Starting phenix.real_space_refine on Thu Jan 16 14:44:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5i_44213/01_2025/9b5i_44213.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5i_44213/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5i_44213/01_2025/9b5i_44213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5i_44213/01_2025/9b5i_44213.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5i_44213/01_2025/9b5i_44213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5i_44213/01_2025/9b5i_44213.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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 Classifications: {'RNA': 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: 3.84, per 1000 atoms: 0.40 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.38 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: 3.69 Time building geometry restraints manager: 2.95 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 119.60 112.56 7.04 3.00e+00 1.11e-01 5.50e+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: 0.000 Normalize map: mean=0, sd=1: 9.390 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 24.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.660 ------------------------------------------------------------------------------- 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 : 0.003 0.073 9745 Z= 0.213 Angle : 0.489 15.914 13200 Z= 0.234 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 PHE 0.009 0.001 PHE A 360 TYR 0.008 0.001 TYR A 736 ARG 0.002 0.000 ARG B 72 *********************** 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 : 1.189 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: 1.5225 time to fit residues: 250.0744 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 : 1.098 ------------------------------------------------------------------------------- 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 100 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.127620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.090336 restraints weight = 11768.476| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.21 r_work: 0.3020 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9745 Z= 0.194 Angle : 0.486 6.648 13200 Z= 0.252 Chirality : 0.042 0.155 1471 Planarity : 0.004 0.041 1709 Dihedral : 6.455 83.494 1311 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.07 % Allowed : 7.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1200 helix: 1.75 (0.24), residues: 492 sheet: 1.19 (0.37), residues: 178 loop : 0.19 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 PHE 0.010 0.001 PHE A 360 TYR 0.009 0.001 TYR A 732 ARG 0.006 0.000 ARG C 143 *********************** 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: 22 poor density : 120 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7313 (tp30) cc_final: 0.6894 (tp30) REVERT: A 135 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7563 (mmmt) REVERT: A 184 MET cc_start: 0.8241 (mtm) cc_final: 0.7548 (mtt) REVERT: A 191 ASP cc_start: 0.7511 (m-30) cc_final: 0.7285 (m-30) REVERT: A 196 MET cc_start: 0.8472 (mmp) cc_final: 0.8115 (mmt) REVERT: A 216 LYS cc_start: 0.6961 (mtmm) cc_final: 0.6589 (mtpp) REVERT: A 286 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7921 (mmp) REVERT: A 455 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8097 (mm-30) REVERT: A 465 ASP cc_start: 0.8498 (t0) cc_final: 0.8090 (t0) REVERT: A 583 GLN cc_start: 0.8185 (mt0) cc_final: 0.7246 (mm110) REVERT: A 614 GLU cc_start: 0.7410 (tp30) cc_final: 0.7087 (tp30) REVERT: A 668 MET cc_start: 0.6305 (mmm) cc_final: 0.5909 (mpt) REVERT: A 699 GLN cc_start: 0.7958 (mp10) cc_final: 0.7628 (mp10) REVERT: A 743 ASP cc_start: 0.6991 (t70) cc_final: 0.6673 (t70) REVERT: A 911 LYS cc_start: 0.7192 (mttt) cc_final: 0.6934 (mttp) REVERT: A 1011 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7199 (mmtt) REVERT: B 11 LYS cc_start: 0.7921 (tttt) cc_final: 0.7587 (tttm) REVERT: B 29 LYS cc_start: 0.6918 (mttp) cc_final: 0.6672 (mttm) REVERT: B 57 SER cc_start: 0.8296 (t) cc_final: 0.8032 (p) REVERT: C 63 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7464 (mtpp) REVERT: C 66 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7315 (mtmt) REVERT: C 114 ASN cc_start: 0.8414 (t0) cc_final: 0.7981 (t0) REVERT: C 136 LEU cc_start: 0.7606 (mm) cc_final: 0.7248 (tt) outliers start: 22 outliers final: 7 residues processed: 130 average time/residue: 1.4542 time to fit residues: 201.2354 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 : 1.036 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.127088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.089018 restraints weight = 11915.503| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.27 r_work: 0.2961 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9745 Z= 0.221 Angle : 0.479 5.828 13200 Z= 0.248 Chirality : 0.042 0.151 1471 Planarity : 0.004 0.045 1709 Dihedral : 6.373 81.848 1309 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.36 % Allowed : 7.63 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1200 helix: 1.66 (0.24), residues: 499 sheet: 1.21 (0.37), residues: 183 loop : 0.19 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 PHE 0.010 0.001 PHE A 360 TYR 0.022 0.001 TYR C 127 ARG 0.003 0.000 ARG C 143 *********************** 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 135 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7252 (tp30) cc_final: 0.6665 (tp30) REVERT: A 135 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7472 (mmmt) REVERT: A 184 MET cc_start: 0.8200 (mtm) cc_final: 0.7549 (mtt) REVERT: A 196 MET cc_start: 0.8466 (mmp) cc_final: 0.8161 (mmt) REVERT: A 216 LYS cc_start: 0.6892 (mtmm) cc_final: 0.6530 (mtpp) REVERT: A 286 MET cc_start: 0.8454 (mmp) cc_final: 0.7295 (pmt) REVERT: A 455 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8075 (mm-30) REVERT: A 583 GLN cc_start: 0.8139 (mt0) cc_final: 0.7178 (mm110) REVERT: A 614 GLU cc_start: 0.7351 (tp30) cc_final: 0.7005 (tp30) REVERT: A 668 MET cc_start: 0.6278 (mmm) cc_final: 0.5881 (mpt) REVERT: A 699 GLN cc_start: 0.7955 (mp10) cc_final: 0.7448 (mp10) REVERT: A 743 ASP cc_start: 0.6945 (t70) cc_final: 0.6605 (t70) REVERT: A 869 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: A 911 LYS cc_start: 0.7096 (mttt) cc_final: 0.6816 (mttp) REVERT: A 1011 LYS cc_start: 0.8012 (ttmm) cc_final: 0.7127 (tptt) REVERT: B 6 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8129 (mmtm) REVERT: B 11 LYS cc_start: 0.7860 (tttt) cc_final: 0.7548 (tttm) REVERT: B 29 LYS cc_start: 0.6895 (mttp) cc_final: 0.6641 (mttm) REVERT: B 57 SER cc_start: 0.8247 (t) cc_final: 0.7961 (p) REVERT: C 63 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7414 (mtpp) REVERT: C 66 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7203 (mtmt) REVERT: C 114 ASN cc_start: 0.8380 (t0) cc_final: 0.7924 (t0) REVERT: C 136 LEU cc_start: 0.7580 (mm) cc_final: 0.7217 (tt) outliers start: 25 outliers final: 13 residues processed: 128 average time/residue: 1.4252 time to fit residues: 194.4170 Evaluate side-chains 124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 0.0040 chunk 118 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.125503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.087288 restraints weight = 11721.230| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.29 r_work: 0.2939 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9745 Z= 0.249 Angle : 0.486 5.839 13200 Z= 0.251 Chirality : 0.043 0.144 1471 Planarity : 0.004 0.047 1709 Dihedral : 6.390 82.890 1309 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.73 % Allowed : 8.29 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.24), residues: 