Starting phenix.real_space_refine on Wed Aug 5 11:09:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5h_44212/08_2026/9b5h_44212.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5h_44212/08_2026/9b5h_44212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b5h_44212/08_2026/9b5h_44212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5h_44212/08_2026/9b5h_44212.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5h_44212/08_2026/9b5h_44212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5h_44212/08_2026/9b5h_44212.map" } resolution = 2.69 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= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6078 2.51 5 N 1575 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9536 Number of models: 1 Model: "" Number of chains: 7 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 2, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 1.91, per 1000 atoms: 0.20 Number of scatterers: 9536 At special positions: 0 Unit cell: (86.184, 98.952, 120.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 2 11.99 O 1836 8.00 N 1575 7.00 C 6078 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=2.91 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: 0.75 Conformation dependent library (CDL) restraints added in 234.5 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 47.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.717A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.692A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.021A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.293A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.520A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.643A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 4.146A pdb=" N GLY A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.319A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.599A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.603A 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 410 through 418 removed outlier: 4.378A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.536A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.654A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 474 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 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: 3.934A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.850A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.601A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.531A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 582' 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 Processing helix chain 'A' and resid 632 through 640 removed outlier: 3.992A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.595A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.979A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 835 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.511A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.645A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 883' 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 86 through 90 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 145 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.791A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.290A 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: 4.158A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.158A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.553A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908 Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 923 removed outlier: 6.419A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 923 removed outlier: 6.419A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.889A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 26 removed outlier: 6.241A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1269 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: 1.51 Time building geometry restraints manager: 0.97 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: 1619 1.27 - 1.40: 2291 1.40 - 1.54: 5639 1.54 - 1.67: 132 1.67 - 1.81: 64 Bond restraints: 9745 