Starting phenix.real_space_refine on Wed Aug 5 11:16:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5i_44213/08_2026/9b5i_44213.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5i_44213/08_2026/9b5i_44213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5i_44213/08_2026/9b5i_44213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5i_44213/08_2026/9b5i_44213.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5i_44213/08_2026/9b5i_44213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5i_44213/08_2026/9b5i_44213.cif" } resolution = 2.7 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= 0.069 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: 2.08, per 1000 atoms: 0.22 Number of scatterers: 9536 At special positions: 0 Unit cell: (85.12, 98.952, 121.296, 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: 1.00 Conformation dependent library (CDL) restraints added in 457.1 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: 51 helices and 10 sheets defined 46.7% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.835A 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 73 through 79 removed outlier: 3.634A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.036A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.235A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.634A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.694A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.135A 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: 4.236A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.611A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.595A 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 415 Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.687A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (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: 3.902A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.829A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.552A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.894A 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 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.719A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.848A pdb=" N VAL A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 679 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 752 removed outlier: 3.874A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 removed outlier: 3.630A pdb=" N LEU A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) 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: 3.649A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.643A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.755A 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 removed outlier: 3.584A pdb=" N GLN B 41 " --> pdb=" O PRO B 38 " (cutoff:3.500A) 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 sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.719A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.312A 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: 4.195A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.327A 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: 4.195A 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: 6.447A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.172A 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 922 removed outlier: 6.390A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.390A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.524A 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: 3.893A 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: 10.660A pdb=" N SER C 22 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N TRP C 33 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N GLY C 24 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N PHE C 31 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL C 26 " --> pdb=" O ASP C 29 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.26 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: 5651 1.54 - 1.67: 120 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 1.32e+01 bond pdb=" O POP A1103 " pdb=" P1 POP A1103 " ideal model delta sigma weight residual 1.660 1.611 0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" O POP A1103 " pdb=" P2 POP A1103 " ideal model delta sigma weight residual 1.661 1.612 0.049 2.00e-02 2.50e+03 5.89e+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 2.82e+00 bond pdb=" C4 AMP B 101 " pdb=" C5 AMP B 101 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.69e+00 ... (remaining 9740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 13138 3.18 - 6.37: 58 6.37 - 9.55: 3 9.55 - 12.73: 0 12.73 - 