Starting phenix.real_space_refine on Wed Apr 30 15:53:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6r_29779/04_2025/8g6r_29779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6r_29779/04_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_29779/04_2025/8g6r_29779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6r_29779/04_2025/8g6r_29779.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6r_29779/04_2025/8g6r_29779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6r_29779/04_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-5669/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: 6.02, per 1000 atoms: 0.64 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: 2.56 Conformation dependent library (CDL) restraints added in 975.1 milliseconds 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: 3.66 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: 3.90 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: 1.050 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.590 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- 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 : 0.982 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: 0.1988 time to fit residues: 49.6585 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 : 0.989 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075775 restraints weight = 22865.593| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.57 r_work: 0.3134 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 10.405 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 5.06757 ( 1195) metal coordination : bond 0.00983 ( 8) metal coordination : angle 1.37481 ( 6) covalent geometry : bond 0.00275 ( 9694) covalent geometry : angle 0.58192 (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 : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9078 (mmm) cc_final: 0.8868 (mmp) REVERT: A 119 MET cc_start: 0.9087 (tpt) cc_final: 0.8461 (tpp) REVERT: A 248 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8620 (mp0) REVERT: A 267 GLU cc_start: 0.8300 (mp0) cc_final: 0.8090 (mp0) REVERT: A 415 TYR cc_start: 0.8311 (t80) cc_final: 0.8085 (t80) REVERT: A 419 LEU cc_start: 0.9290 (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: 0.8764 (mpp) cc_final: 0.8511 (mpp) REVERT: A 660 GLU cc_start: 0.8022 (pm20) cc_final: 0.7628 (pm20) REVERT: A 887 TYR cc_start: 0.9225 (t80) cc_final: 0.8631 (t80) REVERT: A 912 ASP cc_start: 0.8738 (t0) cc_final: 0.8293 (p0) REVERT: A 919 MET cc_start: 0.8986 (mmt) cc_final: 0.8714 (mmt) REVERT: B 137 SER cc_start: 0.9634 (m) cc_final: 0.9274 (p) REVERT: B 159 ILE cc_start: 0.9243 (mp) cc_final: 0.8960 (mp) REVERT: B 160 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8594 (mmmt) REVERT: B 165 LYS cc_start: 0.9403 (ptmm) cc_final: 0.9001 (ptmm) REVERT: B 189 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8398 (tm-30) REVERT: C 8 CYS cc_start: 0.8813 (p) cc_final: 0.8430 (p) REVERT: C 20 MET cc_start: 0.8403 (mtm) cc_final: 0.8150 (ptt) REVERT: C 35 LEU cc_start: 0.9182 (tp) cc_final: 0.8899 (tp) REVERT: C 38 LYS cc_start: 0.8674 (ptmm) cc_final: 0.8311 (ptmm) REVERT: C 46 GLU cc_start: 0.9183 (pm20) cc_final: 0.8972 (pm20) REVERT: C 51 MET cc_start: 0.9514 (mpp) cc_final: 0.9162 (mpp) outliers start: 23 outliers final: 12 residues processed: 187 average time/residue: 0.1977 time to fit residues: 52.7414 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 : 1.112 ------------------------------------------------------------------------------- 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: 5.9990 chunk 72 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.108804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074531 restraints weight = 22351.578| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.55 r_work: 0.3039 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9702 Z= 0.145 Angle : 0.570 13.404 13325 Z= 0.288 Chirality : 0.040 0.235 1516 Planarity : 0.004 0.040 1545 Dihedral : 12.565 79.957 1759 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.95 % Allowed : 11.81 % Favored : 85.23 % 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: 0.64 (0.27), residues: 1065 helix: 1.07 (0.24), residues: 497 sheet: -0.67 (0.52), residues: 108 loop : 0.14 (0.31), residues: 460 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 0.016 0.001 PHE C 58 TYR 0.025 0.002 TYR A 211 ARG 0.004 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 445) hydrogen bonds : angle 4.70002 ( 1195) metal coordination : bond 0.01457 ( 8) metal coordination : angle 1.40816 ( 6) covalent geometry : bond 0.00326 ( 9694) covalent geometry : angle 0.56959 (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: 28 poor density : 161 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9168 (tt0) cc_final: 0.8778 (tp30) REVERT: A 223 MET cc_start: 0.9178 (mmm) cc_final: 0.8764 (ptp) REVERT: A 248 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8598 (mp0) REVERT: A 267 GLU cc_start: 0.8294 (mp0) cc_final: 0.7983 (mp0) REVERT: A 403 GLN cc_start: 0.8729 (tt0) cc_final: 0.7836 (pm20) REVERT: A 415 TYR cc_start: 0.8478 (t80) cc_final: 0.8249 (t80) REVERT: A 419 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8931 (mm) REVERT: A 450 TYR cc_start: 0.8924 (m-80) cc_final: 0.8587 (m-80) REVERT: A 534 MET cc_start: 0.8836 (mpp) cc_final: 0.8508 (mpp) REVERT: A 660 GLU cc_start: 0.8131 (pm20) cc_final: 0.7688 (pm20) REVERT: A 887 TYR cc_start: 0.9337 (t80) cc_final: 0.9092 (t80) REVERT: A 911 TRP cc_start: 0.7824 (t-100) cc_final: 0.7342 (m100) REVERT: A 912 ASP cc_start: 0.8759 (t0) cc_final: 0.8331 (p0) REVERT: A 919 MET cc_start: 0.8907 (mmt) cc_final: 0.8627 (mmt) REVERT: B 91 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7063 (tt) REVERT: B 137 SER cc_start: 0.9641 (m) cc_final: 0.9368 (p) REVERT: B 140 ARG cc_start: 0.9015 (mtm-85) cc_final: 0.8784 (mtm-85) REVERT: B 158 ASP cc_start: 0.9001 (t0) cc_final: 0.8721 (t0) REVERT: B 159 ILE cc_start: 0.9217 (mp) cc_final: 0.8763 (mp) REVERT: B 160 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8627 (mmmt) REVERT: B 165 LYS cc_start: 0.9437 (ptmm) cc_final: 0.9062 (ptmm) REVERT: C 8 CYS cc_start: 0.8918 (p) cc_final: 0.8533 (p) REVERT: C 20 MET cc_start: 0.8459 (mtm) cc_final: 0.8146 (ptt) REVERT: C 35 LEU cc_start: 0.9248 (tp) cc_final: 0.8960 (tp) REVERT: C 38 LYS cc_start: 0.8683 (ptmm) cc_final: 0.8184 (ptmm) REVERT: C 51 MET cc_start: 0.9531 (mpp) cc_final: 0.8714 (ptp) outliers start: 28 outliers final: 17 residues processed: 172 average time/residue: 0.2265 time to fit residues: 55.9971 Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 520 ASP Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 631 MET 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 11 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.109987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075861 restraints weight = 22195.477| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.50 r_work: 0.3078 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9702 Z= 0.120 Angle : 0.563 13.869 13325 Z= 0.278 Chirality : 0.039 0.178 1516 Planarity : 0.003 0.033 1545 Dihedral : 12.497 79.729 1759 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.06 % Allowed : 14.03 % Favored : 82.91 % 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: 0.78 (0.27), residues: 1065 helix: 1.16 (0.24), residues: 497 sheet: -0.60 (0.52), residues: 108 loop : 0.25 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 182 HIS 0.003 0.001 HIS A 304 PHE 0.011 0.001 PHE A 736 TYR 0.024 0.001 TYR A 211 ARG 0.004 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 445) hydrogen bonds : angle 4.45765 ( 1195) metal coordination : bond 0.01177 ( 8) metal coordination : angle 1.49182 ( 6) covalent geometry : bond 0.00265 ( 9694) covalent geometry : angle 0.56259 (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 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9129 (tt0) cc_final: 0.8705 (tp30) REVERT: A 248 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8603 (mp0) REVERT: A 263 TYR cc_start: 0.7784 (p90) cc_final: 0.7566 (p90) REVERT: A 267 GLU cc_start: 0.8370 (mp0) cc_final: 0.8019 (mp0) REVERT: A 419 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8901 (mm) REVERT: A 450 TYR cc_start: 0.8919 (m-80) cc_final: 0.8678 (m-80) REVERT: A 660 GLU cc_start: 0.8110 (pm20) cc_final: 0.7687 (pm20) REVERT: A 887 TYR cc_start: 0.9264 (t80) cc_final: 0.8918 (t80) REVERT: A 912 ASP cc_start: 0.8765 (t0) cc_final: 0.8364 (p0) REVERT: A 919 MET cc_start: 0.8906 (mmt) cc_final: 0.8624 (mmt) REVERT: B 137 SER cc_start: 0.9640 (m) cc_final: 0.9304 (p) REVERT: B 140 ARG cc_start: 0.9016 (mtm-85) cc_final: 0.8756 (mtm-85) REVERT: B 158 ASP cc_start: 0.8983 (t0) cc_final: 0.8649 (t0) REVERT: B 159 ILE cc_start: 0.9159 (mp) cc_final: 0.8702 (mp) REVERT: B 160 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8613 (mmmt) REVERT: B 165 LYS cc_start: 0.9446 (ptmm) cc_final: 0.9113 (ptmm) REVERT: C 8 CYS cc_start: 0.8862 (p) cc_final: 0.8410 (p) REVERT: C 35 LEU cc_start: 0.9272 (tp) cc_final: 0.9001 (tp) REVERT: C 38 LYS cc_start: 0.8697 (ptmm) cc_final: 0.8280 (ptmm) outliers start: 29 outliers final: 21 residues processed: 180 average time/residue: 0.2117 time to fit residues: 54.9394 Evaluate side-chains 176 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 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 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 631 MET 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 A residue 834 SER 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 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: 1.9990 chunk 55 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 GLN B 148 HIS B 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.109758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.076004 restraints weight = 22351.989| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.41 r_work: 0.3120 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9702 Z= 0.164 Angle : 0.587 11.713 13325 Z= 0.291 Chirality : 0.040 0.262 1516 Planarity : 0.004 0.035 1545 Dihedral : 12.501 80.515 1759 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.11 % Allowed : 14.56 % Favored : 81.33 % 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: 0.72 (0.27), residues: 1065 helix: 1.04 (0.23), residues: 504 sheet: -0.54 (0.53), residues: 106 loop : 0.27 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 182 HIS 0.004 0.001 HIS A 342 PHE 0.012 0.001 PHE A 736 TYR 0.025 0.001 TYR A 211 ARG 0.005 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 445) hydrogen bonds : angle 4.50093 ( 1195) metal coordination : bond 0.01776 ( 8) metal coordination : angle 1.55667 ( 6) covalent geometry : bond 0.00371 ( 9694) covalent geometry : angle 0.58582 (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 200 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9106 (tt0) cc_final: 0.8666 (tp30) REVERT: A 248 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8679 (mp0) REVERT: A 263 TYR cc_start: 0.7833 (p90) cc_final: 0.7601 (p90) REVERT: A 267 GLU cc_start: 0.8367 (mp0) cc_final: 0.8003 (mp0) REVERT: A 419 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9013 (mm) REVERT: A 660 GLU cc_start: 0.8069 (pm20) cc_final: 0.7641 (pm20) REVERT: A 887 TYR cc_start: 0.9324 (t80) cc_final: 0.9118 (t80) REVERT: A 912 ASP cc_start: 0.8732 (t0) cc_final: 0.8382 (p0) REVERT: A 919 MET cc_start: 0.9019 (mmt) cc_final: 0.8757 (mmt) REVERT: B 137 SER cc_start: 0.9615 (m) cc_final: 0.9152 (m) REVERT: B 140 ARG cc_start: 0.9042 (mtm-85) cc_final: 0.8661 (mtm-85) REVERT: B 158 ASP cc_start: 0.9006 (t0) cc_final: 0.8640 (t0) REVERT: B 159 ILE cc_start: 0.9125 (mp) cc_final: 0.8629 (mp) REVERT: B 160 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8605 (mmmt) REVERT: B 165 LYS cc_start: 0.9434 (ptmm) cc_final: 0.9127 (ptmm) REVERT: C 8 CYS cc_start: 0.8842 (p) cc_final: 0.8541 (p) REVERT: C 35 LEU cc_start: 0.9289 (tp) cc_final: 0.9036 (tp) REVERT: C 38 LYS cc_start: 0.8690 (ptmm) cc_final: 0.8255 (ptmm) outliers start: 39 outliers final: 29 residues processed: 177 average time/residue: 0.1948 time to fit residues: 49.4778 Evaluate side-chains 