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " ideal model delta sigma weight residual 1.453 1.526 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O POP A1103 " pdb=" P1 POP A1103 " ideal model delta sigma weight residual 1.660 1.610 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" O POP A1103 " pdb=" P2 POP A1103 " ideal model delta sigma weight residual 1.661 1.611 0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" C4 AMP B 101 " pdb=" C5 AMP B 101 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.57e+00 ... (remaining 9740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 13147 3.26 - 6.52: 49 6.52 - 9.78: 3 9.78 - 13.03: 0 13.03 - 16.29: 1 Bond angle restraints: 13200 Sorted by residual: angle pdb=" P1 POP A1103 " pdb=" O POP A1103 " pdb=" P2 POP A1103 " ideal model delta sigma weight residual 139.66 123.37 16.29 3.00e+00 1.11e-01 2.95e+01 angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.78 -7.08 1.80e+00 3.09e-01 1.55e+01 angle pdb=" O POP A1103 " pdb=" P1 POP A1103 " pdb=" O2 POP A1103 " ideal model delta sigma weight residual 102.11 110.62 -8.51 3.00e+00 1.11e-01 8.05e+00 angle pdb=" C5' AMP B 101 " pdb=" O5' AMP B 101 " pdb=" P AMP B 101 " ideal model delta sigma weight residual 120.90 116.78 4.12 1.50e+00 4.44e-01 7.53e+00 angle pdb=" O1P AMP B 101 " pdb=" P AMP B 101 " pdb=" O2P AMP B 101 " ideal model delta sigma weight residual 119.90 112.51 7.39 3.00e+00 1.11e-01 6.07e+00 ... (remaining 13195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 5640 17.22 - 34.44: 218 34.44 - 51.65: 44 51.65 - 68.87: 5 68.87 - 86.09: 4 Dihedral angle restraints: 5911 sinusoidal: 2405 harmonic: 3506 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 -142.16 56.16 1 1.00e+01 1.00e-02 4.25e+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 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR A 277 " pdb=" C TYR A 277 " pdb=" N VAL A 278 " pdb=" CA VAL A 278 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 5908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 915 0.030 - 0.060: 389 0.060 - 0.090: 79 0.090 - 0.120: 73 0.120 - 0.150: 15 Chirality restraints: 1471 Sorted by residual: 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 2.58 -0.15 2.00e-01 2.50e+01 5.60e-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 4.59e-01 chirality pdb=" CA ILE A 188 " pdb=" N ILE A 188 " pdb=" C ILE A 188 " pdb=" CB ILE A 188 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 1468 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 95 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.10e+00 pdb=" N PRO C 121 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 75 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO C 76 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.017 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 40 2.56 - 3.14: 7429 3.14 - 3.73: 14057 3.73 - 4.31: 21271 4.31 - 4.90: 35822 Nonbonded interactions: 78619 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O6 POP A1103 " model vdw 1.969 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2 POP A1103 " model vdw 2.035 2.170 nonbonded pdb="MG MG A1102 " pdb=" O4 POP A1103 " model vdw 2.049 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.064 2.170 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.230 3.040 ... (remaining 78614 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.070 Find NCS groups from input model: 0.030 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:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.009 0.879 9749 Z= 0.485 Angle : 0.653 46.056 13202 Z= 0.314 Chirality : 0.040 0.150 1471 Planarity : 0.004 0.042 1709 Dihedral : 10.008 86.090 3644 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.85 % Allowed : 3.58 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.24), residues: 1200 helix: 1.42 (0.24), residues: 492 sheet: 0.81 (0.37), residues: 183 loop : 0.16 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 830 TYR 0.008 0.001 TYR C 74 PHE 0.010 0.001 PHE A 360 TRP 0.006 0.001 TRP A 608 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 9745) covalent geometry : angle 0.50017 / 0.24 (13200) SS BOND : bond 0.87878 / 46.25 ( 1) SS BOND : angle 34.12442 / 19.71 ( 2) hydrogen bonds : bond 0.14690 / 9.49 ( 453) hydrogen bonds : angle 5.89315 / 3.92 ( 1269) Misc. bond : bond 0.08488 / 3.