15.91: 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 139.66 123.75 15.91 3.00e+00 1.11e-01 2.81e+01 angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.39 -6.69 1.80e+00 3.09e-01 1.38e+01 angle pdb=" O POP A1103 " pdb=" P1 POP A1103 " pdb=" O2 POP A1103 " ideal model delta sigma weight residual 102.11 110.66 -8.55 3.00e+00 1.11e-01 8.12e+00 angle pdb=" C5' AMP B 101 " pdb=" O5' AMP B 101 " pdb=" P AMP B 101 " ideal model delta sigma weight residual 120.90 116.66 4.24 1.50e+00 4.44e-01 7.99e+00 angle pdb=" O1P AMP B 101 " pdb=" P AMP B 101 " pdb=" O2P AMP B 101 " ideal model delta sigma weight residual 119.90 112.56 7.34 3.00e+00 1.11e-01 5.98e+00 ... (remaining 13195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 5663 17.31 - 34.62: 200 34.62 - 51.92: 37 51.92 - 69.23: 8 69.23 - 86.54: 3 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 -136.11 50.11 1 1.00e+01 1.00e-02 3.44e+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 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" N GLN A 80 " pdb=" CA GLN A 80 " pdb=" CB GLN A 80 " pdb=" CG GLN A 80 " ideal model delta sinusoidal sigma weight residual -180.00 -120.30 -59.70 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 878 0.028 - 0.056: 408 0.056 - 0.084: 86 0.084 - 0.112: 65 0.112 - 0.141: 34 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 2.57 -0.14 2.00e-01 2.50e+01 4.94e-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 4.92e-01 chirality pdb=" CA ILE B 36 " pdb=" N ILE B 36 " pdb=" C ILE B 36 " pdb=" CB ILE B 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 1468 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO C 95 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 90 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO A 91 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO C 121 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.015 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 48 2.57 - 3.15: 7639 3.15 - 3.74: 14050 3.74 - 4.32: 21044 4.32 - 4.90: 35678 Nonbonded interactions: 78459 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O6 POP A1103 " model vdw 1.989 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2 POP A1103 " model vdw 2.016 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.040 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.055 2.170 nonbonded pdb="MG MG A1102 " pdb=" O4 POP A1103 " model vdw 2.253 2.170 ... (remaining 78454 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: 0.010 Normalize map: mean=0, sd=1: 4.060 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.440 Find NCS groups from input model: 0.050 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 0.875 9749 Z= 0.487 Angle : 0.609 40.871 13202 Z= 0.290 Chirality : 0.040 0.141 1471 Planarity : 0.003 0.036 1709 Dihedral : 9.583 86.539 3644 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.85 % Allowed : 2.17 % Favored : 96.98 % 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: 1.34 (0.25), residues: 1200 helix: 1.80 (0.25), residues: 488 sheet: 0.86 (0.37), residues: 180 loop : 0.14 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.008 0.001 TYR A 736 PHE 0.009 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9745) covalent geometry : angle 0.48919 / 0.23 (13200) SS BOND : bond 0.87466 / 46.03 ( 1) SS BOND : angle 29.42422 / 17.18 ( 2) hydrogen bonds : bond 0.14990 / 10.11 ( 448) hydrogen bonds : angle 5.61165 / 3.89 ( 1251) Misc. bond : bond 0.08606 / 3.82 ( 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 158 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6890 (tp30) cc_final: 0.6636 (tp30) REVERT: A 110 SER cc_start: 0.8444 (t) cc_final: 0.8198 (m) REVERT: A 135 LYS cc_start: 0.7609 (mmmt) cc_final: 0.7301 (mmmt) REVERT: A 184 MET cc_start: 0.8188 (mtm) cc_final: 0.7664 (mtt) REVERT: A 191 ASP cc_start: 0.7429 (m-30) cc_final: 0.7090 (m-30) REVERT: A 216 LYS cc_start: 0.6684 (mtmm) cc_final: 0.6290 (mtpp) REVERT: A 448 MET cc_start: 0.8311 (mmp) cc_final: 0.8100 (mmp) REVERT: A 455 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7643 (mm-30) REVERT: A 468 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6422 (mm-30) REVERT: A 583 GLN cc_start: 0.8079 (mt0) cc_final: 0.7149 (mm110) REVERT: A 614 GLU cc_start: 0.7178 (tp30) cc_final: 0.6897 (tp30) REVERT: A 668 MET cc_start: 0.6121 (mmm) cc_final: 0.5715 (mpt) REVERT: A 699 GLN cc_start: 0.7859 (mp10) cc_final: 0.7473 (mp10) REVERT: A 911 LYS cc_start: 0.7105 (mttt) cc_final: 0.6884 (mttp) REVERT: A 1011 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7154 (mmtt) REVERT: B 11 LYS cc_start: 0.8541 (tttt) cc_final: 0.8306 (tttm) REVERT: B 29 LYS cc_start: 0.8211 (mttp) cc_final: 0.7969 (mttm) REVERT: C 63 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8043 (mtpp) REVERT: C 79 ASN cc_start: 0.8407 (p0) cc_final: 0.8094 (p0) REVERT: C 81 ASN cc_start: 0.8642 (m-40) cc_final: 0.8062 (m110) REVERT: C 114 ASN cc_start: 0.8777 (t0) cc_final: 0.8409 (t0) REVERT: C 117 ASP cc_start: 0.8444 (t0) cc_final: 0.8130 (t0) REVERT: C 136 LEU cc_start: 0.8024 (mm) cc_final: 0.7632 (tt) outliers start: 9 outliers final: 3 residues processed: 154 average time/residue: 0.6629 time to fit residues: 108.5129 Evaluate side-chains 116 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0040 chunk 113 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 117 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.127687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.090360 restraints weight = 11802.878| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.22 r_work: 0.3019 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9749 Z= 0.128 Angle : 0.495 7.140 13202 Z= 0.255 Chirality : 0.042 0.147 1471 Planarity : 0.004 0.041 1709 Dihedral : 6.428 79.586 1311 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.17 % Allowed : 6.88 % Favored : 90.95 % 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 (0.24), residues: 1200 helix: 1.72 (0.24), residues: 492 sheet: 1.20 (0.37), residues: 178 loop : 0.19 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 143 TYR 0.010 0.001 TYR A 732 PHE 0.010 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9745) covalent geometry : angle 0.49227 / 0.25 (13200) SS BOND : bond 0.01521 / 0.80 ( 1) SS BOND : angle 4.28938 / 2.52 ( 2) hydrogen bonds : bond 0.04123 / 2.92 ( 448) hydrogen bonds : angle 4.51924 / 3.18 ( 1251) Misc. bond : bond 0.00201 / 0.09 ( 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 143 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7321 (tp30) cc_final: 0.6901 (tp30) REVERT: A 135 LYS cc_start: 0.7813 (mmmt) cc_final: 0.7551 (mmmt) REVERT: A 184 MET cc_start: 0.8235 (mtm) cc_final: 0.7553 (mtt) REVERT: A 191 ASP cc_start: 0.7509 (m-30) cc_final: 0.7276 (m-30) REVERT: A 196 MET cc_start: 0.8469 (mmp) cc_final: 0.8140 (mmt) REVERT: A 216 LYS cc_start: 0.6968 (mtmm) cc_final: 0.6597 (mtpp) REVERT: A 286 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7789 (mmp) REVERT: A 455 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8105 (mm-30) REVERT: A 465 ASP cc_start: 0.8508 (t0) cc_final: 0.8101 (t0) REVERT: A 583 GLN cc_start: 0.8187 (mt0) cc_final: 0.7248 (mm110) REVERT: A 614 GLU cc_start: 0.7415 (tp30) cc_final: 0.7100 (tp30) REVERT: A 668 MET cc_start: 0.6296 (mmm) cc_final: 0.5902 (mpt) REVERT: A 699 GLN cc_start: 0.7972 (mp10) cc_final: 0.7640 (mp10) REVERT: A 743 ASP cc_start: 0.6986 (t70) cc_final: 0.6669 (t70) REVERT: A 911 LYS cc_start: 0.7191 (mttt) cc_final: 0.6933 (mttp) REVERT: A 1011 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7183 (tptt) REVERT: B 11 LYS cc_start: 0.7943 (tttt) cc_final: 0.7616 (tttm) REVERT: B 29 LYS cc_start: 0.6921 (mttp) cc_final: 0.6675 (mttm) REVERT: B 57 SER cc_start: 0.8292 (t) cc_final: 0.8030 (p) REVERT: C 63 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7450 (mtpp) REVERT: C 66 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7310 (mtmt) REVERT: C 114 ASN cc_start: 0.8411 (t0) cc_final: 0.7970 (t0) REVERT: C 136 LEU cc_start: 0.7605 (mm) cc_final: 0.7249 (tt) outliers start: 23 outliers final: 7 residues processed: 130 average time/residue: 0.5398 time to fit residues: 74.7366 Evaluate side-chains 119 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 0.0040 chunk 60 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.127557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.089587 restraints weight = 11758.601| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.25 r_work: 0.2968 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1001 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 : 0.475 6.367 13202 Z= 0.245 Chirality : 0.042 0.148 1471 Planarity : 0.004 0.044 1709 Dihedral : 6.325 79.586 1309 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.98 % Allowed : 8.11 % Favored : 89.92 % 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: 1.39 (0.24), residues: 1200 helix: 1.68 (0.24), residues: 499 sheet: 1.13 (0.37), residues: 179 loop : 0.19 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 143 TYR 0.022 0.001 TYR C 127 PHE 0.010 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 9745) covalent geometry : angle 0.47128 / 0.24 (13200) SS BOND : bond 0.01170 / 0.62 ( 1) SS BOND : angle 4.62298 / 2.69 ( 2) hydrogen bonds : bond 0.03994 / 2.84 ( 448) hydrogen bonds : angle 4.41410 / 3.12 ( 