Starting phenix.real_space_refine on Wed Aug 5 14:11:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5l_44216/08_2026/9b5l_44216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5l_44216/08_2026/9b5l_44216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b5l_44216/08_2026/9b5l_44216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5l_44216/08_2026/9b5l_44216.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5l_44216/08_2026/9b5l_44216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5l_44216/08_2026/9b5l_44216.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 43 5.16 5 C 6449 2.51 5 N 1678 2.21 5 O 1946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10117 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "B" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.25 Number of scatterers: 10117 At special positions: 0 Unit cell: (91.504, 98.952, 120.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 1 15.00 O 1946 8.00 N 1678 7.00 C 6449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.90 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 370.9 milliseconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 45.8% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 removed outlier: 3.769A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.769A pdb=" N MET A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.602A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.033A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.215A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.632A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.728A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.276A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.564A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.005A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.567A pdb=" N VAL A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 4.046A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 4.068A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.568A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.872A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 630 removed outlier: 3.579A pdb=" N SER A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 641 removed outlier: 4.076A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.672A pdb=" N VAL A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.772A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.548A pdb=" N GLN A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.889A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.636A pdb=" N LEU A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.678A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 146 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'D' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.948A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR A 385 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.375A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.327A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 460 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 905 through 908 Processing sheet with id=AA6, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.391A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP A 996 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL A 942 " --> pdb=" O ASP A 996 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.391A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.918A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 26 removed outlier: 11.245A pdb=" N GLY C 24 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N PHE C 31 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 26 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 12 through 16 476 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1723 1.27 - 1.40: 2409 1.40 - 1.54: 5972 1.54 - 1.67: 165 1.67 - 1.80: 66 Bond restraints: 10335 Sorted by residual: bond pdb=" C04 A1AIV D 101 " pdb=" C05 A1AIV D 101 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.62e+00 bond pdb=" C4 AMP B 101 " pdb=" C5 AMP B 101 " ideal model delta sigma weight residual 1.490 1.461 0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.131 0.020 2.00e-02 2.50e+03 9.87e-01 ... (remaining 