1200 helix: 1.62 (0.24), residues: 499 sheet: 1.18 (0.37), residues: 183 loop : 0.17 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS A 818 PHE 0.011 0.001 PHE A 237 TYR 0.024 0.001 TYR C 127 ARG 0.012 0.000 ARG C 143 *********************** 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 142 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7298 (tp30) cc_final: 0.6723 (tp30) REVERT: A 135 LYS cc_start: 0.7756 (mmmt) cc_final: 0.7509 (mmmt) REVERT: A 184 MET cc_start: 0.8243 (mtm) cc_final: 0.7569 (mtt) REVERT: A 196 MET cc_start: 0.8496 (mmp) cc_final: 0.8249 (mmt) REVERT: A 216 LYS cc_start: 0.6904 (mtmm) cc_final: 0.6533 (mtpp) REVERT: A 228 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7932 (mmmm) REVERT: A 286 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7899 (mmp) REVERT: A 455 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8051 (mm-30) REVERT: A 583 GLN cc_start: 0.8165 (mt0) cc_final: 0.7211 (mm110) REVERT: A 614 GLU cc_start: 0.7383 (tp30) cc_final: 0.7025 (tp30) REVERT: A 668 MET cc_start: 0.6339 (mmm) cc_final: 0.5949 (mpt) REVERT: A 699 GLN cc_start: 0.7944 (mp10) cc_final: 0.7630 (mp10) REVERT: A 743 ASP cc_start: 0.6956 (t70) cc_final: 0.6610 (t70) REVERT: A 869 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: A 911 LYS cc_start: 0.7152 (mttt) cc_final: 0.6853 (mttp) REVERT: A 1011 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7155 (tptt) REVERT: B 6 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8186 (mmtm) REVERT: B 11 LYS cc_start: 0.7910 (tttt) cc_final: 0.7609 (tttm) REVERT: B 29 LYS cc_start: 0.7075 (mttp) cc_final: 0.6810 (mttm) REVERT: B 58 ASP cc_start: 0.7947 (m-30) cc_final: 0.7691 (m-30) REVERT: B 71 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8678 (pp) REVERT: C 63 LYS cc_start: 0.7971 (mtpp) cc_final: 0.7447 (mtpp) REVERT: C 66 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7266 (mtmt) REVERT: C 114 ASN cc_start: 0.8421 (t0) cc_final: 0.7921 (t0) REVERT: C 136 LEU cc_start: 0.7622 (mm) cc_final: 0.7250 (tt) outliers start: 29 outliers final: 19 residues processed: 129 average time/residue: 1.4644 time to fit residues: 201.5906 Evaluate side-chains 134 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 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 B residue 73 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 86 optimal weight: 0.0370 chunk 2 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 61 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.127451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.089395 restraints weight = 11799.977| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.25 r_work: 0.2960 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9745 Z= 0.188 Angle : 0.462 5.553 13200 Z= 0.239 Chirality : 0.042 0.144 1471 Planarity : 0.004 0.046 1709 Dihedral : 6.346 83.728 1309 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.83 % Allowed : 8.77 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1200 helix: 1.69 (0.24), residues: 499 sheet: 1.16 (0.37), residues: 179 loop : 0.18 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS C 32 PHE 0.010 0.001 PHE A 360 TYR 0.025 0.001 TYR C 127 ARG 0.008 0.000 ARG C 143 *********************** 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: 30 poor density : 111 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7280 (tp30) cc_final: 0.6709 (tp30) REVERT: A 184 MET cc_start: 0.8202 (mtm) cc_final: 0.7417 (mtt) REVERT: A 191 ASP cc_start: 0.7189 (m-30) cc_final: 0.6574 (p0) REVERT: A 196 MET cc_start: 0.8509 (mmp) cc_final: 0.8078 (mmt) REVERT: A 216 LYS cc_start: 0.6919 (mtmm) cc_final: 0.6551 (mtpp) REVERT: A 228 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7903 (mmmm) REVERT: A 286 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7128 (pmt) REVERT: A 455 