1251) Misc. bond : bond 0.00023 / 0.01 ( 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 131 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7271 (tp30) cc_final: 0.6685 (tp30) REVERT: A 135 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7496 (mmmt) REVERT: A 184 MET cc_start: 0.8197 (mtm) cc_final: 0.7552 (mtt) REVERT: A 196 MET cc_start: 0.8458 (mmp) cc_final: 0.8159 (mmt) REVERT: A 216 LYS cc_start: 0.6896 (mtmm) cc_final: 0.6529 (mtpp) REVERT: A 455 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8078 (mm-30) REVERT: A 583 GLN cc_start: 0.8146 (mt0) cc_final: 0.7190 (mm110) REVERT: A 614 GLU cc_start: 0.7370 (tp30) cc_final: 0.7014 (tp30) REVERT: A 668 MET cc_start: 0.6289 (mmm) cc_final: 0.5891 (mpt) REVERT: A 699 GLN cc_start: 0.7989 (mp10) cc_final: 0.7510 (mp10) REVERT: A 743 ASP cc_start: 0.6944 (t70) cc_final: 0.6607 (t70) REVERT: A 869 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: A 911 LYS cc_start: 0.7122 (mttt) cc_final: 0.6839 (mttp) REVERT: A 1011 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7147 (tptt) REVERT: B 11 LYS cc_start: 0.7861 (tttt) cc_final: 0.7562 (tttm) REVERT: B 29 LYS cc_start: 0.6930 (mttp) cc_final: 0.6672 (mttm) REVERT: B 57 SER cc_start: 0.8261 (t) cc_final: 0.7977 (p) REVERT: C 63 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7428 (mtpp) REVERT: C 114 ASN cc_start: 0.8397 (t0) cc_final: 0.7932 (t0) REVERT: C 136 LEU cc_start: 0.7599 (mm) cc_final: 0.7234 (tt) outliers start: 21 outliers final: 12 residues processed: 126 average time/residue: 0.5866 time to fit residues: 78.6697 Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 594 THR 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 33 LYS Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 2.9990 chunk 106 optimal weight: 0.0670 chunk 42 optimal weight: 0.5980 chunk 111 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.2715 > 50:) chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.127809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.089680 restraints weight = 11935.220| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.27 r_work: 0.2965 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1099 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= 0.114 Angle : 0.461 5.666 13202 Z= 0.238 Chirality : 0.041 0.143 1471 Planarity : 0.004 0.045 1709 Dihedral : 6.294 80.483 1309 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.45 % Allowed : 8.67 % 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: 1.43 (0.24), residues: 1200 helix: 1.72 (0.24), residues: 499 sheet: 1.17 (0.37), residues: 179 loop : 0.21 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 143 TYR 0.024 0.001 TYR C 127 PHE 0.010 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 ( 9745) covalent geometry : angle 0.45820 / 0.24 (13200) SS BOND : bond 0.00724 / 0.38 ( 1) SS BOND : angle 4.25684 / 2.45 ( 2) hydrogen bonds : bond 0.03679 / 2.64 ( 448) hydrogen bonds : angle 4.31574 / 3.05 ( 1251) Misc. bond : bond 0.00024 / 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 141 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7268 (tp30) cc_final: 0.6689 (tp30) REVERT: A 184 MET cc_start: 0.8188 (mtm) cc_final: 0.7547 (mtt) REVERT: A 196 MET cc_start: 0.8500 (mmp) cc_final: 0.8230 (mmt) REVERT: A 216 LYS cc_start: 0.6911 (mtmm) cc_final: 0.6542 (mtpp) REVERT: A 286 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7752 (mmp) REVERT: A 455 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8035 (mm-30) REVERT: A 583 GLN cc_start: 0.8164 (mt0) cc_final: 0.7201 (mm110) REVERT: A 614 GLU cc_start: 0.7373 (tp30) cc_final: 0.7005 (tp30) REVERT: A 668 MET cc_start: 0.6310 (mmm) cc_final: 0.5910 (mpt) REVERT: A 699 GLN cc_start: 0.7977 (mp10) cc_final: 0.7589 (mp10) REVERT: A 743 ASP cc_start: 0.6948 (t70) cc_final: 0.6615 (t70) REVERT: A 869 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: A 911 LYS cc_start: 0.7038 (mttt) cc_final: 0.6732 (mttp) REVERT: A 1011 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7137 (tptt) REVERT: B 11 LYS cc_start: 0.7874 (tttt) cc_final: 0.7589 (tttm) REVERT: B 29 LYS cc_start: 0.6928 (mttp) cc_final: 0.6672 (mttm) REVERT: B 57 SER cc_start: 0.8272 (t) cc_final: 0.7993 (p) REVERT: B 71 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8648 (pp) REVERT: C 63 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7431 (mtpp) REVERT: C 66 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7182 (mtmt) REVERT: C 114 ASN cc_start: 0.8387 (t0) cc_final: 0.7878 (t0) REVERT: C 136 LEU cc_start: 0.7614 (mm) cc_final: 0.7244 (tt) outliers start: 26 outliers final: 14 residues processed: 129 average time/residue: 0.5245 time