10330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 13790 1.43 - 2.86: 121 2.86 - 4.29: 75 4.29 - 5.72: 4 5.72 - 7.15: 2 Bond angle restraints: 13992 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 127.77 -6.07 1.80e+00 3.09e-01 1.14e+01 angle pdb=" C5' AMP B 101 " pdb=" O5' AMP B 101 " pdb=" P AMP B 101 " ideal model delta sigma weight residual 120.90 116.54 4.36 1.50e+00 4.44e-01 8.46e+00 angle pdb=" O1P AMP B 101 " pdb=" P AMP B 101 " pdb=" O2P AMP B 101 " ideal model delta sigma weight residual 119.90 112.75 7.15 3.00e+00 1.11e-01 5.67e+00 angle pdb=" C4' AMP B 101 " pdb=" C5' AMP B 101 " pdb=" O5' AMP B 101 " ideal model delta sigma weight residual 111.70 108.67 3.03 1.50e+00 4.44e-01 4.07e+00 angle pdb=" CA TYR A 544 " pdb=" CB TYR A 544 " pdb=" CG TYR A 544 " ideal model delta sigma weight residual 113.90 110.33 3.57 1.80e+00 3.09e-01 3.94e+00 ... (remaining 13987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6005 17.81 - 35.62: 228 35.62 - 53.43: 33 53.43 - 71.24: 11 71.24 - 89.05: 5 Dihedral angle restraints: 6282 sinusoidal: 2561 harmonic: 3721 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -155.12 69.12 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CA ASP D 52 " pdb=" CB ASP D 52 " pdb=" CG ASP D 52 " pdb=" OD1 ASP D 52 " ideal model delta sinusoidal sigma weight residual -30.00 -88.56 58.56 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 163.35 16.65 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 917 0.028 - 0.056: 448 0.056 - 0.083: 100 0.083 - 0.111: 74 0.111 - 0.139: 29 Chirality restraints: 1568 Sorted by residual: chirality pdb=" CA VAL A 852 " pdb=" N VAL A 852 " pdb=" C VAL A 852 " pdb=" CB VAL A 852 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE B 13 " pdb=" N ILE B 13 " pdb=" C ILE B 13 " pdb=" CB ILE B 13 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE B 36 " pdb=" N ILE B 36 " pdb=" C ILE B 36 " pdb=" CB ILE B 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1565 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 659 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 660 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 660 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 660 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 756 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO A 757 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 757 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 757 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 17 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO C 18 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " 0.015 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 63 2.53 - 3.12: 7854 3.12 - 3.71: 14744 3.71 - 4.31: 20966 4.31 - 4.90: 36516 Nonbonded interactions: 80143 Sorted by model distance: nonbonded pdb=" OG SER A 395 " pdb=" OD1 ASP A 875 " model vdw 1.933 3.040 nonbonded pdb=" OE2 GLU C 9 " pdb=" OH TYR C 60 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR A 291 " pdb=" OD2 ASP A 387 " model vdw 2.127 3.040 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.149 3.040 nonbonded pdb=" OG SER A 488 " pdb=" OE1 GLU A 489 " model vdw 2.199 3.040 ... (remaining 80138 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 1 through 75) selection = (chain 'D' and resid 1 through 75) } 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: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.160 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.010 0.867 10339 Z= 0.490 Angle : 0.658 51.466 13994 Z= 0.328 Chirality : 0.040 0.139 1568 Planarity : 0.003 0.029 1812 Dihedral : 10.247 89.049 3875 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.42 % Allowed : 4.16 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.25), residues: 1273 helix: 1.95 (0.25), residues: 505 sheet: 0.53 (0.36), residues: 213 loop : 0.28 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.012 0.001 TYR A 544 PHE 0.011 0.001 PHE A 431 TRP 0.004 0.001 TRP C 141 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (10335) covalent geometry : angle 0.48561 / 0.25 (13992) SS BOND : bond 0.86698 / 45.63 ( 1) SS BOND : angle 37.12965 / 21.67 ( 2) hydrogen bonds : bond 0.14440 / 10.10 ( 472) hydrogen bonds : angle 5.79515 / 4.08 ( 1296) Misc. bond : bond 0.09534 / 4.