Starting phenix.real_space_refine on Sat Aug 23 04:05:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5i_44213/08_2025/9b5i_44213.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5i_44213/08_2025/9b5i_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b5i_44213/08_2025/9b5i_44213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5i_44213/08_2025/9b5i_44213.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5i_44213/08_2025/9b5i_44213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5i_44213/08_2025/9b5i_44213.map" } 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-2.0-5787/lib/python3.9/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: 2.04, per 1000 atoms: 0.21 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: 1.01 Conformation dependent library (CDL) restraints added in 283.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.42 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: 1.83 Time building geometry restraints manager: 1.30 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: 13132 3.18 - 6.37: 62 6.37 - 9.55: 5 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=" C1' AMP B 101 " pdb=" C2' AMP B 101 " pdb=" C3' AMP B 101 " ideal model delta sigma weight residual 111.00 102.06 8.94 3.00e+00 1.11e-01 8.87e+00 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=" C2' AMP B 101 " pdb=" C3' AMP B 101 " pdb=" C4' AMP B 101 " ideal model delta sigma weight residual 111.00 103.93 7.07 3.00e+00 1.11e-01 5.55e+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 - 0.042: 1150 0.042 - 0.084: 222 0.084 - 0.127: 92 0.127 - 0.169: 6 0.169 - 0.211: 1 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C3' AMP B 101 " pdb=" C2' AMP B 101 " pdb=" C4' AMP B 101 " pdb=" O3' AMP B 101 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.11e+00 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 ... (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: 0.000 Normalize map: mean=0, sd=1: 4.550 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.360 Find NCS groups from input model: 0.040 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:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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= 0.488 Angle : 0.622 40.871 13202 Z= 0.292 Chirality : 0.041 0.211 1471 Planarity : 0.003 0.036 1709 Dihedral : 9.580 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 aren 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 covalent geometry : bond 0.00323 ( 9745) covalent geometry : angle 0.50560 (13200) SS BOND : bond 0.87466 ( 1) SS BOND : angle 29.42422 ( 2) hydrogen bonds : bond 0.14990 ( 448) hydrogen bonds : angle 5.61165 ( 1251) Misc. bond : bond 0.08606 ( 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 : 0.409 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: 0.7300 (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: 0.8408 (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: 0.7338 time to fit residues: 119.5976 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 : 0.398 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.090235 restraints weight = 11810.114| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.22 r_work: 0.3016 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 9749 Z= 0.132 Angle : 0.501 7.515 13202 Z= 0.257 Chirality : 0.043 0.161 1471 Planarity : 0.004 0.042 1709 Dihedral : 6.338 79.204 1311 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.98 % Allowed : 7.16 % Favored : 90.86 % 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 aren not related in a simple way. whole: 1.44 (0.25), residues: 1200 helix: 1.77 (0.24), residues: 491 sheet: 1.13 (0.37), residues: 180 loop : 0.20 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 143 TYR 0.009 0.001 TYR A 732 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 covalent geometry : bond 0.00320 ( 9745) covalent geometry : angle 0.49690 (13200) SS BOND : bond 0.02109 ( 1) SS BOND : angle 5.31993 ( 2) hydrogen bonds : bond 0.04360 ( 448) hydrogen bonds : angle 4.59747 ( 1251) Misc. bond : bond 0.00166 ( 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 142 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7369 (tp30) cc_final: 0.6959 (tp30) REVERT: A 184 MET cc_start: 0.8299 (mtm) cc_final: 0.7581 (mtt) REVERT: A 191 