Starting phenix.real_space_refine on Sat Aug 23 06:11:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5l_44216/08_2025/9b5l_44216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5l_44216/08_2025/9b5l_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_2025/9b5l_44216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5l_44216/08_2025/9b5l_44216.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5l_44216/08_2025/9b5l_44216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5l_44216/08_2025/9b5l_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-2.0-5787/lib/python3.9/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: 2.29, per 1000 atoms: 0.23 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: 0.96 Conformation dependent library (CDL) restraints added in 387.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.32 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: 1.50 Time building geometry restraints manager: 1.22 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=" C4' AMP B 101 " pdb=" O4' AMP B 101 " ideal model delta sigma weight residual 1.426 1.450 -0.024 2.00e-02 2.50e+03 1.49e+00 ... (remaining 10330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 13861 1.80 - 3.60: 97 3.60 - 5.41: 30 5.41 - 7.21: 2 7.21 - 9.01: 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=" C1' AMP B 101 " pdb=" C2' AMP B 101 " pdb=" C3' AMP B 101 " ideal model delta sigma weight residual 111.00 101.99 9.01 3.00e+00 1.11e-01 9.02e+00 angle pdb=" C2' AMP B 101 " pdb=" C3' AMP B 101 " pdb=" C4' AMP B 101 " ideal model delta sigma weight residual 111.00 103.74 7.26 3.00e+00 1.11e-01 5.86e+00 angle pdb=" O1P AMP B 101 " pdb=" P AMP B 101 " pdb=" O2P AMP B 101 " ideal model delta sigma weight residual 119.60 112.75 6.85 3.00e+00 1.11e-01 5.21e+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 - 0.035: 1087 0.035 - 0.070: 344 0.070 - 0.106: 88 0.106 - 0.141: 48 0.141 - 0.176: 1 Chirality restraints: 1568 Sorted by residual: chirality pdb=" C3' AMP B 101 " pdb=" C2' AMP B 101 " pdb=" C4' AMP B 101 " pdb=" O3' AMP B 101 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 7.74e-01 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 ... (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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.750 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.669 51.466 13994 Z= 0.329 Chirality : 0.040 0.176 1568 Planarity : 0.003 0.029 1812 Dihedral : 10.250 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 aren 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 covalent geometry : bond 0.00409 (10335) covalent geometry : angle 0.50053 (13992) SS BOND : bond 0.86698 ( 1) SS BOND : angle 37.12965 ( 2) hydrogen bonds : bond 0.14440 ( 472) hydrogen bonds : angle 5.79515 ( 1296) Misc. bond : bond 0.09534 ( 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 : 0.277 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: 0.1178 time to fit residues: 31.3792 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 : 0.411 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.114805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084993 restraints weight = 20818.483| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.25 r_work: 0.3263 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10339 Z= 0.141 Angle : 0.561 9.512 13994 Z= 0.289 Chirality : 0.043 0.159 1568 Planarity : 0.004 0.049 1812 Dihedral : 6.754 89.378 1401 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.21 % Allowed : 7.96 % Favored : 89.82 % 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 aren not related in a simple way. whole: 1.36 (0.25), residues: 1273 helix: 1.80 (0.24), residues: 515 sheet: 0.76 (0.37), residues: 208 loop : 0.19 