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.406 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: symmetry clash REVERT: A 33 LYS cc_start: 0.8228 (mptt) cc_final: 0.7764 (tmtt) REVERT: A 35 MET cc_start: 0.8246 (ttp) cc_final: 0.7978 (ttp) REVERT: A 80 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8281 (tp40) REVERT: A 229 VAL cc_start: 0.9280 (t) cc_final: 0.8925 (p) REVERT: A 464 MET cc_start: 0.8778 (pmt) cc_final: 0.8513 (pmm) REVERT: A 474 ARG cc_start: 0.7667 (ptt-90) cc_final: 0.7382 (ptt180) REVERT: A 587 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8480 (tt0) REVERT: A 623 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6951 (t0) REVERT: A 718 ASN cc_start: 0.8622 (t0) cc_final: 0.8306 (t0) REVERT: A 748 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8537 (pt0) REVERT: A 821 ASP cc_start: 0.9004 (t70) cc_final: 0.8793 (t0) REVERT: A 885 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8601 (m-40) REVERT: B 18 GLU cc_start: 0.8756 (mp0) cc_final: 0.8220 (mp0) REVERT: C 34 GLN cc_start: 0.8767 (tt0) cc_final: 0.7998 (pp30) REVERT: C 66 LYS cc_start: 0.8557 (mttt) cc_final: 0.8283 (mtpt) REVERT: C 72 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8635 (mtp85) REVERT: C 92 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8254 (mm-40) REVERT: C 120 VAL cc_start: 0.8842 (t) cc_final: 0.8571 (m) REVERT: C 137 SER cc_start: 0.9062 (m) cc_final: 0.8775 (p) REVERT: D 31 GLN cc_start: 0.8172 (tt0) cc_final: 0.7599 (tp40) outliers start: 16 outliers final: 7 residues processed: 205 average time/residue: 0.1357 time to fit residues: 36.6743 Evaluate side-chains 132 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.114753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.085047 restraints weight = 20784.117| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.23 r_work: 0.3264 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10339 Z= 0.140 Angle : 0.554 9.443 13994 Z= 0.287 Chirality : 0.043 0.140 1568 Planarity : 0.004 0.049 1812 Dihedral : 6.440 89.216 1401 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.12 % Allowed : 8.14 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1273 helix: 1.80 (0.24), residues: 515 sheet: 0.77 (0.37), residues: 208 loop : 0.19 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 72 TYR 0.023 0.001 TYR C 145 PHE 0.014 0.001 PHE A 633 TRP 0.008 0.001 TRP C 141 HIS 0.008 0.001 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10335) covalent geometry : angle 0.54744 / 0.28 (13992) SS BOND : bond 0.01259 / 0.66 ( 1) SS BOND : angle 6.91861 / 4.01 ( 2) hydrogen bonds : bond 0.04045 / 2.68 ( 472) hydrogen bonds : angle 4.80126 / 3.37 ( 1296) Misc. bond : bond 0.00285 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.406 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 33 LYS cc_start: 0.8526 (mptt) cc_final: 0.8107 (tmtt) REVERT: A 35 MET cc_start: 0.8625 (ttp) cc_final: 0.8377 (ttp) REVERT: A 474 ARG cc_start: 0.8006 (ptt-90) cc_final: 0.7747 (ptt180) REVERT: A 507 THR cc_start: 0.9174 (m) cc_final: 0.8958 (p) REVERT: A 588 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7890 (mmmt) REVERT: A 623 ASN cc_start: 0.7408 (OUTLIER) cc_final: 0.6840 (t0) REVERT: A 717 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8327 (t-90) REVERT: A 718 ASN cc_start: 0.8459 (t0) cc_final: 0.8165 (t0) REVERT: B 18 GLU cc_start: 0.8810 (mp0) cc_final: 0.8124 (mp0) REVERT: B 21 ASP cc_start: 0.8554 (m-30) cc_final: 0.7521 (m-30) REVERT: B 63 LYS cc_start: 0.9643 (ptmm) cc_final: 0.8973 (ptmm) REVERT: B 64 GLU cc_start: 0.9156 (mp0) cc_final: 0.8591 (mp0) REVERT: C 7 ASN cc_start: 0.8760 (t0) cc_final: 0.8536 (t0) REVERT: C 34 GLN cc_start: 0.8892 (tt0) cc_final: 0.8196 (pp30) REVERT: C 38 MET cc_start: 0.8309 (ppp) cc_final: 0.8096 (ppp) REVERT: C 92 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8291 (mm-40) REVERT: D 31 GLN cc_start: 0.7954 (tt0) cc_final: 0.7428 (tp40) REVERT: D 41 GLN cc_start: 0.8112 (mt0) cc_final: 0.7888 (mt0) REVERT: D 72 ARG cc_start: 0.7686 (tmm160) cc_final: 0.7180 (tmm160) outliers start: 24 outliers final: 18 residues processed: 162 average time/residue: 0.1182 time to fit residues: 26.3563 Evaluate side-chains 140 