ASP cc_start: 0.7520 (m-30) cc_final: 0.7301 (m-30) REVERT: A 196 MET cc_start: 0.8510 (mmp) cc_final: 0.8193 (mmt) REVERT: A 216 LYS cc_start: 0.7002 (mtmm) cc_final: 0.6626 (mtpp) REVERT: A 286 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7955 (mmp) REVERT: A 455 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8099 (mm-30) REVERT: A 465 ASP cc_start: 0.8488 (t0) cc_final: 0.8081 (t0) REVERT: A 583 GLN cc_start: 0.8204 (mt0) cc_final: 0.7271 (mm110) REVERT: A 614 GLU cc_start: 0.7452 (tp30) cc_final: 0.7117 (tp30) REVERT: A 668 MET cc_start: 0.6369 (mmm) cc_final: 0.5972 (mpt) REVERT: A 699 GLN cc_start: 0.7969 (mp10) cc_final: 0.7644 (mp10) REVERT: A 743 ASP cc_start: 0.7036 (t70) cc_final: 0.6719 (t70) REVERT: A 911 LYS cc_start: 0.7279 (mttt) cc_final: 0.7012 (mttp) REVERT: A 1011 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7236 (mmtt) REVERT: B 11 LYS cc_start: 0.7961 (tttt) cc_final: 0.7625 (tttm) REVERT: B 29 LYS cc_start: 0.7014 (mttp) cc_final: 0.6762 (mttm) REVERT: B 57 SER cc_start: 0.8279 (t) cc_final: 0.7993 (p) REVERT: C 63 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7528 (mtpp) REVERT: C 114 ASN cc_start: 0.8478 (t0) cc_final: 0.8059 (t0) REVERT: C 136 LEU cc_start: 0.7671 (mm) cc_final: 0.7303 (tt) outliers start: 21 outliers final: 7 residues processed: 130 average time/residue: 0.7000 time to fit residues: 96.6233 Evaluate side-chains 117 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 VAL 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 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: 0.7980 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.088565 restraints weight = 11780.267| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.25 r_work: 0.2952 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9749 Z= 0.159 Angle : 0.507 7.188 13202 Z= 0.259 Chirality : 0.043 0.154 1471 Planarity : 0.004 0.045 1709 Dihedral : 6.312 83.353 1309 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.54 % Allowed : 7.63 % Favored : 89.82 % 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 aren not related in a simple way. whole: 1.35 (0.24), residues: 1200 helix: 1.62 (0.24), residues: 499 sheet: 1.20 (0.37), residues: 183 loop : 0.17 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.023 0.001 TYR C 127 PHE 0.011 0.001 PHE A 237 TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9745) covalent geometry : angle 0.50314 (13200) SS BOND : bond 0.00945 ( 1) SS BOND : angle 5.02939 ( 2) hydrogen bonds : bond 0.04330 ( 448) hydrogen bonds : angle 4.51221 ( 1251) Misc. bond : bond 0.00032 ( 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 143 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7267 (tp30) cc_final: 0.6684 (tp30) REVERT: A 184 MET cc_start: 0.8232 (mtm) cc_final: 0.7617 (mtt) REVERT: A 216 LYS cc_start: 0.6889 (mtmm) cc_final: 0.6530 (mtpp) REVERT: A 455 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8071 (mm-30) REVERT: A 583 GLN cc_start: 0.8142 (mt0) cc_final: 0.7177 (mm110) REVERT: A 614 GLU cc_start: 0.7336 (tp30) cc_final: 0.7001 (tp30) REVERT: A 668 MET cc_start: 0.6290 (mmm) cc_final: 0.5908 (mpt) REVERT: A 699 GLN cc_start: 0.7948 (mp10) cc_final: 0.7513 (mp10) REVERT: A 743 ASP cc_start: 0.6944 (t70) cc_final: 0.6599 (t70) REVERT: A 869 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: A 911 LYS cc_start: 0.7110 (mttt) cc_final: 0.6827 (mttp) REVERT: A 1011 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7210 (tptt) REVERT: B 11 LYS cc_start: 0.7872 (tttt) cc_final: 0.7556 (tttm) REVERT: B 29 LYS cc_start: 0.6900 (mttp) cc_final: 0.6643 (mttm) REVERT: B 57 SER cc_start: 0.8222 (t) cc_final: 0.7921 (p) REVERT: C 63 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7417 (mtpp) REVERT: C 114 ASN cc_start: 0.8364 (t0) cc_final: 0.7927 (t0) REVERT: C 136 LEU cc_start: 0.7583 (mm) cc_final: 0.7219 (tt) outliers start: 27 outliers final: 14 residues processed: 134 average time/residue: 0.6555 time to fit residues: 93.6171 Evaluate side-chains 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 980 LYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 108 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.087304 restraints weight = 11933.586| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.30 r_work: 0.2946 