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7214 (mmp80) cc_final: 0.6891 (mmp80) REVERT: A 196 MET cc_start: 0.8666 (mmp) cc_final: 0.8310 (mmp) REVERT: A 216 LYS cc_start: 0.6970 (mtmm) cc_final: 0.6563 (mttm) REVERT: A 250 TYR cc_start: 0.7423 (m-80) cc_final: 0.6827 (m-80) REVERT: A 262 LYS cc_start: 0.8732 (ttpp) cc_final: 0.8461 (tmtp) REVERT: A 274 ASP cc_start: 0.7724 (t0) cc_final: 0.7201 (p0) REVERT: A 333 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8378 (mp10) REVERT: A 406 ARG cc_start: 0.7869 (mtm180) cc_final: 0.6723 (mtp85) REVERT: A 516 GLU cc_start: 0.8211 (mp0) cc_final: 0.7967 (pm20) REVERT: A 540 GLU cc_start: 0.7291 (tt0) cc_final: 0.7039 (mp0) REVERT: A 583 GLN cc_start: 0.7969 (mt0) cc_final: 0.7243 (mm110) REVERT: A 611 ASP cc_start: 0.7460 (m-30) cc_final: 0.7203 (m-30) REVERT: A 626 MET cc_start: 0.7243 (ttt) cc_final: 0.6844 (mpt) REVERT: A 668 MET cc_start: 0.7090 (mmm) cc_final: 0.6846 (mmm) REVERT: A 699 GLN cc_start: 0.7780 (mm110) cc_final: 0.7543 (mp10) REVERT: A 738 LEU cc_start: 0.7659 (mt) cc_final: 0.7438 (mt) REVERT: A 879 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8148 (mmtt) REVERT: A 909 ASN cc_start: 0.7480 (t0) cc_final: 0.7260 (t0) REVERT: A 1004 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7641 (mt-10) REVERT: B 29 LYS cc_start: 0.8291 (mttp) cc_final: 0.8024 (mttm) REVERT: C 72 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: C 111 THR cc_start: 0.8950 (t) cc_final: 0.8677 (m) REVERT: C 139 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7547 (ttm-80) REVERT: C 143 ARG cc_start: 0.7858 (ttp-170) cc_final: 0.7507 (ttp-110) outliers start: 9 outliers final: 2 residues processed: 138 average time/residue: 0.6674 time to fit residues: 97.7519 Evaluate side-chains 111 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0000 chunk 113 optimal weight: 0.0060 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.088492 restraints weight = 11649.609| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.22 r_work: 0.2981 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9749 Z= 0.115 Angle : 0.477 7.151 13202 Z= 0.249 Chirality : 0.042 0.150 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.607 79.452 1311 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.51 % Allowed : 7.16 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.25), residues: 1200 helix: 1.69 (0.25), residues: 489 sheet: 1.10 (0.37), residues: 178 loop : 0.28 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 8 TYR 0.015 0.001 TYR C 145 PHE 0.011 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 9745) covalent geometry : angle 0.47234 / 0.25 (13200) SS BOND : bond 0.00857 / 0.45 ( 1) SS BOND : angle 5.23953 / 3.04 ( 2) hydrogen bonds : bond 0.04148 / 2.87 ( 453) hydrogen bonds : angle 4.65888 / 3.17 ( 1269) Misc. bond : bond 0.00263 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.8732 (mmp) cc_final: 0.8315 (mmp) REVERT: A 216 LYS cc_start: 0.7373 (mtmm) cc_final: 0.7029 (mttp) REVERT: A 250 TYR cc_start: 0.7569 (m-80) cc_final: 0.7081 (m-80) REVERT: A 262 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8610 (tmtp) REVERT: A 274 ASP cc_start: 0.7777 (t0) cc_final: 0.7198 (p0) REVERT: A 333 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8398 (mp10) REVERT: A 406 ARG cc_start: 0.8016 (mtm180) cc_final: 0.6815 (mtp85) REVERT: A 516 GLU cc_start: 0.8371 (mp0) cc_final: 0.8008 (pm20) REVERT: A 540 GLU cc_start: 0.7699 (tt0) cc_final: 0.7254 (mp0) REVERT: A 583 GLN cc_start: 0.8118 (mt0) cc_final: 0.7323 (mm110) REVERT: A 611 ASP cc_start: 0.7780 (m-30) cc_final: 0.7560 (m-30) REVERT: A 626 MET cc_start: 0.7293 (ttt) cc_final: 0.6868 (mpt) REVERT: A 668 MET cc_start: 0.7481 (mmm) cc_final: 0.7254 (mmm) REVERT: A 699 GLN cc_start: 0.7898 (mm110) cc_final: 0.7637 (mp10) REVERT: A 879 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8259 (mmtt) REVERT: A 909 ASN cc_start: 0.7418 (t0) cc_final: 0.7134 (t0) REVERT: A 1004 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 139 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.7093 (ttm-80) REVERT: C 143 ARG cc_start: 0.7661 (ttp-170) cc_final: 0.7325 (ttp-110) outliers start: 16 outliers final: 6 residues processed: 128 average time/residue: 0.5945 time to fit residues: 80.9404 Evaluate side-chains 117 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.090256 restraints weight = 11609.089| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.15 r_work: 0.3027 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9749 Z= 0.131 Angle : 0.477 7.321 13202 Z= 0.248 Chirality : 0.042 0.154 1471 Planarity : 0.004 0.042 1709 Dihedral : 5.231 69.225 1311 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.32 % Allowed : 8.67 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1200 helix: 1.67 (0.24), residues: 489 sheet: 1.07 (0.37), residues: 178 loop : 0.29 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 8 TYR 0.008 0.001 TYR A 736 PHE 0.011 0.001 PHE A 237 TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 9745) covalent geometry : angle 0.47282 / 0.25 (13200) SS BOND : bond 0.01365 / 0.72 ( 1) SS BOND : angle 5.21235 / 3.06 ( 2) hydrogen bonds : bond 0.04113 / 2.84 ( 453) hydrogen bonds : angle 4.50226 / 3.07 ( 1269) Misc. bond : bond 0.00105 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.8743 (mmp) cc_final: 0.8381 (mmp) REVERT: A 216 LYS cc_start: 0.7440 (mtmm) cc_final: 0.7078 (mttp) REVERT: A 250 TYR cc_start: 0.7625 (m-80) cc_final: 0.7174 (m-80) REVERT: A 262 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8638 (tmtp) REVERT: A 274 ASP cc_start: 0.7811 (t0) cc_final: 0.7217 (p0) REVERT: A 333 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8391 (mp10) REVERT: A 406 ARG cc_start: 0.8048 (mtm180) cc_final: 0.6872 (mtp85) REVERT: A 516 GLU cc_start: 0.8353 (mp0) cc_final: 0.8004 (pm20) REVERT: A 540 GLU cc_start: 0.7750 (tt0) cc_final: 0.7289 (mp0) REVERT: A 583 GLN cc_start: 0.8202 (mt0) cc_final: 0.7371 (mm110) REVERT: A 611 ASP cc_start: 0.7794 (m-30) cc_final: 0.7547 (m-30) REVERT: A 626 MET cc_start: 0.7338 (ttt) cc_final: 0.6924 (mpt) REVERT: A 668 MET cc_start: 0.7580 (mmm) cc_final: 0.7353 (mmm) REVERT: A 699 GLN cc_start: 0.7950 (mm110) cc_final: 0.7694 (mp10) REVERT: A 879 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8312 (mmtt) REVERT: A 909 ASN cc_start: 0.7421 (t0) cc_final: 0.7161 (t0) REVERT: B 71 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8649 (pp) REVERT: C 139 ARG cc_start: 0.7436 (ttm-80) cc_final: 0.7177 (ttm-80) REVERT: C 143 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7373 (ttp-110) outliers start: 14 outliers final: 7 residues processed: 116 average time/residue: 0.6208 time to fit residues: 76.8269 Evaluate side-chains 111 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 91 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.089423 restraints weight = 11812.987| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.21 r_work: 0.3007 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9749 Z= 0.159 Angle : 0.488 6.412 13202 Z= 0.253 Chirality : 0.043 0.150 1471 Planarity : 0.004 0.043 1709 Dihedral : 5.216 65.184 1311 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.79 % Allowed : 9.33 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.24), residues: 1200 helix: 1.62 (0.24), residues: 489 sheet: 1.04 (0.38), residues: 178 loop : 0.28 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 8 TYR 0.009 0.001 TYR A 150 PHE 0.012 0.001 PHE A 237 TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 ( 9745) covalent geometry : angle 0.48441 / 0.25 (13200) SS BOND : bond 0.01326 / 0.70 ( 1) SS BOND : angle 4.59261 / 2.69 ( 2) hydrogen bonds : bond 0.04287 / 2.97 ( 453) hydrogen bonds : angle 4.48899 / 3.06 ( 1269) Misc. bond : bond 0.00016 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.8755 (mmp) cc_final: 0.8423 (mmp) REVERT: A 216 LYS cc_start: 0.7438 (mtmm) cc_final: 0.7071 (mttp) REVERT: A 250 TYR cc_start: 0.7632 (m-80) cc_final: 0.7190 (m-80) REVERT: A 262 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8630 (tmtp) REVERT: A 274 ASP cc_start: 0.7772 (t0) cc_final: 0.7186 (p0) REVERT: A 333 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8384 (mp10) REVERT: A 406 ARG cc_start: 0.8069 (mtm180) cc_final: 0.6888 (mtp85) REVERT: A 516 GLU cc_start: 0.8384 (mp0) cc_final: 0.8035 (pm20) REVERT: A 540 GLU cc_start: 0.7790 (tt0) cc_final: 0.7304 (mp0) REVERT: A 583 GLN cc_start: 0.8218 (mt0) cc_final: 0.7363 (mm110) REVERT: A 611 ASP cc_start: 0.7864 (m-30) cc_final: 0.7662 (m-30) REVERT: A 626 MET cc_start: 0.7355 (ttt) cc_final: 0.6926 (mpt) REVERT: A 668 MET cc_start: 0.7607 (mmm) cc_final: 0.7380 (mmm) REVERT: A 699 GLN cc_start: 0.7969 (mm110) cc_final: 0.7700 (mp10) REVERT: A 879 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8386 (mmtt) REVERT: A 909 ASN cc_start: 0.7420 (t0) cc_final: 0.7145 (t0) REVERT: B 71 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8663 (pp) REVERT: C 139 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.7254 (ttm-80) REVERT: C 143 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7371 (ttp-170) outliers start: 19 outliers final: 10 residues processed: 118 average time/residue: 0.6476 time to fit residues: 81.5536 Evaluate side-chains 115 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 42 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.088104 restraints weight = 11667.611| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.23 r_work: 0.2988 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9749 Z= 0.129 Angle : 0.468 5.756 13202 Z= 0.243 Chirality : 0.042 0.148 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.239 69.859 1311 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.79 % Allowed : 10.37 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.24), residues: 1200 helix: 1.68 (0.24), residues: 489 sheet: 1.02 (0.37), residues: 180 loop : 0.30 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 8 TYR 0.008 0.001 TYR A 736 PHE 0.011 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 9745) covalent geometry : angle 0.46530 / 0.24 (13200) SS BOND : bond 0.00846 / 0.45 ( 1) SS BOND : angle 4.26639 / 2.46 ( 2) hydrogen bonds : bond 0.03959 / 2.75 ( 453) hydrogen bonds : angle 4.40663 / 3.00 ( 1269) Misc. bond : bond 0.00017 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.325 Fit side-chains REVERT: A 196 MET cc_start: 0.8709 (mmp) cc_final: 0.8404 (mmp) REVERT: A 216 LYS cc_start: 0.7348 (mtmm) cc_final: 0.6953 (mttp) REVERT: A 250 TYR cc_start: 0.7570 (m-80) cc_final: 0.7152 (m-80) REVERT: A 262 LYS cc_start: 0.8870 (ttpp) cc_final: 0.8575 (tmtp) REVERT: A 274 ASP cc_start: 0.7727 (t0) cc_final: 0.7125 (p0) REVERT: A 286 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7986 (mmp) REVERT: A 333 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8357 (mp10) REVERT: A 406 ARG cc_start: 0.8000 (mtm180) cc_final: 0.6824 (mtp85) REVERT: A 516 GLU cc_start: 0.8363 (mp0) cc_final: 0.8001 (pm20) REVERT: A 540 GLU cc_start: 0.7682 (tt0) cc_final: 0.7230 (mp0) REVERT: A 583 GLN cc_start: 0.8173 (mt0) cc_final: 0.7356 (mm110) REVERT: A 611 ASP cc_start: 0.7789 (m-30) cc_final: 0.7550 (m-30) REVERT: A 626 MET cc_start: 0.7314 (ttt) cc_final: 0.6891 (mpt) REVERT: A 699 GLN cc_start: 0.7941 (mm110) cc_final: 0.7665 (mp10) REVERT: A 879 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8312 (mmtt) REVERT: A 909 ASN cc_start: 0.7372 (t0) cc_final: 0.7101 (t0) REVERT: B 71 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8643 (pp) REVERT: C 139 ARG cc_start: 0.7397 (ttm-80) cc_final: 0.7194 (ttm-80) REVERT: C 143 ARG cc_start: 0.7731 (ttp-170) cc_final: 0.7444 (ttp-170) outliers start: 19 outliers final: 11 residues processed: 113 average time/residue: 0.6330 time to fit residues: 76.1282 Evaluate side-chains 114 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 0.0980 chunk 32 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 39 optimal weight: 0.0270 chunk 10 optimal weight: 0.0470 chunk 65 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.1514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.092862 restraints weight = 