185 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 A residue 834 SER Chi-restraints excluded: chain A residue 911 TRP 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 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: 5.9990 chunk 82 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.110601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.075385 restraints weight = 22802.390| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.61 r_work: 0.3127 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9702 Z= 0.139 Angle : 0.587 16.673 13325 Z= 0.287 Chirality : 0.039 0.248 1516 Planarity : 0.003 0.034 1545 Dihedral : 12.468 80.972 1759 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.69 % Allowed : 15.40 % 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: 0.76 (0.27), residues: 1065 helix: 1.06 (0.24), residues: 509 sheet: -0.55 (0.55), residues: 94 loop : 0.27 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 182 HIS 0.003 0.001 HIS A 342 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 0.03458 ( 445) hydrogen bonds : angle 4.43442 ( 1195) metal coordination : bond 0.01429 ( 8) metal coordination : angle 1.49983 ( 6) covalent geometry : bond 0.00314 ( 9694) covalent geometry : angle 0.58659 (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 195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9083 (tt0) cc_final: 0.8640 (tp30) REVERT: A 248 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8694 (mp0) REVERT: A 263 TYR cc_start: 0.7798 (p90) cc_final: 0.7564 (p90) REVERT: A 267 GLU cc_start: 0.8390 (mp0) cc_final: 0.7998 (mp0) REVERT: A 419 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9003 (mm) REVERT: A 450 TYR cc_start: 0.8944 (m-80) cc_final: 0.8662 (m-80) REVERT: A 614 TYR cc_start: 0.8962 (m-10) cc_final: 0.8742 (m-10) REVERT: A 660 GLU cc_start: 0.8071 (pm20) cc_final: 0.7623 (pm20) REVERT: A 887 TYR cc_start: 0.9315 (t80) cc_final: 0.8342 (t80) REVERT: A 912 ASP cc_start: 0.8699 (t0) cc_final: 0.8408 (p0) REVERT: A 919 MET cc_start: 0.8998 (mmt) cc_final: 0.8716 (mmt) REVERT: B 137 SER cc_start: 0.9606 (m) cc_final: 0.9187 (p) REVERT: B 140 ARG cc_start: 0.9068 (mtm-85) cc_final: 0.8808 (mtm-85) REVERT: B 158 ASP cc_start: 0.9025 (t0) cc_final: 0.8622 (t0) REVERT: B 159 ILE cc_start: 0.9107 (mp) cc_final: 0.8609 (mp) REVERT: B 160 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8589 (mmmt) REVERT: B 165 LYS cc_start: 0.9410 (ptmm) cc_final: 0.9128 (ptmm) REVERT: B 171 GLU cc_start: 0.8921 (pm20) cc_final: 0.8682 (pm20) REVERT: C 8 CYS cc_start: 0.8861 (p) cc_final: 0.8618 (p) REVERT: C 35 LEU cc_start: 0.9282 (tp) cc_final: 0.9014 (tp) REVERT: C 38 LYS cc_start: 0.8688 (ptmm) cc_final: 0.8247 (ptmm) outliers start: 35 outliers final: 31 residues processed: 174 average time/residue: 0.1969 time to fit residues: 48.8194 Evaluate side-chains 189 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 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 631 MET Chi-restraints excluded: chain A residue 654 LEU 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 A residue 834 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3929 r_free = 0.3929 target = 0.109872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074523 restraints weight = 23164.713| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.62 r_work: 0.3088 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9702 Z= 0.190 Angle : 0.621 16.682 13325 Z= 0.306 Chirality : 0.040 0.278 1516 Planarity : 0.004 0.037 1545 Dihedral : 12.453 82.048 1759 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.80 % Allowed : 15.72 % Favored : 80.49 % 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: 0.67 (0.27), residues: 1065 helix: 1.01 (0.24), residues: 507 sheet: -0.57 (0.53), residues: 106 loop : 0.23 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 182 HIS 0.005 0.001 HIS B 168 PHE 0.012 0.001 PHE A 736 TYR 0.024 0.002 TYR A 211 ARG 0.006 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 445) hydrogen bonds : angle 4.55639 ( 1195) metal coordination : bond 0.02053 ( 8) metal coordination : angle 1.62950 ( 6) covalent geometry : bond 0.00431 ( 9694) covalent geometry : angle 0.62005 (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 193 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9092 (tt0) cc_final: 0.8658 (tp30) REVERT: A 248 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8757 (mp0) REVERT: A 263 TYR cc_start: 0.7857 (p90) cc_final: 0.7626 (p90) REVERT: A 267 GLU cc_start: 0.8437 (mp0) cc_final: 0.8035 (mp0) REVERT: A 403 GLN cc_start: 0.8726 (tt0) cc_final: 0.7997 (pm20) REVERT: A 419 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9036 (mm) REVERT: A 536 GLN cc_start: 0.8221 (tt0) cc_final: 0.7961 (tt0) REVERT: A 660 GLU cc_start: 0.8111 (pm20) cc_final: 0.7654 (pm20) REVERT: A 912 ASP cc_start: 0.8609 (t0) cc_final: 0.8381 (p0) REVERT: A 919 MET cc_start: 0.9045 (mmt) cc_final: 0.8799 (mmt) REVERT: B 137 SER cc_start: 0.9598 (m) cc_final: 0.9341 (p) REVERT: B 158 ASP cc_start: 0.9033 (t0) cc_final: 0.8486 (t0) REVERT: B 159 ILE cc_start: 0.9112 (mp) cc_final: 0.8441 (mp) REVERT: B 160 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8603 (mmmt) REVERT: B 165 LYS cc_start: 0.9418 (ptmm) cc_final: 0.9144 (ptmm) REVERT: C 8 CYS cc_start: 0.8874 (p) cc_final: 0.8613 (p) REVERT: C 35 LEU cc_start: 0.9305 (tp) cc_final: 0.9021 (tp) REVERT: C 38 LYS cc_start: 0.8686 (ptmm) cc_final: 0.8249 (ptmm) REVERT: C 46 GLU cc_start: 0.9170 (pm20) cc_final: 0.8965 (pm20) REVERT: C 51 MET cc_start: 0.9532 (OUTLIER) cc_final: 0.9102 (mpp) outliers start: 36 outliers final: 28 residues processed: 174 average time/residue: 0.1999 time to fit residues: 49.8171 Evaluate side-chains 185 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 597 LEU 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 A residue 834 SER 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 153 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.6969 > 50: distance: 8 - 26: 23.225 distance: 15 - 35: 22.812 distance: 19 - 43: 15.483 distance: 22 - 26: 20.581 distance: 23 - 51: 22.537 distance: 26 - 27: 16.508 distance: 27 - 28: 13.170 distance: 27 - 30: 32.928 distance: 28 - 29: 25.499 distance: 28 - 35: 32.684 distance: 29 - 59: 31.900 distance: 30 - 31: 43.943 distance: 31 - 32: 12.090 distance: 32 - 33: 36.841 distance: 33 - 34: 36.065 distance: 35 - 36: 29.850 distance: 36 - 37: 17.172 distance: 36 - 39: 26.413 distance: 37 - 38: 14.672 distance: 37 - 43: 31.350 distance: 39 - 40: 15.262 distance: 40 - 41: 26.087 distance: 40 - 42: 28.094 distance: 43 - 44: 16.697 distance: 44 - 45: 30.067 distance: 44 - 47: 10.638 distance: 45 - 46: 35.227 distance: 45 - 51: 25.660 distance: 47 - 48: 24.568 distance: 48 - 49: 20.133 distance: 48 - 50: 19.141 distance: 51 - 52: 19.008 distance: 52 - 53: 25.958 distance: 52 - 55: 13.176 distance: 53 - 54: 22.983 distance: 53 - 59: 26.885 distance: 55 - 56: 37.805 distance: 55 - 57: 27.662 distance: 56 - 58: 38.394 distance: 59 - 60: 19.239 distance: 60 - 61: 24.563 distance: 60 - 63: 12.031 distance: 61 - 62: 16.791 distance: 61 - 67: 15.666 distance: 63 - 64: 28.840 distance: 64 - 65: 5.832 distance: 64 - 66: 31.832 distance: 67 - 68: 34.118 distance: 68 - 69: 32.411 distance: 69 - 70: 38.064 distance: 69 - 71: 42.825 distance: 71 - 72: 13.204 distance: 72 - 73: 32.086 distance: 72 - 75: 11.180 distance: 73 - 74: 16.626 distance: 73 - 78: 30.212 distance: 75 - 76: 37.992 distance: 75 - 77: 29.308 distance: 78 - 79: 25.435 distance: 79 - 80: 16.884 distance: 79 - 82: 34.212 distance: 80 - 81: 22.233 distance: 80 - 87: 17.394 distance: 82 - 83: 23.712 distance: 83 - 84: 10.641 distance: 84 - 85: 4.492 distance: 84 - 86: 3.350 distance: 87 - 88: 47.310 distance: 88 - 89: 19.981 distance: 88 - 91: 24.857 distance: 89 - 90: 28.383 distance: 89 - 95: 15.920 distance: 91 - 92: 14.309 distance: 92 - 93: 18.071 distance: 92 - 94: 25.580 distance: 95 - 96: 27.582 distance: 95 - 101: 25.932 distance: 96 - 97: 11.537 distance: 96 - 99: 11.950 distance: 97 - 98: 29.236 distance: 97 - 102: 8.324 distance: 99 - 100: 14.995 distance: 100 - 101: 5.364