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.004 0.050 9749 Z= 0.151 Angle : 0.498 7.109 13202 Z= 0.254 Chirality : 0.043 0.151 1471 Planarity : 0.004 0.046 1709 Dihedral : 6.152 81.670 1309 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.73 % Allowed : 8.20 % Favored : 89.07 % 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 aren not related in a simple way. whole: 1.33 (0.24), residues: 1200 helix: 1.61 (0.24), residues: 499 sheet: 1.16 (0.37), residues: 183 loop : 0.16 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 143 TYR 0.025 0.001 TYR C 127 PHE 0.011 0.001 PHE A 360 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9745) covalent geometry : angle 0.49563 (13200) SS BOND : bond 0.01690 ( 1) SS BOND : angle 4.19036 ( 2) hydrogen bonds : bond 0.04132 ( 448) hydrogen bonds : angle 4.42322 ( 1251) Misc. bond : bond 0.00035 ( 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 139 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7283 (tp30) cc_final: 0.6710 (tp30) REVERT: A 184 MET cc_start: 0.8222 (mtm) cc_final: 0.7569 (mtt) REVERT: A 216 LYS cc_start: 0.6906 (mtmm) cc_final: 0.6536 (mtpp) REVERT: A 228 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7928 (mmmm) REVERT: A 286 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7807 (mmp) REVERT: A 455 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8060 (mm-30) REVERT: A 583 GLN cc_start: 0.8168 (mt0) cc_final: 0.7213 (mm110) REVERT: A 614 GLU cc_start: 0.7378 (tp30) cc_final: 0.7011 (tp30) REVERT: A 668 MET cc_start: 0.6321 (mmm) cc_final: 0.5937 (mpt) REVERT: A 699 GLN cc_start: 0.7939 (mp10) cc_final: 0.7629 (mp10) REVERT: A 743 ASP cc_start: 0.6960 (t70) cc_final: 0.6611 (t70) REVERT: A 869 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 911 LYS cc_start: 0.7139 (mttt) cc_final: 0.6835 (mttp) REVERT: A 1011 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7148 (tptt) REVERT: B 11 LYS cc_start: 0.7914 (tttt) cc_final: 0.7616 (tttm) REVERT: B 29 LYS cc_start: 0.7067 (mttp) cc_final: 0.6801 (mttm) REVERT: B 58 ASP cc_start: 0.7808 (m-30) cc_final: 0.7574 (m-30) REVERT: B 71 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8661 (pp) REVERT: C 63 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7431 (mtpp) REVERT: C 66 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7196 (mtmt) REVERT: C 114 ASN cc_start: 0.8296 (t0) cc_final: 0.7830 (t0) REVERT: C 136 LEU cc_start: 0.7618 (mm) cc_final: 0.7249 (tt) outliers start: 29 outliers final: 15 residues processed: 125 average time/residue: 0.6857 time to fit residues: 91.0371 Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 191 ASP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 228 LYS 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 66 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=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: 0.5980 chunk 79 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 75 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.087571 restraints weight = 11806.207| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.30 r_work: 0.2948 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9749 Z= 0.131 Angle : 0.484 7.028 13202 Z= 0.247 Chirality : 0.042 0.146 1471 Planarity : 0.004 0.053 1709 Dihedral : 6.068 79.522 1309 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.64 % Allowed : 8.86 % Favored : 88.50 % 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 aren not related in a simple way. whole: 1.36 (0.24), residues: 1200 helix: 1.64 (0.24), residues: 499 sheet: 1.17 (0.37), residues: 183 loop : 0.17 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 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 0.003 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9745) covalent geometry : angle 0.48152 (13200) SS BOND : bond 0.01073 ( 1) SS BOND : angle 3.92132 ( 2) hydrogen bonds : bond 0.03923 ( 448) hydrogen bonds : angle 4.37398 ( 1251) Misc. bond : bond 0.00022 ( 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 140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7270 (tp30) cc_final: 0.6699 (tp30) REVERT: A 184 MET cc_start: 0.8172 (mtm) cc_final: 0.7568 (mtt) REVERT: A 191 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6585 (p0) REVERT: A 216 LYS cc_start: 0.6910 (mtmm) cc_final: 