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 72 TYR 0.023 0.001 TYR C 145 PHE 0.014 0.001 PHE A 633 TRP 0.010 0.001 TRP C 141 HIS 0.008 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00325 (10335) covalent geometry : angle 0.55457 (13992) SS BOND : bond 0.01710 ( 1) SS BOND : angle 6.94665 ( 2) hydrogen bonds : bond 0.04114 ( 472) hydrogen bonds : angle 4.81036 ( 1296) Misc. bond : bond 0.00455 ( 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: 25 poor density : 147 time to evaluate : 0.372 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: 0.8524 (mptt) cc_final: 0.8105 (tmtt) REVERT: A 35 MET cc_start: 0.8622 (ttp) cc_final: 0.8372 (ttp) REVERT: A 474 ARG cc_start: 0.8025 (ptt-90) cc_final: 0.7702 (ptt90) REVERT: A 507 THR cc_start: 0.9173 (m) cc_final: 0.8955 (p) REVERT: A 588 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7891 (mmmt) REVERT: A 623 ASN cc_start: 0.7412 (OUTLIER) cc_final: 0.6841 (t0) REVERT: A 717 HIS cc_start: 0.8860 (OUTLIER) cc_final: 0.8328 (t-90) REVERT: A 718 ASN cc_start: 0.8460 (t0) cc_final: 0.8168 (t0) REVERT: B 18 GLU cc_start: 0.8796 (mp0) cc_final: 0.8101 (mp0) REVERT: B 21 ASP cc_start: 0.8555 (m-30) cc_final: 0.7525 (m-30) REVERT: B 63 LYS cc_start: 0.9641 (ptmm) cc_final: 0.8971 (ptmm) REVERT: B 64 GLU cc_start: 0.9156 (mp0) cc_final: 0.8591 (mp0) REVERT: C 7 ASN cc_start: 0.8768 (t0) cc_final: 0.8528 (t0) REVERT: C 34 GLN cc_start: 0.8891 (tt0) cc_final: 0.8196 (pp30) REVERT: C 38 MET cc_start: 0.8314 (ppp) cc_final: 0.8100 (ppp) REVERT: C 72 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8597 (mtp85) REVERT: C 92 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8292 (mm-40) REVERT: D 31 GLN cc_start: 0.7931 (tt0) cc_final: 0.7393 (tp40) REVERT: D 41 GLN cc_start: 0.8119 (mt0) cc_final: 0.7894 (mt0) REVERT: D 72 ARG cc_start: 0.7717 (tmm160) cc_final: 0.7176 (tmm160) outliers start: 25 outliers final: 18 residues processed: 162 average time/residue: 0.0999 time to fit residues: 22.3492 Evaluate side-chains 139 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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: 0.0050 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.113495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084537 restraints weight = 20890.396| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.16 r_work: 0.3296 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10339 Z= 0.142 Angle : 0.526 8.472 13994 Z= 0.271 Chirality : 0.042 0.139 1568 Planarity : 0.004 0.036 1812 Dihedral : 5.751 86.907 1394 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.83 % Allowed : 8.76 % Favored : 88.41 % 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 aren not related in a simple way. whole: 1.36 (0.24), residues: 1273 helix: 1.82 (0.24), residues: 511 sheet: 0.71 (0.36), residues: 215 loop : 0.20 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 919 TYR 0.014 0.001 TYR C 145 PHE 0.023 0.001 PHE A 846 TRP 0.006 0.001 TRP A 669 HIS 0.011 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00332 (10335) covalent geometry : angle 0.52104 (13992) SS BOND : bond 0.00696 ( 1) SS BOND : angle 6.22994 ( 2) hydrogen bonds : bond 0.03626 ( 472) hydrogen bonds : angle 4.68458 ( 1296) Misc. bond : bond 0.00160 ( 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 : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8608 (mptt) cc_final: 0.8144 (tmtt) REVERT: A 35 MET cc_start: 0.8603 (ttp) cc_final: 0.8352 (ttp) REVERT: A 474 ARG cc_start: 0.8059 (ptt-90) cc_final: 0.7766 (ptt90) REVERT: A 653 ASP cc_start: 0.8539 (m-30) cc_final: 0.7534 (m-30) REVERT: A 668 MET cc_start: 0.7647 (tpp) cc_final: 0.7444 (tpp) REVERT: A 717 HIS cc_start: 0.8769 (OUTLIER) cc_final: 0.8363 (t-90) REVERT: A 718 ASN cc_start: 0.8363 (t0) cc_final: 0.8070 (t0) REVERT: B 18 GLU cc_start: 0.8805 (mp0) cc_final: 0.8187 (mp0) REVERT: B 21 ASP cc_start: 0.8561 (m-30) cc_final: 0.7625 (m-30) REVERT: B 64 GLU cc_start: 0.9063 (mp0) cc_final: 0.8729 (mp0) REVERT: C 34 GLN cc_start: 0.8841 (tt0) cc_final: 0.8367 (pp30) REVERT: C 92 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8254 (mm-40) REVERT: D 14 THR cc_start: 0.6453 (OUTLIER) cc_final: 0.6252 (t) REVERT: D 18 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8040 (tm-30) REVERT: D 31 GLN cc_start: 0.7944 (tt0) cc_final: 0.7429 (tp40) REVERT: D 45 PHE cc_start: 0.7650 (t80) cc_final: 0.7419 (t80) REVERT: D 72 ARG cc_start: 0.7619 (tmm160) cc_final: 0.7407 (tmm160) outliers start: 32 outliers final: 19 residues processed: 148 average time/residue: 0.1024 time to fit residues: 20.6052 Evaluate side-chains 129 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 14 THR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 57 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.113581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.085036 restraints weight = 21097.953| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.13 r_work: 0.3247 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10339 Z= 0.156 Angle : 0.532 6.390 13994 Z= 0.273 Chirality : 0.042 0.140 1568 Planarity : 0.004 0.054 1812 Dihedral : 5.642 88.337 1391 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.65 % Allowed : 10.53 % Favored : 86.81 % 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 aren not related in a simple way. whole: 1.34 (0.24), residues: 1273 helix: 1.83 (0.24), residues: 509 sheet: 0.74 (0.36), residues: 215 loop : 0.14 (0.27), residues: 549 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 0.006 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00370 (10335) covalent geometry : angle 0.52948 (13992) SS BOND : bond 0.01014 ( 1) SS BOND : angle 4.68052 ( 2) hydrogen bonds : bond 0.03547 ( 472) hydrogen bonds : angle 4.59387 ( 1296) Misc. bond : bond 0.00035 ( 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 147 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.289 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: 0.8541 (mptt) cc_final: 0.8017 (tmtt) REVERT: A 35 MET cc_start: 0.8576 (ttp) cc_final: 0.8341 (ttp) REVERT: A 145 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8568 (ttmt) REVERT: A 474 ARG cc_start: 0.8147 (ptt-90) cc_final: 0.7717 (ptt90) REVERT: A 668 MET cc_start: 0.7557 (tpp) cc_final: 0.7332 (tpp) REVERT: A 717 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.8414 (t-90) REVERT: A 718 ASN cc_start: 0.8465 (t0) cc_final: 0.8085 (t0) REVERT: B 18 GLU cc_start: 0.8838 (mp0) cc_final: 0.8070 (mp0) REVERT: B 21 ASP cc_start: 0.8557 (m-30) cc_final: 0.7367 (m-30) REVERT: B 64 GLU cc_start: 0.9146 (mp0) cc_final: 0.8768 (mp0) REVERT: C 34 GLN cc_start: 0.8901 (tt0) cc_final: 0.8292 (pp30) REVERT: C 38 MET cc_start: 0.8194 (ppp) cc_final: 0.7971 (ppp) REVERT: C 92 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8248 (mm-40) REVERT: D 18 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7949 (tm-30) REVERT: D 31 GLN cc_start: 0.7968 (tt0) cc_final: 0.7415 (tp40) REVERT: D 41 GLN cc_start: 0.8080 (mt0) cc_final: 0.7872 (mt0) outliers start: 30 outliers final: 21 residues processed: 138 average time/residue: 0.1025 time to fit residues: 19.1446 Evaluate side-chains 134 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 0.0170 chunk 94 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.114344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084875 restraints weight = 20923.495| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.27 r_work: 0.3256 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10339 Z= 0.109 Angle : 0.507 7.674 13994 Z= 0.258 Chirality : 0.041 0.165 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.528 88.635 1391 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.39 % Allowed : 10.97 % 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 aren not related in a simple way. whole: 1.35 (0.24), residues: 1273 helix: 1.82 (0.24), residues: 510 sheet: 0.89 (0.36), residues: 208 loop : 0.10 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.017 0.001 TYR C 145 PHE 0.025 0.001 PHE A 846 TRP 0.006 0.001 TRP A 669 HIS 0.005 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00252 (10335) covalent geometry : angle 0.50490 (13992) SS BOND : bond 0.00841 ( 1) SS BOND : angle 3.49353 ( 2) hydrogen bonds : bond 0.03200 ( 472) hydrogen bonds : angle 4.46967 ( 1296) Misc. bond : bond 0.00305 ( 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 143 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.391 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: 0.8527 (mptt) cc_final: 0.7992 (tmtt) REVERT: A 35 MET cc_start: 0.8564 (ttp) cc_final: 0.8339 (ttp) REVERT: A 474 ARG cc_start: 0.8132 (ptt-90) cc_final: 0.7661 (ptt90) REVERT: A 668 MET cc_start: 0.7543 (tpp) cc_final: 0.7307 (tpp) REVERT: A 717 HIS cc_start: 0.8831 (OUTLIER) cc_final: 0.8411 (t-90) REVERT: A 718 ASN cc_start: 0.8424 (t0) cc_final: 0.8035 (t0) REVERT: A 818 HIS cc_start: 0.7363 (m90) cc_final: 0.6858 (m170) REVERT: B 18 GLU cc_start: 0.8834 (mp0) cc_final: 0.8035 (mp0) REVERT: B 21 ASP cc_start: 0.8599 (m-30) cc_final: 0.7357 (m-30) REVERT: B 24 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7719 (p0) REVERT: B 64 GLU cc_start: 0.9147 (mp0) cc_final: 0.8761 (mp0) REVERT: B 74 ARG cc_start: 0.8436 (ptt-90) cc_final: 0.7899 (ptp90) REVERT: C 34 GLN cc_start: 0.8911 (tt0) cc_final: 0.8140 (pp30) REVERT: C 38 MET cc_start: 0.8232 (ppp) cc_final: 0.7953 (ppp) REVERT: C 92 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8247 (mm-40) REVERT: D 18 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7992 (tm-30) REVERT: D 31 GLN cc_start: 0.7962 (tt0) cc_final: 0.7407 (tp40) REVERT: D 41 GLN cc_start: 0.8122 (mt0) cc_final: 0.7907 (mt0) outliers start: 27 outliers final: 19 residues processed: 133 average time/residue: 0.1111 time to fit residues: 19.8231 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 : 0.322 ------------------------------------------------------------------------------- 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 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 576 THR 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 24 ASP 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 71 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: 3.9990 chunk 76 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 23 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 92 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.115132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.085700 restraints weight = 21192.771| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.28 r_work: 0.3262 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2517 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= 0.099 Angle : 0.490 6.307 13994 Z= 0.248 Chirality : 0.041 0.130 1568 Planarity : 0.003 0.040 1812 Dihedral : 5.389 88.685 1391 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.30 % Allowed : 11.33 % Favored : 86.37 % 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 aren not related in a simple way. whole: 1.38 (0.24), residues: 1273 helix: 1.91 (0.24), residues: 504 sheet: 0.85 (0.38), residues: 196 loop : 0.11 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00227 (10335) covalent geometry : angle 0.48769 (13992) SS BOND : bond 0.00192 ( 1) SS BOND : angle 3.60554 ( 