to fit residues: 72.0928 Evaluate side-chains 130 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 594 THR 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 33 LYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 75 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.126787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.088567 restraints weight = 11786.318| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.30 r_work: 0.2962 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1168 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= 0.115 Angle : 0.459 5.567 13202 Z= 0.237 Chirality : 0.041 0.140 1471 Planarity : 0.004 0.046 1709 Dihedral : 6.278 79.845 1309 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.45 % Allowed : 8.95 % Favored : 88.60 % 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: 1.46 (0.25), residues: 1200 helix: 1.74 (0.24), residues: 500 sheet: 1.20 (0.38), residues: 179 loop : 0.21 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 143 TYR 0.023 0.001 TYR C 127 PHE 0.010 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.11 ( 9745) covalent geometry : angle 0.45585 / 0.24 (13200) SS BOND : bond 0.00489 / 0.26 ( 1) SS BOND : angle 4.23245 / 2.42 ( 2) hydrogen bonds : bond 0.03629 / 2.60 ( 448) hydrogen bonds : angle 4.27595 / 3.03 ( 1251) Misc. bond : bond 0.00047 / 0.02 ( 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 141 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7264 (tp30) cc_final: 0.6681 (tp30) REVERT: A 184 MET cc_start: 0.8165 (mtm) cc_final: 0.7538 (mtt) REVERT: A 196 MET cc_start: 0.8483 (mmp) cc_final: 0.8235 (mmt) REVERT: A 216 LYS cc_start: 0.6910 (mtmm) cc_final: 0.6541 (mtpp) REVERT: A 286 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7697 (mmp) REVERT: A 455 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8036 (mm-30) REVERT: A 583 GLN cc_start: 0.8164 (mt0) cc_final: 0.7196 (mm110) REVERT: A 614 GLU cc_start: 0.7356 (tp30) cc_final: 0.6967 (tp30) REVERT: A 668 MET cc_start: 0.6305 (mmm) cc_final: 0.5906 (mpt) REVERT: A 699 GLN cc_start: 0.7927 (mp10) cc_final: 0.7644 (mp10) REVERT: A 743 ASP cc_start: 0.6921 (t70) cc_final: 0.6580 (t70) REVERT: A 869 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: A 911 LYS cc_start: 0.7115 (mttt) cc_final: 0.6816 (mttp) REVERT: A 1011 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7122 (tptt) REVERT: B 11 LYS cc_start: 0.7858 (tttt) cc_final: 0.7577 (tttm) REVERT: B 29 LYS cc_start: 0.6921 (mttp) cc_final: 0.6664 (mttm) REVERT: B 57 SER cc_start: 0.8251 (t) cc_final: 0.7977 (p) REVERT: B 71 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8646 (pp) REVERT: C 63 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7400 (mttm) REVERT: C 114 ASN cc_start: 0.8376 (t0) cc_final: 0.7874 (t0) REVERT: C 136 LEU cc_start: 0.7608 (mm) cc_final: 0.7236 (tt) outliers start: 26 outliers final: 14 residues processed: 132 average time/residue: 0.6358 time to fit residues: 89.2681 Evaluate side-chains 131 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 594 THR 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 33 LYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.125414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.087165 restraints weight = 11910.114| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.25 r_work: 0.2921 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9749 Z= 0.213 Angle : 0.534 6.772 13202 Z= 0.275 Chirality : 0.045 0.151 1471 Planarity : 0.004 0.049 1709 Dihedral : 6.450 83.053 1309 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.73 % Allowed : 9.24 % Favored : 88.03 % 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: 1.27 (0.24), residues: 1200 helix: 1.57 (0.24), residues: 499 sheet: 1.06 (0.37), residues: 188 loop : 0.12 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 143 TYR 0.025 0.002 TYR C 127 PHE 0.013 0.002 PHE A 237 TRP 0.007 0.001 TRP A 608 HIS 0.004 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.21 ( 9745) covalent geometry : angle 0.53057 / 0.27 (13200) SS BOND : bond 0.01162 / 0.61 ( 1) SS BOND : angle 5.01037 / 2.90 ( 2) hydrogen bonds : bond 0.04718 / 3.36 ( 448) hydrogen bonds : angle 4.52390 / 3.20 ( 1251) Misc. bond : bond 0.00049 / 0.02 ( 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 139 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7308 (tp30) cc_final: 0.6726 (tp30) REVERT: A 184 MET cc_start: 0.8421 (mtm) cc_final: 0.7728 (mtt) REVERT: A 196 MET cc_start: 0.8524 (mmp) cc_final: 0.8158 (mmt) REVERT: A 216 LYS cc_start: 0.6880 (mtmm) cc_final: 0.6518 (mtpp) REVERT: A 286 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7243 (pmt) REVERT: A 