0.6543 (mtpp) REVERT: A 228 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7916 (mmmm) REVERT: A 286 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7232 (pmt) REVERT: A 455 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8058 (mm-30) REVERT: A 583 GLN cc_start: 0.8171 (mt0) cc_final: 0.7214 (mm110) REVERT: A 614 GLU cc_start: 0.7338 (tp30) cc_final: 0.6966 (tp30) REVERT: A 668 MET cc_start: 0.6315 (mmm) cc_final: 0.5920 (mpt) REVERT: A 699 GLN cc_start: 0.7942 (mp10) cc_final: 0.7655 (mp10) REVERT: A 743 ASP cc_start: 0.6946 (t70) cc_final: 0.6592 (t70) REVERT: A 869 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: A 911 LYS cc_start: 0.7137 (mttt) cc_final: 0.6824 (mttp) REVERT: A 1011 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7141 (tptt) REVERT: B 11 LYS cc_start: 0.7904 (tttt) cc_final: 0.7615 (tttm) REVERT: B 29 LYS cc_start: 0.7048 (mttp) cc_final: 0.6785 (mttm) REVERT: B 71 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8658 (pp) REVERT: C 63 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7435 (mtpp) REVERT: C 66 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7259 (mtmt) REVERT: C 114 ASN cc_start: 0.8356 (t0) cc_final: 0.7847 (t0) REVERT: C 136 LEU cc_start: 0.7616 (mm) cc_final: 0.7238 (tt) outliers start: 28 outliers final: 16 residues processed: 130 average time/residue: 0.6137 time to fit residues: 84.9383 Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 228 LYS 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 22 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.086701 restraints weight = 11864.805| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.31 r_work: 0.2926 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9749 Z= 0.174 Angle : 0.508 7.218 13202 Z= 0.259 Chirality : 0.043 0.144 1471 Planarity : 0.004 0.048 1709 Dihedral : 6.008 80.245 1309 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.64 % Allowed : 9.61 % Favored : 87.75 % 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 aren not related in a simple way. whole: 1.27 (0.24), residues: 1200 helix: 1.57 (0.24), residues: 499 sheet: 1.12 (0.37), residues: 183 loop : 0.12 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 143 TYR 0.024 0.001 TYR C 127 PHE 0.011 0.001 PHE A 237 TRP 0.006 0.001 TRP A 669 HIS 0.004 0.001 HIS C 55 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 9745) covalent geometry : angle 0.50591 (13200) SS BOND : bond 0.01030 ( 1) SS BOND : angle 4.13888 ( 2) hydrogen bonds : bond 0.04264 ( 448) hydrogen bonds : angle 4.44068 ( 1251) Misc. bond : bond 0.00037 ( 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: 28 poor density : 111 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7297 (tp30) cc_final: 0.6717 (tp30) REVERT: A 184 MET cc_start: 0.8180 (mtm) cc_final: 0.7613 (mtt) REVERT: A 191 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6606 (p0) REVERT: A 216 LYS cc_start: 0.6906 (mtmm) cc_final: 0.6541 (mtpp) REVERT: A 286 MET cc_start: 0.8426 (mmp) cc_final: 0.7265 (pmt) REVERT: A 455 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8064 (mm-30) REVERT: A 583 GLN cc_start: 0.8189 (mt0) cc_final: 0.7234 (mm110) REVERT: A 614 GLU cc_start: 0.7358 (tp30) cc_final: 0.6975 (tp30) REVERT: A 668 MET cc_start: 0.6328 (mmm) cc_final: 0.5913 (mpt) REVERT: A 699 GLN cc_start: 0.7973 (mp10) cc_final: 0.7679 (mp10) REVERT: A 743 ASP cc_start: 0.6964 (t70) cc_final: 0.6597 (t70) REVERT: A 869 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: A 911 LYS cc_start: 0.7121 (mttt) cc_final: 0.6796 (mttp) REVERT: A 1011 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7167 (tptt) REVERT: B 11 LYS cc_start: 0.7866 (tttt) cc_final: 0.7576 (tttm) REVERT: B 29 LYS cc_start: 0.7078 (mttp) cc_final: 0.6824 (mttm) REVERT: B 71 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8660 (pp) REVERT: C 32 HIS cc_start: 0.7363 (t-90) cc_final: 0.7070 (t70) REVERT: C 63 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7445 (mtpp) REVERT: C 66 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7289 (mtmt) REVERT: C 114 ASN cc_start: 0.8387 (t0) cc_final: 0.7901 (t0) REVERT: C 136 LEU cc_start: 0.7597 (mm) cc_final: 0.7284 (tt) outliers start: 28 outliers final: 17 residues processed: 128 average time/residue: 0.6437 time to fit residues: 