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.113422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084622 restraints weight = 20878.620| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.14 r_work: 0.3296 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10339 Z= 0.149 Angle : 0.523 8.512 13994 Z= 0.272 Chirality : 0.042 0.135 1568 Planarity : 0.004 0.037 1812 Dihedral : 5.858 86.526 1394 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.83 % Allowed : 8.85 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.24), residues: 1273 helix: 1.83 (0.24), residues: 511 sheet: 0.71 (0.36), residues: 215 loop : 0.18 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.015 0.001 TYR C 145 PHE 0.023 0.001 PHE A 846 TRP 0.006 0.001 TRP A 669 HIS 0.007 0.001 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (10335) covalent geometry : angle 0.51769 / 0.27 (13992) SS BOND : bond 0.01029 / 0.54 ( 1) SS BOND : angle 6.28578 / 3.64 ( 2) hydrogen bonds : bond 0.03670 / 2.42 ( 472) hydrogen bonds : angle 4.69293 / 3.28 ( 1296) Misc. bond : bond 0.00145 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8607 (mptt) cc_final: 0.8147 (tmtt) REVERT: A 35 MET cc_start: 0.8609 (ttp) cc_final: 0.8358 (ttp) REVERT: A 442 MET cc_start: 0.8594 (tpp) cc_final: 0.8330 (tpp) REVERT: A 474 ARG cc_start: 0.8059 (ptt-90) cc_final: 0.7754 (ptt90) REVERT: A 653 ASP cc_start: 0.8536 (m-30) cc_final: 0.7533 (m-30) REVERT: A 668 MET cc_start: 0.7648 (tpp) cc_final: 0.7444 (tpp) REVERT: A 717 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8359 (t-90) REVERT: A 718 ASN cc_start: 0.8365 (t0) cc_final: 0.8075 (t0) REVERT: B 18 GLU cc_start: 0.8808 (mp0) cc_final: 0.8185 (mp0) REVERT: B 21 ASP cc_start: 0.8566 (m-30) cc_final: 0.7630 (m-30) REVERT: B 24 ASP cc_start: 0.8275 (m-30) cc_final: 0.7764 (p0) REVERT: B 64 GLU cc_start: 0.9068 (mp0) cc_final: 0.8734 (mp0) REVERT: C 34 GLN cc_start: 0.8838 (tt0) cc_final: 0.8364 (pp30) REVERT: C 92 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8257 (mm-40) REVERT: D 18 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8201 (tm-30) REVERT: D 31 GLN cc_start: 0.7942 (tt0) cc_final: 0.7428 (tp40) REVERT: D 45 PHE cc_start: 0.7642 (t80) cc_final: 0.7416 (t80) REVERT: D 72 ARG cc_start: 0.7553 (tmm160) cc_final: 0.7318 (tmm160) outliers start: 32 outliers final: 18 residues processed: 149 average time/residue: 0.1199 time to fit residues: 24.4851 Evaluate side-chains 127 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 64 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 57 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.113375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.083493 restraints weight = 21353.392| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.34 r_work: 0.3213 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10339 Z= 0.183 Angle : 0.541 6.993 13994 Z= 0.280 Chirality : 0.042 0.143 1568 Planarity : 0.004 0.057 1812 Dihedral : 5.832 86.770 1391 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.74 % Allowed : 10.18 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.24), residues: 1273 helix: 1.79 (0.24), residues: 510 sheet: 0.69 (0.36), residues: 215 loop : 0.08 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 652 TYR 0.015 0.001 TYR C 145 PHE 0.024 0.001 PHE A 846 TRP 0.006 0.001 TRP A 669 HIS 0.007 0.001 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (10335) covalent geometry : angle 0.53730 / 0.28 (13992) SS BOND : bond 0.00800 / 0.42 ( 1) SS BOND : angle 5.16948 / 2.99 ( 2) hydrogen bonds : bond 0.03700 / 2.44 ( 472) hydrogen bonds : angle 4.64271 / 3.24 ( 1296) Misc. bond : bond 0.00165 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.406 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 33 LYS cc_start: 0.8536 (mptt) cc_final: 0.8001 (tmtt) REVERT: A 35 MET cc_start: 0.8602 (ttp) cc_final: 0.8364 (ttp) REVERT: A 474 ARG cc_start: 0.8151 (ptt-90) cc_final: 0.7778 (ptt90) REVERT: A 717 HIS cc_start: 0.8880 (OUTLIER) cc_final: 0.8433 (t-90) REVERT: A 718 ASN cc_start: 0.8504 (t0) cc_final: 0.8097 (t0) REVERT: B 18 GLU cc_start: 0.8851 (mp0) cc_final: 0.8078 (mp0) REVERT: B 21 ASP cc_start: 0.8591 (m-30) cc_final: 0.7412 (m-30) REVERT: B 24 ASP cc_start: 0.8352 (m-30) cc_final: 0.7791 (p0) REVERT: B 64 GLU cc_start: 0.9177 (mp0) cc_final: 0.8738 (mp0) REVERT: C 34 GLN cc_start: 0.8919 (tt0) cc_final: 0.8275 (pp30) REVERT: C 38 MET cc_start: 0.8234 (ppp) cc_final: 0.7992 (ppp) REVERT: C 92 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8246 (mm-40) REVERT: D 18 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7998 (tm-30) REVERT: D 31 GLN cc_start: 0.7996 (tt0) cc_final: 0.7438 (tp40) outliers start: 31 outliers final: 25 residues processed: 137 average time/residue: 0.1208 time to fit residues: 22.8758 Evaluate side-chains 138 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 0.0370 chunk 94 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.0170 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.115467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085954 restraints weight = 20998.859| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.26 r_work: 0.3297 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 : 0.002 0.031 10339 Z= 0.097 Angle : 0.491 6.950 13994 Z= 0.253 Chirality : 0.041 0.167 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.639 88.377 1391 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.12 % Allowed : 11.24 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1273 helix: 1.83 (0.24), residues: 510 sheet: 0.85 (0.37), residues: 202 loop : 0.10 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.017 0.001 TYR A 250 PHE 0.026 0.001 PHE A 846 TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (10335) covalent geometry : angle 0.48913 / 0.25 (13992) SS BOND : bond 0.00750 / 0.39 ( 1) SS BOND : angle 3.97797 / 2.28 ( 2) hydrogen bonds : bond 0.03047 / 2.02 ( 472) hydrogen bonds : angle 4.44412 / 3.11 ( 1296) Misc. bond : bond 0.00128 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.422 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 33 LYS cc_start: 0.8552 (mptt) cc_final: 0.8040 (tmtt) REVERT: A 35 MET cc_start: 0.8521 (ttp) cc_final: 0.8298 (ttp) REVERT: A 474 ARG cc_start: 0.8073 (ptt-90) cc_final: 0.7648 (ptt90) REVERT: A 717 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8410 (t-90) REVERT: A 718 ASN cc_start: 0.8363 (t0) cc_final: 0.7986 (t0) REVERT: A 818 HIS cc_start: 0.7139 (m90) cc_final: 0.6635 (m170) REVERT: B 18 GLU cc_start: 0.8796 (mp0) cc_final: 0.8021 (mp0) REVERT: B 21 ASP cc_start: 0.8597 (m-30) cc_final: 0.7391 (m-30) REVERT: B 24 ASP cc_start: 0.8270 (m-30) cc_final: 0.7797 (p0) REVERT: B 64 GLU cc_start: 0.9091 (mp0) cc_final: 0.8765 (mp0) REVERT: B 74 ARG cc_start: 0.8389 (ptt-90) cc_final: 0.7868 (ptp90) REVERT: C 34 GLN cc_start: 0.8897 (tt0) cc_final: 0.8194 (pp30) REVERT: C 38 MET cc_start: 0.8229 (ppp) cc_final: 0.7967 (ppp) REVERT: C 92 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8209 (mm-40) REVERT: C 144 LYS cc_start: 0.9018 (tttm) cc_final: 0.8810 (tttp) REVERT: D 18 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7972 (tm-30) REVERT: D 31 GLN cc_start: 0.7929 (tt0) cc_final: 0.7391 (tp40) outliers start: 24 outliers final: 19 residues processed: 141 average time/residue: 0.1231 time to fit residues: 23.7550 Evaluate side-chains 134 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 76 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.0270 chunk 110 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.115240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.085971 restraints weight = 21090.398| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.23 r_work: 0.3256 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10339 Z= 0.111 Angle : 0.494 6.817 13994 Z= 0.254 Chirality : 0.041 0.143 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.606 89.840 1391 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.21 % Allowed : 11.77 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.24), residues: 1273 helix: 1.90 (0.24), residues: 503 sheet: 0.80 (0.38), residues: 196 loop : 0.07 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.015 0.001 TYR C 145 PHE 0.027 0.001 PHE A 846 TRP 0.006 0.001 TRP A 669 HIS 0.004 0.001 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (10335) covalent geometry : angle 0.49224 / 0.25 (13992) SS BOND : bond 0.00578 / 0.30 ( 1) SS BOND : angle 3.62285 / 2.08 ( 2) hydrogen bonds : bond 0.03082 / 2.05 ( 472) hydrogen