455 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8055 (mm-30) REVERT: A 583 GLN cc_start: 0.8168 (mt0) cc_final: 0.7202 (mm110) REVERT: A 614 GLU cc_start: 0.7324 (tp30) cc_final: 0.6933 (tp30) REVERT: A 668 MET cc_start: 0.6283 (mmm) cc_final: 0.5864 (mpt) REVERT: A 699 GLN cc_start: 0.7958 (mp10) cc_final: 0.7652 (mp10) REVERT: A 743 ASP cc_start: 0.6962 (t70) cc_final: 0.6592 (t70) REVERT: A 869 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: A 911 LYS cc_start: 0.7100 (mttt) cc_final: 0.6778 (mttp) REVERT: A 1011 LYS cc_start: 0.8070 (ttmm) cc_final: 0.7147 (tptt) REVERT: B 11 LYS cc_start: 0.7820 (tttt) cc_final: 0.7522 (tttm) REVERT: B 71 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8677 (pp) REVERT: C 32 HIS cc_start: 0.7326 (t70) cc_final: 0.6967 (t70) REVERT: C 63 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7557 (mtpp) REVERT: C 114 ASN cc_start: 0.8399 (t0) cc_final: 0.7912 (t0) REVERT: C 136 LEU cc_start: 0.7555 (mm) cc_final: 0.7239 (tt) outliers start: 29 outliers final: 18 residues processed: 128 average time/residue: 0.6073 time to fit residues: 83.0559 Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 114 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.125489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.087209 restraints weight = 11921.535| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.31 r_work: 0.2947 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9749 Z= 0.136 Angle : 0.485 7.193 13202 Z= 0.251 Chirality : 0.042 0.168 1471 Planarity : 0.004 0.047 1709 Dihedral : 6.241 82.749 1309 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.36 % Allowed : 9.99 % Favored : 87.65 % 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: 1.30 (0.24), residues: 1200 helix: 1.63 (0.24), residues: 500 sheet: 1.12 (0.37), residues: 178 loop : 0.10 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 143 TYR 0.024 0.001 TYR C 127 PHE 0.010 0.001 PHE A 360 TRP 0.006 0.001 TRP A 669 HIS 0.005 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 9745) covalent geometry : angle 0.48182 / 0.25 (13200) SS BOND : bond 0.02127 / 1.12 ( 1) SS BOND : angle 4.61574 / 2.66 ( 2) hydrogen bonds : bond 0.04002 / 2.85 ( 448) hydrogen bonds : angle 4.37845 / 3.09 ( 1251) Misc. bond : bond 0.00155 / 0.07 ( 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 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7297 (tp30) cc_final: 0.6737 (tp30) REVERT: A 184 MET cc_start: 0.8255 (mtm) cc_final: 0.7513 (mtt) REVERT: A 191 ASP cc_start: 0.7219 (m-30) cc_final: 0.6579 (p0) REVERT: A 196 MET cc_start: 0.8545 (mmp) cc_final: 0.8183 (mmt) REVERT: A 216 LYS cc_start: 0.6945 (mtmm) cc_final: 0.6581 (mtpp) REVERT: A 286 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7411 (pmt) REVERT: A 455 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8094 (mm-30) REVERT: A 583 GLN cc_start: 0.8209 (mt0) cc_final: 0.7260 (mm110) REVERT: A 614 GLU cc_start: 0.7358 (tp30) cc_final: 0.6964 (tp30) REVERT: A 668 MET cc_start: 0.6315 (mmm) cc_final: 0.5922 (mpt) REVERT: A 699 GLN cc_start: 0.7976 (mp10) cc_final: 0.7673 (mp10) REVERT: A 743 ASP cc_start: 0.6952 (t70) cc_final: 0.6588 (t70) REVERT: A 869 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: A 911 LYS cc_start: 0.7082 (mttt) cc_final: 0.6763 (mttp) REVERT: A 1011 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7187 (tptt) REVERT: B 11 LYS cc_start: 0.7879 (tttt) cc_final: 0.7605 (tttm) REVERT: B 57 SER cc_start: 0.8315 (t) cc_final: 0.8035 (p) REVERT: B 71 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8691 (pp) REVERT: C 32 HIS cc_start: 0.7416 (t70) cc_final: 0.7104 (t70) REVERT: C 63 LYS cc_start: 0.7981 (mtpp) cc_final: 0.7486 (mtpp) REVERT: C 114 ASN cc_start: 0.8425 (t0) cc_final: 0.7947 (t0) REVERT: C 136 LEU cc_start: 0.7572 (mm) cc_final: 0.7254 (tt) outliers start: 25 outliers final: 15 residues processed: 125 average time/residue: 0.6070 time to fit residues: 80.9078 Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 107 optimal weight: 0.0060 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 0.0670 chunk 18 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 overall best weight: 0.2734 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.127444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.089551 restraints weight = 11733.942| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.28 r_work: 0.2981 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9749 Z= 0.096 Angle : 0.446 6.252 13202 Z= 0.231 Chirality : 0.041 0.142 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.864 85.995 1309 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.70 % Allowed : 10.46 % 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: 1.41 (0.25), residues: 1200 helix: 1.77 (0.24), residues: 500 sheet: 1.11 (0.37), residues: 187 loop : 0.12 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 143 TYR 0.026 0.001 TYR C 127 PHE 0.009 0.001 PHE A 360 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9745) covalent geometry : angle 0.44437 / 0.23 (13200) SS BOND : bond 0.01106 / 0.58 ( 1) SS BOND : angle 2.91057 / 1.70 ( 2) hydrogen bonds : bond 0.03288 / 2.36 ( 448) hydrogen bonds : angle 4.17316 / 2.94 ( 1251) Misc. bond : bond 0.00047 / 0.02 ( 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 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7249 (tp30) cc_final: 0.6686 (tp30) REVERT: A 184 MET cc_start: 0.8155 (mtm) cc_final: 0.7446 (mtt) REVERT: A 191 ASP cc_start: 0.7198 (m-30) cc_final: 0.6561 (p0) REVERT: A 196 MET cc_start: 0.8486 (mmp) cc_final: 0.8082 (mmt) REVERT: A 216 LYS cc_start: 0.6854 (mtmm) cc_final: 0.6481 (mtpp) REVERT: A 286 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7175 (pmt) REVERT: A 455 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8015 (mm-30) REVERT: A 583 GLN cc_start: 0.8173 (mt0) cc_final: 0.7206 (mm110) REVERT: A 614 GLU cc_start: 0.7266 (tp30) cc_final: 0.6859 (tp30) REVERT: A 668 MET cc_start: 0.6217 (mmm) cc_final: 0.5847 (mpt) REVERT: A 699 GLN cc_start: 0.7946 (mp10) cc_final: 0.7625 (mp10) REVERT: A 743 ASP cc_start: 0.6923 (t70) cc_final: 0.6666 (t70) REVERT: A 911 LYS cc_start: 0.7001 (mttt) cc_final: 0.6664 (mttp) REVERT: A 1011 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7139 (tppt) REVERT: B 6 LYS cc_start: 0.8337 (mmtp) cc_final: 0.8031 (mmtm) REVERT: B 57 SER cc_start: 0.8290 (t) cc_final: 0.8010 (p) REVERT: C 63 LYS cc_start: 0.7946 (mtpp) cc_final: 0.7434 (mtpp) REVERT: C 114 ASN cc_start: 0.8360 (t0) cc_final: 0.7846 (t0) REVERT: C 136 LEU cc_start: 0.7558 (mm) cc_final: 0.7243 (tt) outliers start: 18 outliers final: 9 residues processed: 123 average time/residue: 0.5762 time to fit residues: 75.5033 Evaluate side-chains 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 101 optimal weight: 0.0670 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 = 0.126777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.088522 restraints weight = 11856.628| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.32 r_work: 0.2959 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9749 Z= 0.117 Angle : 0.460 6.121 13202 Z= 0.237 Chirality : 0.041 0.140 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.303 82.512 1308 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.32 % Allowed : 11.22 % Favored : 87.46 % 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: 1.46 (0.25), residues: 1200 helix: 1.77 (0.24), residues: 500 sheet: 1.18 (0.38), residues: 179 loop : 0.18 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 8 TYR 0.024 0.001 TYR C 127 PHE 0.010 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 9745) covalent geometry : angle 0.45873 / 0.24 (13200) SS BOND : bond 0.01222 / 0.64 ( 1) SS BOND : angle 3.05604 / 1.80 ( 2) hydrogen bonds : bond 0.03540 / 2.54 ( 448) hydrogen bonds : angle 4.18646 / 2.96 ( 1251) Misc. bond : bond 0.00047 / 0.02 ( 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 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7041 (tp30) cc_final: 0.6505 (tp30) REVERT: A 184 MET cc_start: 0.8158 (mtm) cc_final: 0.7417 (mtt) REVERT: A 191 ASP cc_start: 0.7207 (m-30) cc_final: 0.6566 (p0) REVERT: A 196 MET cc_start: 0.8499 (mmp) cc_final: 0.8089 (mmt) REVERT: A 216 LYS cc_start: 0.6870 (mtmm) cc_final: 0.6495 (mtpp) REVERT: A 286 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7278 (pmt) REVERT: A 455 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8068 (mm-30) REVERT: A 583 GLN cc_start: 0.8187 (mt0) cc_final: 0.7214 (mm110) REVERT: A 614 GLU cc_start: 0.7285 (tp30) cc_final: 0.6874 (tp30) REVERT: A 668 MET cc_start: 0.6263 (mmm) cc_final: 0.5878 (mpt) REVERT: A 699 GLN cc_start: 0.7963 (mp10) cc_final: 0.7390 (mp10) REVERT: A 743 ASP cc_start: 0.6943 (t70) cc_final: 0.6606 (t70) REVERT: A 869 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: A 911 LYS cc_start: 0.7113 (mttt) cc_final: 0.6784 (mttp) REVERT: A 1011 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7115 (tptt) REVERT: B 6 LYS cc_start: 0.8381 (mmtp) cc_final: 0.8074 (mmtm) REVERT: B 57 SER cc_start: 0.8300 (t) cc_final: 0.8018 (p) REVERT: B 71 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8688 (pp) REVERT: C 63 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7503 (mttm) REVERT: C 114 ASN cc_start: 0.8381 (t0) cc_final: 0.7867 (t0) REVERT: C 