2) hydrogen bonds : bond 0.02951 ( 472) hydrogen bonds : angle 4.36931 ( 1296) Misc. bond : bond 0.00005 ( 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 150 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.357 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: 0.8540 (mptt) cc_final: 0.8012 (tmtt) REVERT: A 35 MET cc_start: 0.8546 (ttp) cc_final: 0.8288 (ttm) REVERT: A 474 ARG cc_start: 0.8107 (ptt-90) cc_final: 0.7642 (ptt90) REVERT: A 668 MET cc_start: 0.7615 (tpp) cc_final: 0.7357 (tpp) REVERT: A 699 GLN cc_start: 0.8723 (mp10) cc_final: 0.8465 (mp10) REVERT: A 717 HIS cc_start: 0.8831 (OUTLIER) cc_final: 0.8443 (t-90) REVERT: A 718 ASN cc_start: 0.8370 (t0) cc_final: 0.7976 (t0) REVERT: A 818 HIS cc_start: 0.7205 (m90) cc_final: 0.6679 (m170) REVERT: B 18 GLU cc_start: 0.8823 (mp0) cc_final: 0.8018 (mp0) REVERT: B 21 ASP cc_start: 0.8596 (m-30) cc_final: 0.7340 (m-30) REVERT: B 24 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7731 (p0) REVERT: B 31 GLN cc_start: 0.8779 (tt0) cc_final: 0.8482 (tt0) REVERT: B 64 GLU cc_start: 0.9126 (mp0) cc_final: 0.8756 (mp0) REVERT: B 74 ARG cc_start: 0.8397 (ptt-90) cc_final: 0.7847 (ptp90) REVERT: C 34 GLN cc_start: 0.8902 (tt0) cc_final: 0.8148 (pp30) REVERT: C 38 MET cc_start: 0.8234 (ppp) cc_final: 0.7945 (ppp) REVERT: C 92 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8205 (mm-40) REVERT: D 1 MET cc_start: 0.8011 (pmm) cc_final: 0.7780 (pmm) REVERT: D 18 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8042 (tm-30) REVERT: D 31 GLN cc_start: 0.7938 (tt0) cc_final: 0.7386 (tp40) REVERT: D 41 GLN cc_start: 0.8109 (mt0) cc_final: 0.7867 (mt0) outliers start: 26 outliers final: 19 residues processed: 140 average time/residue: 0.1012 time to fit residues: 19.3687 Evaluate side-chains 136 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 568 THR Chi-restraints excluded: chain A residue 576 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 24 ASP 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: 1.9990 chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.114544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.085667 restraints weight = 20953.698| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.18 r_work: 0.3281 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10339 Z= 0.132 Angle : 0.504 7.918 13994 Z= 0.256 Chirality : 0.041 0.149 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.378 88.697 1391 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.04 % Allowed : 12.12 % Favored : 85.84 % 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 aren not related in a simple way. whole: 1.39 (0.25), residues: 1273 helix: 1.96 (0.24), residues: 503 sheet: 0.81 (0.37), residues: 202 loop : 0.09 (0.27), residues: 568 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 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00312 (10335) covalent geometry : angle 0.50189 (13992) SS BOND : bond 0.00495 ( 1) SS BOND : angle 3.41747 ( 2) hydrogen bonds : bond 0.03131 ( 472) hydrogen bonds : angle 4.38227 ( 1296) Misc. bond : bond 0.00036 ( 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 135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.287 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: 0.8579 (mptt) cc_final: 0.8061 (tmtt) REVERT: A 35 MET cc_start: 0.8603 (ttp) cc_final: 0.8381 (ttm) REVERT: A 474 ARG cc_start: 0.8162 (ptt-90) cc_final: 0.7688 (ptt90) REVERT: A 558 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7650 (mm-30) REVERT: A 668 MET cc_start: 0.7627 (tpp) cc_final: 0.7381 (tpp) REVERT: A 717 HIS cc_start: 0.8827 (OUTLIER) cc_final: 0.8423 (t-90) REVERT: A 718 ASN cc_start: 0.8348 (t0) cc_final: 0.7978 (t0) REVERT: A 818 HIS cc_start: 0.7264 (m90) cc_final: 0.6730 (m170) REVERT: B 18 GLU cc_start: 0.8820 (mp0) cc_final: 0.8029 (mp0) REVERT: B 21 ASP cc_start: 0.8562 (m-30) cc_final: 0.7301 (m-30) REVERT: B 24 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7727 (p0) REVERT: B 31 GLN cc_start: 0.8836 (tt0) cc_final: 0.8569 (tt0) REVERT: B 64 GLU cc_start: 0.9082 (mp0) cc_final: 0.8780 (mp0) REVERT: B 74 ARG cc_start: 0.8414 (ptt-90) cc_final: 0.7879 (ptp90) REVERT: C 34 GLN cc_start: 0.8864 (tt0) cc_final: 0.8230 (tm-30) REVERT: C 38 MET cc_start: 0.8235 (ppp) cc_final: 0.7938 (ppp) REVERT: C 92 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8201 (mm-40) REVERT: D 18 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8054 (tm-30) REVERT: D 31 GLN cc_start: 0.7906 (tt0) cc_final: 0.7650 (tp40) outliers start: 23 outliers final: 19 residues processed: 127 average time/residue: 0.1122 time to fit residues: 19.1026 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 : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 24 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 0.0000 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 73 optimal weight: 0.0570 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.115088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.085898 restraints weight = 21052.563| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.28 r_work: 0.3268 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10339 Z= 0.098 Angle : 0.497 7.453 13994 Z= 0.252 Chirality : 0.041 0.132 1568 Planarity : 0.003 0.040 1812 Dihedral : 5.220 88.148 1388 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.77 % Allowed : 12.92 % Favored : 85.31 % 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 aren not related in a simple way. whole: 1.41 (0.25), residues: 1273 helix: 1.96 (0.24), residues: 504 sheet: 0.86 (0.37), residues: 207 loop : 0.09 (0.27), residues: 562 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 0.030 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 covalent geometry : bond 0.00225 (10335) covalent geometry : angle 0.49516 (13992) SS BOND : bond 0.00478 ( 1) SS BOND : angle 3.21813 ( 2) hydrogen bonds : bond 0.02907 ( 472) hydrogen bonds : angle 4.32907 ( 1296) Misc. bond : bond 0.00034 ( 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 140 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.277 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: 0.8515 (mptt) cc_final: 0.7967 (tmtt) REVERT: A 35 MET cc_start: 0.8537 (ttp) cc_final: 0.8260 (ttm) REVERT: A 474 ARG cc_start: 0.8097 (ptt-90) cc_final: 0.7626 (ptt90) REVERT: A 558 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7756 (mm-30) REVERT: A 567 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8429 (p0) REVERT: A 668 MET cc_start: 0.7637 (tpp) cc_final: 0.7383 (tpp) REVERT: A 717 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.8438 (t-90) REVERT: A 718 ASN cc_start: 0.8339 (t0) cc_final: 0.7918 (t0) REVERT: A 818 HIS cc_start: 0.7110 (m90) cc_final: 0.6597 (m170) REVERT: B 18 GLU cc_start: 0.8844 (mp0) cc_final: 0.8018 (mp0) REVERT: B 21 ASP cc_start: 0.8561 (m-30) cc_final: 0.7263 (m-30) REVERT: B 24 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7737 (p0) REVERT: B 31 GLN cc_start: 0.8705 (tt0) cc_final: 0.8443 (tt0) REVERT: B 64 GLU cc_start: 0.9146 (mp0) cc_final: 0.8752 (mp0) REVERT: B 74 ARG cc_start: 0.8400 (ptt-90) cc_final: 0.7843 (ptp90) REVERT: C 34 GLN cc_start: 0.8879 (tt0) cc_final: 0.8147 (tm-30) REVERT: C 38 MET cc_start: 0.8260 (ppp) cc_final: 0.7943 (ppp) REVERT: C 92 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8176 (mm-40) REVERT: D 18 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8019 (tm-30) REVERT: D 31 GLN cc_start: 0.7898 (tt0) cc_final: 0.7669 (tp40) outliers start: 20 outliers