bonds : angle 4.40442 / 3.08 ( 1296) Misc. bond : bond 0.00015 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8557 (mptt) cc_final: 0.8036 (tmtt) REVERT: A 35 MET cc_start: 0.8553 (ttp) cc_final: 0.8303 (ttm) REVERT: A 474 ARG cc_start: 0.8110 (ptt-90) cc_final: 0.7674 (ptt90) REVERT: A 717 HIS cc_start: 0.8829 (OUTLIER) cc_final: 0.8419 (t-90) REVERT: A 718 ASN cc_start: 0.8372 (t0) cc_final: 0.7985 (t0) REVERT: A 818 HIS cc_start: 0.7184 (m90) cc_final: 0.6653 (m170) REVERT: B 18 GLU cc_start: 0.8819 (mp0) cc_final: 0.8027 (mp0) REVERT: B 21 ASP cc_start: 0.8605 (m-30) cc_final: 0.7375 (m-30) REVERT: B 24 ASP cc_start: 0.8286 (m-30) cc_final: 0.7803 (p0) REVERT: B 64 GLU cc_start: 0.9120 (mp0) cc_final: 0.8771 (mp0) REVERT: B 74 ARG cc_start: 0.8416 (ptt-90) cc_final: 0.7877 (ptp90) REVERT: C 34 GLN cc_start: 0.8912 (tt0) cc_final: 0.8186 (pp30) REVERT: C 38 MET cc_start: 0.8223 (ppp) cc_final: 0.7934 (ppp) REVERT: C 92 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8185 (mm-40) REVERT: D 1 MET cc_start: 0.7900 (pmm) cc_final: 0.7626 (pmm) REVERT: D 18 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8035 (tm-30) REVERT: D 31 GLN cc_start: 0.7899 (tt0) cc_final: 0.7659 (tp40) REVERT: D 42 ARG cc_start: 0.7329 (mmm-85) cc_final: 0.6912 (mmm-85) outliers start: 25 outliers final: 17 residues processed: 134 average time/residue: 0.1056 time to fit residues: 19.3787 Evaluate side-chains 131 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 124 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.114486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.085326 restraints weight = 20871.875| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.24 r_work: 0.3272 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10339 Z= 0.119 Angle : 0.495 8.375 13994 Z= 0.254 Chirality : 0.041 0.130 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.573 88.529 1391 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.21 % Allowed : 12.21 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.24), residues: 1273 helix: 1.92 (0.24), residues: 503 sheet: 0.79 (0.37), residues: 201 loop : 0.03 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.016 0.001 TYR C 145 PHE 0.025 0.001 PHE A 846 TRP 0.006 0.001 TRP A 669 HIS 0.004 0.001 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (10335) covalent geometry : angle 0.49311 / 0.25 (13992) SS BOND : bond 0.00485 / 0.26 ( 1) SS BOND : angle 3.54912 / 2.02 ( 2) hydrogen bonds : bond 0.03060 / 2.04 ( 472) hydrogen bonds : angle 4.37422 / 3.06 ( 1296) Misc. bond : bond 0.00048 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.365 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 33 LYS cc_start: 0.8537 (mptt) cc_final: 0.8000 (tmtt) REVERT: A 35 MET cc_start: 0.8584 (ttp) cc_final: 0.8320 (ttm) REVERT: A 474 ARG cc_start: 0.8120 (ptt-90) cc_final: 0.7664 (ptt90) REVERT: A 717 HIS cc_start: 0.8857 (OUTLIER) cc_final: 0.8450 (t-90) REVERT: A 718 ASN cc_start: 0.8416 (t0) cc_final: 0.8019 (t0) REVERT: A 818 HIS cc_start: 0.7217 (m90) cc_final: 0.6709 (m170) REVERT: B 18 GLU cc_start: 0.8833 (mp0) cc_final: 0.8016 (mp0) REVERT: B 21 ASP cc_start: 0.8581 (m-30) cc_final: 0.7290 (m-30) REVERT: B 24 ASP cc_start: 0.8302 (m-30) cc_final: 0.7807 (p0) REVERT: B 64 GLU cc_start: 0.9154 (mp0) cc_final: 0.8767 (mp0) REVERT: B 74 ARG cc_start: 0.8399 (ptt-90) cc_final: 0.7849 (ptp90) REVERT: C 34 GLN cc_start: 0.8911 (tt0) cc_final: 0.8168 (tm-30) REVERT: C 38 MET cc_start: 0.8261 (ppp) cc_final: 0.7950 (ppp) REVERT: C 92 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8189 (mm-40) REVERT: D 1 MET cc_start: 0.7853 (pmm) cc_final: 0.7584 (pmm) REVERT: D 18 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7998 (tm-30) REVERT: D 31 GLN cc_start: 0.7917 (tt0) cc_final: 0.7658 (tp40) REVERT: D 42 ARG cc_start: 0.7384 (mmm-85) cc_final: 0.6937 (mmm-85) outliers start: 25 outliers final: 22 residues processed: 132 average time/residue: 0.1123 time to fit residues: 20.1396 Evaluate side-chains 135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.114698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.085844 restraints weight = 20988.994| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.23 r_work: 0.3259 