11695.430| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.17 r_work: 0.3056 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9749 Z= 0.087 Angle : 0.451 11.441 13202 Z= 0.230 Chirality : 0.040 0.157 1471 Planarity : 0.004 0.042 1709 Dihedral : 5.095 82.900 1310 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.51 % Allowed : 11.31 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.25), residues: 1200 helix: 1.83 (0.24), residues: 489 sheet: 1.09 (0.37), residues: 185 loop : 0.42 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 8 TYR 0.016 0.001 TYR C 145 PHE 0.008 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS A 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 ( 9745) covalent geometry : angle 0.45075 / 0.23 (13200) SS BOND : bond 0.02003 / 1.05 ( 1) SS BOND : angle 1.77670 / 0.96 ( 2) hydrogen bonds : bond 0.03242 / 2.28 ( 453) hydrogen bonds : angle 4.21691 / 2.87 ( 1269) Misc. bond : bond 0.00076 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.251 Fit side-chains REVERT: A 196 MET cc_start: 0.8690 (mmp) cc_final: 0.8338 (mmp) REVERT: A 216 LYS cc_start: 0.7419 (mtmm) cc_final: 0.7035 (mttp) REVERT: A 250 TYR cc_start: 0.7611 (m-80) cc_final: 0.7200 (m-80) REVERT: A 262 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8720 (tmtp) REVERT: A 274 ASP cc_start: 0.7788 (t0) cc_final: 0.7182 (p0) REVERT: A 286 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7945 (mmp) REVERT: A 406 ARG cc_start: 0.8037 (mtm180) cc_final: 0.6864 (mtp85) REVERT: A 516 GLU cc_start: 0.8411 (mp0) cc_final: 0.8014 (pm20) REVERT: A 540 GLU cc_start: 0.7742 (tt0) cc_final: 0.7289 (mp0) REVERT: A 583 GLN cc_start: 0.8104 (mt0) cc_final: 0.7372 (mm110) REVERT: A 611 ASP cc_start: 0.7822 (m-30) cc_final: 0.7573 (m-30) REVERT: A 626 MET cc_start: 0.7343 (ttt) cc_final: 0.6933 (mpt) REVERT: A 699 GLN cc_start: 0.7954 (mm110) cc_final: 0.7704 (mp10) REVERT: A 879 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8314 (mmtt) REVERT: A 909 ASN cc_start: 0.7386 (t0) cc_final: 0.7128 (t0) REVERT: A 981 LYS cc_start: 0.8475 (mmtp) cc_final: 0.8132 (mtpp) REVERT: B 71 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8640 (pp) REVERT: C 143 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7435 (ttp-170) outliers start: 16 outliers final: 6 residues processed: 116 average time/residue: 0.6097 time to fit residues: 75.1845 Evaluate side-chains 110 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 114 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.089594 restraints weight = 11801.015| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.17 r_work: 0.2993 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9749 Z= 0.161 Angle : 0.497 11.138 13202 Z= 0.256 Chirality : 0.043 0.168 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.259 83.576 1310 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.23 % Allowed : 12.35 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.25), residues: 1200 helix: 1.71 (0.24), residues: 490 sheet: 1.07 (0.37), residues: 180 loop : 0.38 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 8 TYR 0.016 0.001 TYR C 145 PHE 0.012 0.001 PHE A 237 TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 ( 9745) covalent geometry : angle 0.49688 / 0.26 (13200) SS BOND : bond 0.01515 / 0.80 ( 1) SS BOND : angle 1.64852 / 0.83 ( 2) hydrogen bonds : bond 0.04184 / 2.91 ( 453) hydrogen bonds : angle 4.38534 / 2.98 ( 1269) Misc. bond : bond 0.00075 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.384 Fit side-chains REVERT: A 196 MET cc_start: 0.8678 (mmp) cc_final: 0.8352 (mmp) REVERT: A 216 LYS cc_start: 0.7305 (mtmm) cc_final: 0.6914 (mttp) REVERT: A 250 TYR cc_start: 0.7531 (m-80) cc_final: 0.7105 (m-80) REVERT: A 262 LYS cc_start: 0.8947 (ttpp) cc_final: 0.8668 (tmtp) REVERT: A 274 ASP cc_start: 0.7750 (t0) cc_final: 0.7116 (p0) REVERT: A 516 GLU cc_start: 0.8357 (mp0) cc_final: 0.7969 (pm20) REVERT: A 540 GLU cc_start: 0.7721 (tt0) cc_final: 0.7205 (mp0) REVERT: A 583 GLN cc_start: 0.8102 (mt0) cc_final: 0.7284 (mm110) REVERT: A 626 MET cc_start: 0.7322 (ttt) cc_final: 0.6912 (mpt) REVERT: A 699 GLN cc_start: 0.7922 (mm110) cc_final: 