final: 14 residues processed: 132 average time/residue: 0.1127 time to fit residues: 20.3348 Evaluate side-chains 129 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 24 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 123 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 10 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 110 optimal weight: 0.7980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.115536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.086327 restraints weight = 20992.181| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.27 r_work: 0.3264 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10339 Z= 0.098 Angle : 0.500 9.641 13994 Z= 0.253 Chirality : 0.040 0.130 1568 Planarity : 0.003 0.040 1812 Dihedral : 5.137 88.151 1388 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.59 % Allowed : 13.10 % Favored : 85.31 % 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 aren not related in a simple way. whole: 1.43 (0.25), residues: 1273 helix: 1.96 (0.24), residues: 504 sheet: 0.92 (0.37), residues: 207 loop : 0.10 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 54 TYR 0.016 0.001 TYR C 145 PHE 0.028 0.001 PHE A 846 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00226 (10335) covalent geometry : angle 0.49852 (13992) SS BOND : bond 0.00073 ( 1) SS BOND : angle 3.36903 ( 2) hydrogen bonds : bond 0.02838 ( 472) hydrogen bonds : angle 4.30474 ( 1296) Misc. bond : bond 0.00039 ( 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 136 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.254 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: 0.8528 (mptt) cc_final: 0.7988 (tmtt) REVERT: A 35 MET cc_start: 0.8543 (ttp) cc_final: 0.8266 (ttm) REVERT: A 474 ARG cc_start: 0.8083 (ptt-90) cc_final: 0.7609 (ptt90) REVERT: A 558 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 567 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8417 (p0) REVERT: A 668 MET cc_start: 0.7657 (tpp) cc_final: 0.7407 (tpp) REVERT: A 717 HIS cc_start: 0.8854 (OUTLIER) cc_final: 0.8418 (t-90) REVERT: A 718 ASN cc_start: 0.8348 (t0) cc_final: 0.7938 (t0) REVERT: A 818 HIS cc_start: 0.7138 (m90) cc_final: 0.6627 (m170) REVERT: B 18 GLU cc_start: 0.8853 (mp0) cc_final: 0.8031 (mp0) REVERT: B 21 ASP cc_start: 0.8584 (m-30) cc_final: 0.7264 (m-30) REVERT: B 24 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7741 (p0) REVERT: B 31 GLN cc_start: 0.8702 (tt0) cc_final: 0.8454 (tt0) REVERT: B 64 GLU cc_start: 0.9139 (mp0) cc_final: 0.8749 (mp0) REVERT: B 74 ARG cc_start: 0.8382 (ptt-90) cc_final: 0.7843 (ptp90) REVERT: C 34 GLN cc_start: 0.8873 (tt0) cc_final: 0.8161 (tm-30) REVERT: C 38 MET cc_start: 0.8213 (ppp) cc_final: 0.7870 (ppp) REVERT: C 92 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8212 (mm-40) REVERT: D 1 MET cc_start: 0.8031 (pmm) cc_final: 0.7737 (pmm) REVERT: D 18 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 31 GLN cc_start: 0.7890 (tt0) cc_final: 0.7649 (tp40) outliers start: 18 outliers final: 12 residues processed: 129 average time/residue: 0.1154 time to fit residues: 19.9821 Evaluate side-chains 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 24 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 103 optimal weight: 0.0070 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.115354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.086512 restraints weight = 20703.724| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.25 r_work: 0.3252 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10339 Z= 0.114 Angle : 0.511 11.143 13994 Z= 0.258 Chirality : 0.041 0.130 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.099 84.784 1388 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.59 % Allowed : 13.19 % 