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10339 Z= 0.109 Angle : 0.502 8.916 13994 Z= 0.259 Chirality : 0.041 0.137 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.387 87.269 1388 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.04 % Allowed : 12.39 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.24), residues: 1273 helix: 1.93 (0.24), residues: 504 sheet: 0.79 (0.38), residues: 196 loop : -0.01 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.016 0.001 TYR C 145 PHE 0.024 0.001 PHE A 846 TRP 0.006 0.001 TRP A 669 HIS 0.003 0.000 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10335) covalent geometry : angle 0.50060 / 0.26 (13992) SS BOND : bond 0.00293 / 0.15 ( 1) SS BOND : angle 3.30469 / 1.85 ( 2) hydrogen bonds : bond 0.02970 / 1.99 ( 472) hydrogen bonds : angle 4.32429 / 3.02 ( 1296) Misc. bond : bond 0.00037 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.296 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: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8537 (mptt) cc_final: 0.7995 (tmtt) REVERT: A 35 MET cc_start: 0.8567 (ttp) cc_final: 0.8295 (ttm) REVERT: A 474 ARG cc_start: 0.8104 (ptt-90) cc_final: 0.7652 (ptt90) REVERT: A 717 HIS cc_start: 0.8854 (OUTLIER) cc_final: 0.8412 (t-90) REVERT: A 718 ASN cc_start: 0.8405 (t0) cc_final: 0.8012 (t0) REVERT: B 18 GLU cc_start: 0.8842 (mp0) cc_final: 0.8021 (mp0) REVERT: B 21 ASP cc_start: 0.8584 (m-30) cc_final: 0.7286 (m-30) REVERT: B 24 ASP cc_start: 0.8294 (m-30) cc_final: 0.7813 (p0) REVERT: B 64 GLU cc_start: 0.9154 (mp0) cc_final: 0.8761 (mp0) REVERT: B 74 ARG cc_start: 0.8379 (ptt-90) cc_final: 0.7858 (ptp90) REVERT: C 34 GLN cc_start: 0.8884 (tt0) cc_final: 0.8168 (tm-30) REVERT: C 38 MET cc_start: 0.8258 (ppp) cc_final: 0.7925 (ppp) REVERT: C 92 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8178 (mm-40) REVERT: D 1 MET cc_start: 0.7858 (pmm) cc_final: 0.7507 (pmm) REVERT: D 18 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7750 (tm-30) REVERT: D 50 LEU cc_start: 0.7553 (mp) cc_final: 0.7269 (mt) outliers start: 23 outliers final: 21 residues processed: 130 average time/residue: 0.1045 time to fit residues: 18.3849 Evaluate side-chains 134 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 0.0000 chunk 123 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.115735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086050 restraints weight = 21041.449| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.35 r_work: 0.3291 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10339 Z= 0.105 Angle : 0.498 9.187 13994 Z= 0.254 Chirality : 0.040 0.131 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.340 85.292 1388 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.21 % Allowed : 12.12 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1273 helix: 1.97 (0.24), residues: 503 sheet: 0.81 (0.38), residues: 196 loop : 0.00 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.016 0.001 TYR C 145 PHE 0.023 0.001 PHE A 846 TRP 0.006 0.001 TRP A 669 HIS 0.003 0.000 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (10335) covalent geometry : angle 0.49696 / 0.25 (13992) SS BOND : bond 0.00172 / 0.09 ( 1) SS BOND : angle 3.17806 / 1.76 ( 2) hydrogen bonds : bond 0.02900 / 1.94 ( 472) hydrogen bonds : angle 4.30796 / 3.02 ( 1296) Misc. bond : bond 0.00038 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.282 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: symmetry clash REVERT: A 33 LYS cc_start: 0.8541 (mptt) cc_final: 0.8001 (tmtt) REVERT: A 35 MET cc_start: 0.8575 (ttp) cc_final: 0.8308 (ttm) REVERT: A 474 ARG cc_start: 0.8093 (ptt-90) cc_final: 0.7622 (ptt90) REVERT: A 567 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8463 (p0) REVERT: A 717 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8421 (t-90) REVERT: A 718 ASN cc_start: 0.8375 (t0) cc_final: 0.7979 (t0) REVERT: B 18 GLU cc_start: 0.8836 (mp0) cc_final: 0.8014 (mp0) REVERT: B 21 ASP cc_start: 0.8602 (m-30) cc_final: 0.7276 (m-30) REVERT: B 24 ASP cc_start: 0.8297 (m-30) cc_final: 0.7822 (p0) REVERT: B 64 GLU cc_start: 0.9146 (mp0) cc_final: 0.8764 (mp0) REVERT: B 74 ARG cc_start: 0.8360 (ptt-90) cc_final: 0.7837 (ptp90) REVERT: C 34 GLN cc_start: 0.8889 (tt0) cc_final: 0.8169 (tm-30) REVERT: C 38 MET