87.5829 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 : 0.275 ------------------------------------------------------------------------------- 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 273 LYS 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 980 LYS 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 Chi-restraints excluded: chain C residue 122 GLU 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: 0.8980 chunk 60 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 109 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.087484 restraints weight = 11900.754| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.31 r_work: 0.2945 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9749 Z= 0.134 Angle : 0.485 7.045 13202 Z= 0.248 Chirality : 0.042 0.144 1471 Planarity : 0.004 0.048 1709 Dihedral : 5.689 81.926 1309 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.26 % Allowed : 10.37 % 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 aren not related in a simple way. whole: 1.34 (0.24), residues: 1200 helix: 1.62 (0.24), residues: 500 sheet: 1.13 (0.37), residues: 184 loop : 0.16 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 143 TYR 0.025 0.001 TYR C 127 PHE 0.010 0.001 PHE A 360 TRP 0.006 0.001 TRP A 669 HIS 0.004 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9745) covalent geometry : angle 0.48239 (13200) SS BOND : bond 0.00970 ( 1) SS BOND : angle 4.03352 ( 2) hydrogen bonds : bond 0.03894 ( 448) hydrogen bonds : angle 4.35516 ( 1251) Misc. bond : bond 0.00037 ( 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 135 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7279 (tp30) cc_final: 0.6718 (tp30) REVERT: A 184 MET cc_start: 0.8176 (mtm) cc_final: 0.7610 (mtt) REVERT: A 191 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6603 (p0) REVERT: A 216 LYS cc_start: 0.6925 (mtmm) cc_final: 0.6561 (mtpp) REVERT: A 286 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7298 (pmt) REVERT: A 455 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8060 (mm-30) REVERT: A 583 GLN cc_start: 0.8196 (mt0) cc_final: 0.7234 (mm110) REVERT: A 614 GLU cc_start: 0.7353 (tp30) cc_final: 0.6963 (tp30) REVERT: A 668 MET cc_start: 0.6307 (mmm) cc_final: 0.5914 (mpt) REVERT: A 699 GLN cc_start: 0.7952 (mp10) cc_final: 0.7640 (mp10) REVERT: A 743 ASP cc_start: 0.6964 (t70) cc_final: 0.6608 (t70) REVERT: A 869 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: A 911 LYS cc_start: 0.7108 (mttt) cc_final: 0.6776 (mttp) REVERT: A 1011 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7141 (tptt) REVERT: B 71 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8643 (pp) REVERT: C 32 HIS cc_start: 0.7325 (t-90) cc_final: 0.6976 (t70) REVERT: C 63 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7491 (mttm) REVERT: C 66 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7249 (mtmt) REVERT: C 114 ASN cc_start: 0.8342 (t0) cc_final: 0.7831 (t0) REVERT: C 136 LEU cc_start: 0.7576 (mm) cc_final: 0.7257 (tt) outliers start: 24 outliers final: 13 residues processed: 125 average time/residue: 0.6325 time to fit residues: 84.0991 Evaluate side-chains 126 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 191 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 110 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.086833 restraints weight = 11800.295| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.30 r_work: 0.2934 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9749 Z= 0.172 Angle : 0.506 7.205 13202 Z= 0.257 Chirality : 0.043 0.142 1471 Planarity : 0.004 0.055 1709 Dihedral : 5.492 83.335 1309 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.17 % Allowed : 10.74 % Favored : 87.09 % 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 aren not related in a simple way. whole: 1.28 (0.24), residues: 1200 helix: 1.57 (0.24), residues: 500 sheet: 1.13 (0.37), residues: 183 loop : 0.12 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 5 TYR 0.026 0.001 TYR C 127 PHE 0.011 0.001 PHE A 237 TRP 0.007 0.001 TRP A 669 HIS 0.005 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9745) covalent geometry : angle 0.50287 (13200) SS BOND : bond 0.00935 ( 1) SS BOND : angle 4.24846 ( 2) hydrogen bonds : bond 0.04181 ( 448) hydrogen bonds : angle 4.39992 ( 1251) Misc. bond : bond 0.00039 ( 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 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7306 (tp30) cc_final: 0.6736 (tp30) REVERT: A 184 MET cc_start: 0.8181 (mtm) cc_final: 0.7623 (mtt) REVERT: A 191 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6612 (p0) REVERT: A 216 LYS cc_start: 0.6920 (mtmm) cc_final: 0.6558 (mtpp) REVERT: A 286 MET cc_start: 0.8411 (mmp) cc_final: 0.7248 (pmt) REVERT: A 455 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8094 (mm-30) REVERT: A 583 GLN cc_start: 0.8197 (mt0) cc_final: 0.7233 (mm110) REVERT: A 614 GLU cc_start: 0.7365 (tp30) cc_final: 0.6971 (tp30) REVERT: A 668 MET cc_start: 0.6298 (mmm) cc_final: 0.5896 (mpt) REVERT: A 699 GLN cc_start: 0.7988 (mp10) cc_final: 0.7676 (mp10) REVERT: A 743 ASP cc_start: 0.6985 (t70) cc_final: 0.6629 (t70) REVERT: A 869 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: A 911 LYS cc_start: 0.7121 (mttt) cc_final: 0.6777 (mttp) REVERT: A 1011 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7162 (tptt) REVERT: B 71 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8658 (pp) REVERT: C 32 HIS cc_start: 0.7412 (t-90) cc_final: 0.7060 (t70) REVERT: C 63 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7466 (mtpp) REVERT: C 66 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7261 (mtmt) REVERT: C 114 ASN cc_start: 0.8371 (t0) cc_final: 0.7870 (t0) REVERT: C 136 LEU cc_start: 0.7582 (mm) cc_final: 0.7260 (tt) outliers start: 23 outliers final: 16 residues processed: 122 average time/residue: 0.6124 time to fit residues: 79.4218 Evaluate side-chains 128 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 111 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.088508 restraints weight = 11906.934| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.26 r_work: 0.2940 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1275 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= 0.153 Angle : 0.496 7.118 13202 Z= 0.253 Chirality : 0.043 0.140 1471 Planarity : 0.004 0.047 1709 Dihedral : 5.205 83.686 1309 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.36 % Allowed : 10.37 % Favored : 87.28 % 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 aren not related in a simple way. whole: 1.30 (0.24), residues: 1200 helix: 1.60 (0.24), residues: 500 sheet: 1.16 (0.37), residues: 183 loop : 0.12 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 5 TYR 0.027 0.001 TYR C 127 PHE 0.011 0.001 PHE A 237 TRP 0.007 0.001 TRP A 669 HIS 0.005 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9745) covalent geometry : angle 0.49296 (13200) SS BOND : bond 0.00948 ( 1) SS BOND : angle 4.22257 ( 2) hydrogen bonds : bond 0.04060 ( 448) hydrogen bonds : angle 4.36740 ( 1251) Misc. bond : bond 0.00030 ( 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 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7288 (tp30) cc_final: 0.6719 (tp30) REVERT: A 184 MET cc_start: 0.8168 (mtm) cc_final: 0.7611 (mtt) REVERT: A 191 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6584 (p0) REVERT: A 216 LYS cc_start: 0.6900 (mtmm) cc_final: 0.6542 (mtpp) REVERT: A 286 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7297 (pmt) REVERT: A 455 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8102 (mm-30) REVERT: A 583 GLN cc_start: 0.8195 (mt0) cc_final: 0.7231 (mm110) REVERT: A 614 GLU cc_start: 0.7331 (tp30) cc_final: 0.6936 (tp30) REVERT: A 668 MET cc_start: 0.6245 (mmm) cc_final: 0.5869 (mpt) REVERT: A 699 GLN cc_start: 0.7996 (mp10) cc_final: 0.7606 (mp10) REVERT: A 743 ASP cc_start: 0.6977 (t70) cc_final: 0.6622 (t70) REVERT: A 869 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: A 911 LYS cc_start: 0.7094 (mttt) cc_final: 0.6750 (mttp) REVERT: A 1011 LYS cc_start: 0.8061 (ttmm) cc_final: 0.7125 (tptt) REVERT: B 71 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8634 (pp) REVERT: C 32 HIS cc_start: 0.7324 (t-90) cc_final: 0.6979 (t70) REVERT: C 63 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7439 (mtpp) REVERT: C 66 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7258 (mtmt) REVERT: C 114 ASN cc_start: 0.8359 (t0) cc_final: 0.7867 (t0) REVERT: C 136 LEU cc_start: 0.7562 (mm) cc_final: 0.7242 (tt) outliers start: 25 outliers final: 15 residues processed: 120 average