0.27), residues: 1065 helix: 1.16 (0.24), residues: 508 sheet: -0.77 (0.57), residues: 93 loop : 0.33 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 182 HIS 0.003 0.001 HIS A 304 PHE 0.010 0.001 PHE A 736 TYR 0.022 0.001 TYR A 211 ARG 0.007 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 445) hydrogen bonds : angle 4.35777 ( 1195) metal coordination : bond 0.01007 ( 8) metal coordination : angle 1.35488 ( 6) covalent geometry : bond 0.00276 ( 9694) covalent geometry : angle 0.62051 (13319) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8630 (mp0) REVERT: A 263 TYR cc_start: 0.7804 (p90) cc_final: 0.7555 (p90) REVERT: A 267 GLU cc_start: 0.8411 (mp0) cc_final: 0.7976 (mp0) REVERT: A 403 GLN cc_start: 0.8738 (tt0) cc_final: 0.8418 (mm110) REVERT: A 412 LYS cc_start: 0.9428 (tttp) cc_final: 0.9007 (tppt) REVERT: A 419 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9054 (mm) REVERT: A 536 GLN cc_start: 0.8199 (tt0) cc_final: 0.7838 (tt0) REVERT: A 660 GLU cc_start: 0.8008 (pm20) cc_final: 0.7692 (pm20) REVERT: A 887 TYR cc_start: 0.9231 (t80) cc_final: 0.8808 (t80) REVERT: B 134 ASP cc_start: 0.8565 (t0) cc_final: 0.8351 (t0) REVERT: B 158 ASP cc_start: 0.9021 (t0) cc_final: 0.8592 (t0) REVERT: B 159 ILE cc_start: 0.9052 (mp) cc_final: 0.8570 (mp) REVERT: B 160 LYS cc_start: 0.9071 (mmmt) cc_final: 0.8609 (mmmt) REVERT: C 8 CYS cc_start: 0.8862 (p) cc_final: 0.8590 (p) REVERT: C 38 LYS cc_start: 0.8567 (ptmm) cc_final: 0.8159 (ptmm) REVERT: C 55 LEU cc_start: 0.9492 (mt) cc_final: 0.9284 (mt) outliers start: 30 outliers final: 26 residues processed: 168 average time/residue: 0.2021 time to fit residues: 48.6368 Evaluate side-chains 178 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.112801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.077932 restraints weight = 22903.014| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.64 r_work: 0.3158 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9702 Z= 0.121 Angle : 0.632 17.886 13325 Z= 0.303 Chirality : 0.040 0.349 1516 Planarity : 0.003 0.035 1545 Dihedral : 12.314 81.961 1759 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.95 % Allowed : 17.19 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.27), residues: 1065 helix: 1.23 (0.24), residues: 502 sheet: -0.77 (0.56), residues: 93 loop : 0.31 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 182 HIS 0.003 0.001 HIS A 304 PHE 0.011 0.001 PHE A 689 TYR 0.023 0.001 TYR A 211 ARG 0.008 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 445) hydrogen bonds : angle 4.33501 ( 1195) metal coordination : bond 0.00940 ( 8) metal coordination : angle 1.33314 ( 6) covalent geometry : bond 0.00277 ( 9694) covalent geometry : angle 0.63173 (13319) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8623 (mp0) REVERT: A 263 TYR cc_start: 0.7817 (p90) cc_final: 0.7569 (p90) REVERT: A 267 GLU cc_start: 0.8401 (mp0) cc_final: 0.7951 (mp0) REVERT: A 403 GLN cc_start: 0.8743 (tt0) cc_final: 0.8424 (mm110) REVERT: A 412 LYS cc_start: 0.9446 (tttp) cc_final: 0.9016 (tppt) REVERT: A 419 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9081 (mm) REVERT: A 536 GLN cc_start: 0.8184 (tt0) cc_final: 0.7823 (tt0) REVERT: A 660 GLU cc_start: 0.7954 (pm20) cc_final: 0.7645 (pm20) REVERT: A 887 TYR cc_start: 0.9206 (t80) cc_final: 0.8798 (t80) REVERT: A 919 MET cc_start: 0.9243 (tpp) cc_final: 0.8786 (mmt) REVERT: B 134 ASP cc_start: 0.8257 (t0) cc_final: 0.7828 (t0) REVERT: B 158 ASP cc_start: 0.9031 (t0) cc_final: 0.8613 (t0) REVERT: B 159 ILE cc_start: 0.9048 (mp) cc_final: 0.8569 (mp) REVERT: B 160 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8578 (mmmt) REVERT: C 8 CYS cc_start: 0.8864 (p) cc_final: 0.8585 (p) REVERT: C 38 LYS cc_start: 0.8579 (ptmm) cc_final: 0.8072 (ptmm) REVERT: C 44 ASP cc_start: 0.8650 (t0) cc_final: 0.8031 (t0) REVERT: C 51 MET cc_start: 0.9510 (OUTLIER) cc_final: 0.9137 (mtp) outliers start: 28 outliers final: 23 residues processed: 171 average time/residue: 0.2000 time to fit residues: 49.0258 Evaluate side-chains 178 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 40.0000 chunk 38 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.112572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.077253 restraints weight = 22829.153| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.69 r_work: 0.3154 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9702 Z= 0.128 Angle : 0.641 17.470 13325 Z= 0.308 Chirality : 0.040 0.346 1516 Planarity : 0.003 0.035 1545 Dihedral : 12.320 81.829 1759 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.95 % Allowed : 17.72 % Favored : 79.32 % 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: 0.79 (0.27), residues: 1065 helix: 1.17 (0.23), residues: 512 sheet: -1.16 (0.53), residues: 103 loop : 0.37 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 911 HIS 0.003 0.001 HIS A 304 PHE 0.010 0.001 PHE A 736 TYR 0.023 0.001 TYR A 211 ARG 0.008 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 445) hydrogen bonds : angle 4.31849 ( 1195) metal coordination : bond 0.01017 ( 8) metal coordination : angle 1.45755 ( 6) covalent geometry : bond 0.00296 ( 9694) covalent geometry : angle 0.64001 (13319) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4848.67 seconds wall clock time: 84 minutes 55.17 seconds (5095.17 seconds total)