cc_start: 0.8216 (ppp) cc_final: 0.7869 (ppp) REVERT: C 92 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8180 (mm-40) REVERT: D 18 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7767 (tm-30) REVERT: D 41 GLN cc_start: 0.7372 (pm20) cc_final: 0.7148 (pm20) REVERT: D 50 LEU cc_start: 0.7478 (mp) cc_final: 0.7219 (mt) outliers start: 25 outliers final: 19 residues processed: 130 average time/residue: 0.0948 time to fit residues: 16.9107 Evaluate side-chains 131 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 72 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.114035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.085199 restraints weight = 20761.742| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.23 r_work: 0.3239 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10339 Z= 0.129 Angle : 0.522 8.685 13994 Z= 0.269 Chirality : 0.041 0.194 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.328 81.988 1388 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.95 % Allowed : 12.83 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.24), residues: 1273 helix: 1.93 (0.24), residues: 503 sheet: 0.83 (0.38), residues: 201 loop : 0.01 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 54 TYR 0.016 0.001 TYR C 145 PHE 0.023 0.001 PHE A 846 TRP 0.004 0.001 TRP A 669 HIS 0.003 0.000 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10335) covalent geometry : angle 0.51983 / 0.27 (13992) SS BOND : bond 0.00294 / 0.15 ( 1) SS BOND : angle 3.54904 / 2.04 ( 2) hydrogen bonds : bond 0.03097 / 2.07 ( 472) hydrogen bonds : angle 4.39235 / 3.11 ( 1296) Misc. bond : bond 0.00045 / 0.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.312 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: symmetry clash REVERT: A 33 LYS cc_start: 0.8525 (mptt) cc_final: 0.7989 (tmtt) REVERT: A 35 MET cc_start: 0.8626 (ttp) cc_final: 0.8380 (ttm) REVERT: A 474 ARG cc_start: 0.8107 (ptt-90) cc_final: 0.7634 (ptt90) REVERT: A 567 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8451 (p0) REVERT: A 717 HIS cc_start: 0.8873 (OUTLIER) cc_final: 0.8458 (t-90) REVERT: A 718 ASN cc_start: 0.8385 (t0) cc_final: 0.8027 (t0) REVERT: B 18 GLU cc_start: 0.8868 (mp0) cc_final: 0.8030 (mp0) REVERT: B 21 ASP cc_start: 0.8574 (m-30) cc_final: 0.7228 (m-30) REVERT: B 24 ASP cc_start: 0.8262 (m-30) cc_final: 0.7800 (p0) REVERT: B 64 GLU cc_start: 0.9165 (mp0) cc_final: 0.8770 (mp0) REVERT: B 74 ARG cc_start: 0.8386 (ptt-90) cc_final: 0.7866 (ptp90) REVERT: C 34 GLN cc_start: 0.8874 (tt0) cc_final: 0.8158 (tm-30) REVERT: C 38 MET cc_start: 0.8169 (ppp) cc_final: 0.7850 (ppp) REVERT: C 92 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8185 (mm-40) REVERT: D 18 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8046 (tm-30) REVERT: D 50 LEU cc_start: 0.7527 (mp) cc_final: 0.7267 (mt) outliers start: 22 outliers final: 18 residues processed: 126 average time/residue: 0.0958 time to fit residues: 16.5731 Evaluate side-chains 131 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 72 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.114714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.086197 restraints weight = 20888.419| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.18 r_work: 0.3254 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10339 Z= 0.122 Angle : 0.516 9.581 13994 Z= 0.266 Chirality : 0.041 0.162 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.293 79.094 1388 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.68 % Allowed : 12.92 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.24), residues: 1273 helix: 1.95 (0.24), residues: 497 sheet: 0.80 (0.38), residues: 201 loop : 0.00 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 54 TYR 0.016 0.001 TYR C 145 PHE 0.022 0.001 PHE A 846 TRP 0.006 0.001 TRP A 669 HIS 0.003 0.000 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (10335) covalent geometry : angle 0.51446 / 0.27 (13992) SS BOND : bond 0.00393 / 0.21 ( 1) SS BOND : angle 3.26931 / 1.86 ( 2) hydrogen bonds : bond 0.03018 / 2.01 ( 472) hydrogen bonds : angle 4.38049 / 3.12 ( 1296) Misc. bond : bond 0.00014 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2154.98 seconds wall clock time: 37 minutes 23.30 seconds (2243.30 seconds total)