0.7644 (mp10) REVERT: A 909 ASN cc_start: 0.7341 (t0) cc_final: 0.7077 (t0) REVERT: A 981 LYS cc_start: 0.8440 (mmtp) cc_final: 0.8069 (mtpp) REVERT: B 71 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8633 (pp) REVERT: C 143 ARG cc_start: 0.7694 (ttp-170) cc_final: 0.7446 (ttp-170) outliers start: 13 outliers final: 8 residues processed: 117 average time/residue: 0.5972 time to fit residues: 74.4846 Evaluate side-chains 111 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 0.0770 chunk 18 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.088015 restraints weight = 11676.143| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.20 r_work: 0.2978 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9749 Z= 0.135 Angle : 0.485 10.644 13202 Z= 0.249 Chirality : 0.042 0.162 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.253 84.563 1310 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.51 % Allowed : 12.16 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.25), residues: 1200 helix: 1.72 (0.24), residues: 490 sheet: 1.08 (0.37), residues: 180 loop : 0.38 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 8 TYR 0.019 0.001 TYR C 145 PHE 0.011 0.001 PHE A 237 TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.13 ( 9745) covalent geometry : angle 0.48474 / 0.25 (13200) SS BOND : bond 0.01958 / 1.03 ( 1) SS BOND : angle 1.57756 / 0.81 ( 2) hydrogen bonds : bond 0.03953 / 2.76 ( 453) hydrogen bonds : angle 4.34993 / 2.96 ( 1269) Misc. bond : bond 0.00018 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.367 Fit side-chains REVERT: A 196 MET cc_start: 0.8696 (mmp) cc_final: 0.8375 (mmp) REVERT: A 216 LYS cc_start: 0.7347 (mtmm) cc_final: 0.6958 (mttp) REVERT: A 250 TYR cc_start: 0.7548 (m-80) cc_final: 0.7125 (m-80) REVERT: A 262 LYS cc_start: 0.8960 (ttpp) cc_final: 0.8689 (tmtp) REVERT: A 274 ASP cc_start: 0.7783 (t0) cc_final: 0.7167 (p0) REVERT: A 516 GLU cc_start: 0.8400 (mp0) cc_final: 0.8010 (pm20) REVERT: A 540 GLU cc_start: 0.7758 (tt0) cc_final: 0.7274 (mp0) REVERT: A 583 GLN cc_start: 0.8136 (mt0) cc_final: 0.7351 (mm110) REVERT: A 626 MET cc_start: 0.7311 (ttt) cc_final: 0.6904 (mpt) REVERT: A 699 GLN cc_start: 0.7964 (mm110) cc_final: 0.7695 (mp10) REVERT: A 909 ASN cc_start: 0.7375 (t0) cc_final: 0.7109 (t0) REVERT: A 981 LYS cc_start: 0.8467 (mmtp) cc_final: 0.8098 (mtpp) REVERT: B 71 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8670 (pp) REVERT: C 143 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.7511 (ttp-170) outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.6102 time to fit residues: 74.9010 Evaluate side-chains 116 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.091570 restraints weight = 11694.339| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.15 r_work: 0.3024 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9749 Z= 0.105 Angle : 0.465 9.546 13202 Z= 0.238 Chirality : 0.041 0.150 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.230 88.663 1310 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.32 % Allowed : 12.72 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.25), residues: 1200 helix: 1.73 (0.24), residues: 496 sheet: 1.11 (0.37), residues: 181 loop : 0.46 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 8 TYR 0.016 0.001 TYR C 145 PHE 0.009 0.001 PHE A 237 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 ( 9745) covalent geometry : angle 0.46499 / 0.24 (13200) SS BOND : bond 0.02256 / 1.19 ( 1) SS BOND : angle 0.24591 / 0.14 ( 2) hydrogen bonds : bond 0.03504 / 2.46 ( 453) hydrogen bonds : angle 4.23677 / 2.88 ( 1269) Misc. bond : bond 0.00021 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.249 Fit side-chains REVERT: A 196 MET cc_start: 0.8639 (mmp) cc_final: 0.8326 (mmp) REVERT: A 216 LYS cc_start: 0.7304 (mtmm) cc_final: 0.6911 (mttp) REVERT: A 250 TYR cc_start: 0.7400 (m-80) cc_final: 0.7055 (m-80) REVERT: A 262 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8679 (tmtp) REVERT: A 274 ASP cc_start: 0.7766 (t0) cc_final: 0.7106 (p0) REVERT: A 516 GLU cc_start: 0.8374 (mp0) cc_final: 0.7979 (pm20) REVERT: A 540 GLU cc_start: 