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 aren not related in a simple way. whole: 1.43 (0.25), residues: 1273 helix: 1.98 (0.24), residues: 503 sheet: 0.93 (0.37), residues: 207 loop : 0.08 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 54 TYR 0.016 0.001 TYR C 145 PHE 0.028 0.001 PHE A 846 TRP 0.005 0.001 TRP A 669 HIS 0.003 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00270 (10335) covalent geometry : angle 0.51002 (13992) SS BOND : bond 0.00532 ( 1) SS BOND : angle 3.17295 ( 2) hydrogen bonds : bond 0.02922 ( 472) hydrogen bonds : angle 4.29374 ( 1296) Misc. bond : bond 0.00023 ( 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 133 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.308 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: 0.8511 (mptt) cc_final: 0.7981 (tmtt) REVERT: A 35 MET cc_start: 0.8609 (ttp) cc_final: 0.8363 (ttm) REVERT: A 327 LYS cc_start: 0.8836 (mttm) cc_final: 0.8526 (mtmm) REVERT: A 474 ARG cc_start: 0.8106 (ptt-90) cc_final: 0.7617 (ptt90) REVERT: A 558 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 567 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8426 (p0) REVERT: A 668 MET cc_start: 0.7667 (tpp) cc_final: 0.7417 (tpp) REVERT: A 717 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.8482 (t-90) REVERT: A 718 ASN cc_start: 0.8367 (t0) cc_final: 0.7946 (t0) REVERT: A 818 HIS cc_start: 0.7207 (m90) cc_final: 0.6722 (m170) REVERT: B 18 GLU cc_start: 0.8872 (mp0) cc_final: 0.8041 (mp0) REVERT: B 21 ASP cc_start: 0.8583 (m-30) cc_final: 0.7247 (m-30) REVERT: B 24 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7753 (p0) REVERT: B 64 GLU cc_start: 0.9162 (mp0) cc_final: 0.8762 (mp0) REVERT: B 74 ARG cc_start: 0.8390 (ptt-90) cc_final: 0.7853 (ptp90) REVERT: C 34 GLN cc_start: 0.8871 (tt0) cc_final: 0.8146 (tm-30) REVERT: C 38 MET cc_start: 0.8148 (ppp) cc_final: 0.7819 (ppp) REVERT: C 92 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8182 (mm-40) REVERT: D 1 MET cc_start: 0.8012 (pmm) cc_final: 0.7686 (pmm) REVERT: D 18 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8066 (tm-30) REVERT: D 31 GLN cc_start: 0.7876 (tt0) cc_final: 0.7652 (tp40) outliers start: 18 outliers final: 14 residues processed: 124 average time/residue: 0.1164 time to fit residues: 19.4960 Evaluate side-chains 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 357 MET 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 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 24 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.115511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.085927 restraints weight = 21071.890| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.34 r_work: 0.3239 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10339 Z= 0.124 Angle : 0.510 10.476 13994 Z= 0.258 Chirality : 0.041 0.130 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.069 81.951 1388 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.59 % Allowed : 12.92 % Favored : 85.49 % 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 aren not related in a simple way. whole: 1.42 (0.25), residues: 1273 helix: 2.03 (0.24), residues: 497 sheet: 0.66 (0.37), residues: 218 loop : 0.14 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 54 TYR 0.015 0.001 TYR C 145 PHE 0.027 0.001 PHE A 846 TRP 0.005 0.001 TRP A 669 HIS 0.003 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00295 (10335) covalent geometry : angle 0.50820 (13992) SS BOND : bond 0.00454 ( 1) SS BOND : angle 3.18129 ( 2) hydrogen bonds : bond 0.02978 ( 472) hydrogen bonds : angle 4.30086 ( 1296) Misc. bond : bond 0.00013 ( 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: 1959.15 seconds wall clock time: 34 minutes 3.26 seconds (2043.26 seconds total)