136 LEU cc_start: 0.7565 (mm) cc_final: 0.7245 (tt) outliers start: 14 outliers final: 9 residues processed: 120 average time/residue: 0.6823 time to fit residues: 87.0854 Evaluate side-chains 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 71 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: 0.6980 chunk 74 optimal weight: 0.7980 chunk 112 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 114 optimal weight: 0.0270 overall best weight: 0.3038 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.127592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.089591 restraints weight = 11779.970| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.28 r_work: 0.2981 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9749 Z= 0.097 Angle : 0.445 5.857 13202 Z= 0.229 Chirality : 0.041 0.141 1471 Planarity : 0.004 0.046 1709 Dihedral : 4.724 79.357 1307 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.32 % Allowed : 11.31 % Favored : 87.37 % 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: 1.83 (0.24), residues: 500 sheet: 1.13 (0.37), residues: 187 loop : 0.16 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 8 TYR 0.024 0.001 TYR C 127 PHE 0.009 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.001 0.000 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 9745) covalent geometry : angle 0.44325 / 0.23 (13200) SS BOND : bond 0.00749 / 0.39 ( 1) SS BOND : angle 2.74676 / 1.62 ( 2) hydrogen bonds : bond 0.03283 / 2.36 ( 448) hydrogen bonds : angle 4.10813 / 2.90 ( 1251) Misc. bond : bond 0.00025 / 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 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7006 (tp30) cc_final: 0.6459 (tp30) REVERT: A 184 MET cc_start: 0.8108 (mtm) cc_final: 0.7758 (mtt) REVERT: A 191 ASP cc_start: 0.7203 (m-30) cc_final: 0.6565 (p0) REVERT: A 196 MET cc_start: 0.8471 (mmp) cc_final: 0.8108 (mmm) REVERT: A 216 LYS cc_start: 0.6842 (mtmm) cc_final: 0.6484 (mtpp) REVERT: A 286 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7297 (pmt) REVERT: A 455 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8069 (mm-30) REVERT: A 583 GLN cc_start: 0.8176 (mt0) cc_final: 0.7215 (mm110) REVERT: A 614 GLU cc_start: 0.7297 (tp30) cc_final: 0.6889 (tp30) REVERT: A 668 MET cc_start: 0.6238 (mmm) cc_final: 0.5853 (mpt) REVERT: A 699 GLN cc_start: 0.7967 (mp10) cc_final: 0.7656 (mp10) REVERT: A 743 ASP cc_start: 0.6915 (t70) cc_final: 0.6651 (t70) REVERT: A 869 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: A 911 LYS cc_start: 0.7010 (mttt) cc_final: 0.6670 (mttp) REVERT: A 1011 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7089 (tptt) REVERT: B 6 LYS cc_start: 0.8370 (mmtp) cc_final: 0.8056 (mmtm) REVERT: B 19 SER cc_start: 0.8364 (p) cc_final: 0.8162 (t) REVERT: B 57 SER cc_start: 0.8323 (t) cc_final: 0.8094 (p) REVERT: B 71 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8675 (pp) REVERT: C 32 HIS cc_start: 0.7206 (t-90) cc_final: 0.6883 (t70) REVERT: C 63 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7429 (mttm) REVERT: C 114 ASN cc_start: 0.8376 (t0) cc_final: 0.7869 (t0) REVERT: C 136 LEU cc_start: 0.7622 (mm) cc_final: 0.7243 (tt) outliers start: 14 outliers final: 9 residues processed: 120 average time/residue: 0.5714 time to fit residues: 72.9607 Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 71 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: 0.8980 chunk 56 optimal weight: 0.3980 chunk 76 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 45 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.126759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.088636 restraints weight = 11827.212| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.31 r_work: 0.2960 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9749 Z= 0.122 Angle : 0.458 5.777 13202 Z= 0.235 Chirality : 0.041 0.141 1471 Planarity : 0.004 0.046 1709 Dihedral : 4.624 76.439 1307 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.23 % Allowed : 11.40 % Favored : 87.37 % 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: 1.80 (0.24), residues: 500 sheet: 1.19 (0.38), residues: 179 loop : 0.20 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 8 TYR 0.025 0.001 TYR C 127 PHE 0.010 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 ( 9745) covalent geometry : angle 0.45632 / 0.23 (13200) SS BOND : bond 0.01002 / 0.53 ( 1) SS BOND : angle 3.05051 / 1.79 ( 2) hydrogen bonds : bond 0.03506 / 2.52 ( 448) hydrogen bonds : angle 4.14427 / 2.93 ( 1251) Misc. bond : bond 0.00034 / 0.02 ( 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: 3416.56 seconds wall clock time: 58 minutes 34.83 seconds (3514.83 seconds total)