0.7718 (tt0) cc_final: 0.7240 (mp0) REVERT: A 583 GLN cc_start: 0.8072 (mt0) cc_final: 0.7299 (mm110) REVERT: A 626 MET cc_start: 0.7288 (ttt) cc_final: 0.6885 (mpt) REVERT: A 699 GLN cc_start: 0.7917 (mm110) cc_final: 0.7637 (mp10) REVERT: A 909 ASN cc_start: 0.7343 (t0) cc_final: 0.7086 (t0) REVERT: A 981 LYS cc_start: 0.8434 (mmtp) cc_final: 0.8063 (mtpp) REVERT: B 71 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8609 (pp) REVERT: C 143 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7442 (ttp-170) outliers start: 14 outliers final: 9 residues processed: 115 average time/residue: 0.5544 time to fit residues: 68.0239 Evaluate side-chains 113 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.0970 chunk 74 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.090892 restraints weight = 11659.016| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.16 r_work: 0.3031 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9749 Z= 0.129 Angle : 0.478 9.812 13202 Z= 0.245 Chirality : 0.042 0.156 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.273 89.812 1310 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.23 % Allowed : 12.72 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.25), residues: 1200 helix: 1.67 (0.24), residues: 496 sheet: 1.10 (0.37), residues: 187 loop : 0.48 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 8 TYR 0.017 0.001 TYR C 145 PHE 0.010 0.001 PHE A 237 TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 9745) covalent geometry : angle 0.47834 / 0.24 (13200) SS BOND : bond 0.02202 / 1.16 ( 1) SS BOND : angle 0.53360 / 0.30 ( 2) hydrogen bonds : bond 0.03729 / 2.61 ( 453) hydrogen bonds : angle 4.28113 / 2.91 ( 1269) Misc. bond : bond 0.00020 / 0.01 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.269 Fit side-chains REVERT: A 196 MET cc_start: 0.8693 (mmp) cc_final: 0.8377 (mmp) REVERT: A 216 LYS cc_start: 0.7395 (mtmm) cc_final: 0.7003 (mttp) REVERT: A 250 TYR cc_start: 0.7455 (m-80) cc_final: 0.7115 (m-80) REVERT: A 262 LYS cc_start: 0.8958 (ttpp) cc_final: 0.8718 (tmtp) REVERT: A 274 ASP cc_start: 0.7801 (t0) cc_final: 0.7165 (p0) REVERT: A 516 GLU cc_start: 0.8373 (mp0) cc_final: 0.8049 (pm20) REVERT: A 540 GLU cc_start: 0.7799 (tt0) cc_final: 0.7344 (mp0) REVERT: A 583 GLN cc_start: 0.8133 (mt0) cc_final: 0.7375 (mm110) REVERT: A 626 MET cc_start: 0.7338 (ttt) cc_final: 0.6943 (mpt) REVERT: A 699 GLN cc_start: 0.7973 (mm110) cc_final: 0.7713 (mp10) REVERT: A 909 ASN cc_start: 0.7385 (t0) cc_final: 0.7118 (t0) REVERT: A 981 LYS cc_start: 0.8481 (mmtp) cc_final: 0.8112 (mtpp) REVERT: B 71 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8665 (pp) REVERT: C 143 ARG cc_start: 0.7780 (ttp-170) cc_final: 0.7503 (ttp-170) outliers start: 13 outliers final: 10 residues processed: 115 average time/residue: 0.5110 time to fit residues: 62.8225 Evaluate side-chains 114 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 101 optimal weight: 0.0040 chunk 13 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.090925 restraints weight = 11696.753| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.16 r_work: 0.3030 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9749 Z= 0.125 Angle : 0.476 9.998 13202 Z= 0.244 Chirality : 0.042 0.152 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.234 86.710 1310 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.32 % Allowed : 12.63 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.25), residues: 1200 helix: 1.68 (0.24), residues: 496 sheet: 1.15 (0.36), residues: 186 loop : 0.47 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 8 TYR 0.017 0.001 TYR C 145 PHE 0.010 0.001 PHE A 237 TRP 0.006 0.001 TRP A 608 HIS 0.001 0.000 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.12 ( 9745) covalent geometry : angle 0.47647 / 0.24 (13200) SS BOND : bond 0.02104 / 1.11 ( 1) SS BOND : angle 0.41741 / 0.24 ( 2) hydrogen bonds : bond 0.03731 / 2.62 ( 453) hydrogen bonds : angle 4.27845 / 2.90 ( 1269) Misc. bond : bond 0.00016 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3261.79 seconds wall clock time: 55 minutes 56.07 seconds (3356.07 seconds total)