time/residue: 0.6183 time to fit residues: 79.2249 Evaluate side-chains 127 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 461 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 980 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.8980 chunk 74 optimal weight: 0.0270 chunk 112 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 19 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 114 optimal weight: 0.0030 overall best weight: 0.2448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.089458 restraints weight = 11788.250| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.31 r_work: 0.2972 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9749 Z= 0.091 Angle : 0.455 6.658 13202 Z= 0.233 Chirality : 0.041 0.144 1471 Planarity : 0.004 0.045 1709 Dihedral : 4.811 83.050 1309 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.41 % Allowed : 11.31 % Favored : 87.28 % 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 aren not related in a simple way. whole: 1.41 (0.25), residues: 1200 helix: 1.75 (0.24), residues: 500 sheet: 1.11 (0.37), residues: 187 loop : 0.15 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 8 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 0.004 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 9745) covalent geometry : angle 0.45289 (13200) SS BOND : bond 0.00574 ( 1) SS BOND : angle 3.63576 ( 2) hydrogen bonds : bond 0.03239 ( 448) hydrogen bonds : angle 4.15899 ( 1251) Misc. bond : bond 0.00004 ( 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 128 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7266 (tp30) cc_final: 0.6704 (tp30) REVERT: A 184 MET cc_start: 0.8092 (mtm) cc_final: 0.7577 (mtt) REVERT: A 191 ASP cc_start: 0.7203 (m-30) cc_final: 0.6583 (p0) REVERT: A 216 LYS cc_start: 0.6854 (mtmm) cc_final: 0.6485 (mtpp) REVERT: A 286 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7224 (pmt) REVERT: A 455 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8129 (mm-30) REVERT: A 583 GLN cc_start: 0.8189 (mt0) cc_final: 0.7226 (mm110) REVERT: A 614 GLU cc_start: 0.7366 (tp30) cc_final: 0.6965 (tp30) REVERT: A 668 MET cc_start: 0.6221 (mmm) cc_final: 0.5844 (mpt) REVERT: A 699 GLN cc_start: 0.7970 (mp10) cc_final: 0.7462 (mp10) REVERT: A 743 ASP cc_start: 0.6947 (t70) cc_final: 0.6679 (t70) REVERT: A 911 LYS cc_start: 0.7017 (mttt) cc_final: 0.6671 (mttp) REVERT: A 1011 LYS cc_start: 0.8034 (ttmm) cc_final: 0.7102 (tptt) REVERT: B 57 SER cc_start: 0.8271 (t) cc_final: 0.7978 (p) REVERT: C 32 HIS cc_start: 0.7313 (t-90) cc_final: 0.6943 (t70) REVERT: C 63 LYS cc_start: 0.7934 (mtpp) cc_final: 0.7424 (mttm) REVERT: C 79 ASN cc_start: 0.7662 (p0) cc_final: 0.7386 (p0) REVERT: C 114 ASN cc_start: 0.8354 (t0) cc_final: 0.7834 (t0) REVERT: C 136 LEU cc_start: 0.7626 (mm) cc_final: 0.7238 (tt) outliers start: 15 outliers final: 10 residues processed: 123 average time/residue: 0.6353 time to fit residues: 83.3174 Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 335 ASP Chi-restraints excluded: chain A residue 461 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 101 optimal weight: 0.0020 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.088602 restraints weight = 11846.850| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.28 r_work: 0.2960 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1336 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= 0.129 Angle : 0.475 6.731 13202 Z= 0.242 Chirality : 0.042 0.142 1471 Planarity : 0.004 0.046 1709 Dihedral : 4.841 83.503 1309 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.04 % Allowed : 11.78 % 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 aren not related in a simple way. whole: 1.44 (0.25), residues: 1200 helix: 1.74 (0.24), residues: 500 sheet: 1.19 (0.38), residues: 179 loop : 0.19 (0.28), 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 0.006 0.001 TRP A 669 HIS 0.004 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9745) covalent geometry : angle 0.47228 (13200) SS BOND : bond 0.00665 ( 1) SS BOND : angle 3.80725 ( 2) hydrogen bonds : bond 0.03577 ( 448) hydrogen bonds : angle 4.20652 ( 1251) Misc. bond : bond 0.00029 ( 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: 3545.03 seconds wall clock time: 60 minutes 43.48 seconds (3643.48 seconds total)