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8040 (mm-30) REVERT: A 583 GLN cc_start: 0.8168 (mt0) cc_final: 0.7214 (mm110) REVERT: A 614 GLU cc_start: 0.7365 (tp30) cc_final: 0.6983 (tp30) REVERT: A 668 MET cc_start: 0.6322 (mmm) cc_final: 0.5924 (mpt) REVERT: A 699 GLN cc_start: 0.7951 (mp10) cc_final: 0.7661 (mp10) REVERT: A 743 ASP cc_start: 0.6948 (t70) cc_final: 0.6601 (t70) REVERT: A 869 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: A 911 LYS cc_start: 0.7141 (mttt) cc_final: 0.6834 (mttp) REVERT: A 1011 LYS cc_start: 0.8038 (ttmm) cc_final: 0.7134 (tptt) REVERT: B 6 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8184 (mmtm) REVERT: B 11 LYS cc_start: 0.7893 (tttt) cc_final: 0.7596 (tttm) REVERT: B 29 LYS cc_start: 0.7047 (mttp) cc_final: 0.6783 (mttm) REVERT: B 71 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8648 (pp) REVERT: C 32 HIS cc_start: 0.7260 (t-90) cc_final: 0.6966 (t70) REVERT: C 63 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7437 (mtpp) REVERT: C 66 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7238 (mtmt) REVERT: C 114 ASN cc_start: 0.8376 (t0) cc_final: 0.7888 (t0) REVERT: C 136 LEU cc_start: 0.7616 (mm) cc_final: 0.7240 (tt) outliers start: 30 outliers final: 14 residues processed: 130 average time/residue: 1.4148 time to fit residues: 196.2800 Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 0.0040 chunk 33 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 73 optimal weight: 0.0270 chunk 106 optimal weight: 0.0670 chunk 112 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.0270 overall best weight: 0.2246 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.129312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.091356 restraints weight = 11837.764| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.26 r_work: 0.2986 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.002 0.063 9745 Z= 0.131 Angle : 0.441 6.951 13200 Z= 0.228 Chirality : 0.041 0.141 1471 Planarity : 0.004 0.045 1709 Dihedral : 6.047 85.645 1309 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.89 % Allowed : 10.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1200 helix: 1.81 (0.24), residues: 500 sheet: 1.13 (0.37), residues: 187 loop : 0.18 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.003 0.000 HIS C 32 PHE 0.009 0.001 PHE A 360 TYR 0.025 0.001 TYR C 127 ARG 0.009 0.000 ARG C 143 *********************** 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 135 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7064 (tp30) cc_final: 0.6519 (tp30) REVERT: A 184 MET cc_start: 0.8136 (mtm) cc_final: 0.7391 (mtt) REVERT: A 191 ASP cc_start: 0.7116 (m-30) cc_final: 0.6558 (p0) REVERT: A 196 MET cc_start: 0.8483 (mmp) cc_final: 0.8012 (mmt) REVERT: A 216 LYS cc_start: 0.6894 (mtmm) cc_final: 0.6525 (mtpp) REVERT: A 286 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7171 (pmt) REVERT: A 455 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 583 GLN cc_start: 0.8177 (mt0) cc_final: 0.7227 (mm110) REVERT: A 614 GLU cc_start: 0.7360 (tp30) cc_final: 0.7034 (tp30) REVERT: A 668 MET cc_start: 0.6250 (mmm) cc_final: 0.5868 (mpt) REVERT: A 699 GLN cc_start: 0.7954 (mp10) cc_final: 0.7653 (mp10) REVERT: A 743 ASP cc_start: 0.6923 (t70) cc_final: 0.6669 (t70) REVERT: A 869 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: A 911 LYS cc_start: 0.7024 (mttt) cc_final: 0.6696 (mttp) REVERT: A 1011 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7105 (tptt) REVERT: B 6 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8077 (mmtm) REVERT: B 34 GLU cc_start: 0.7771 (tp30) cc_final: 0.7557 (mm-30) REVERT: B 57 SER cc_start: 0.8261 (t) cc_final: 0.7993 (p) REVERT: C 32 HIS cc_start: 0.7265 (t-90) cc_final: 0.6935 (t70) REVERT: C 63 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7421 (mttm) REVERT: C 114 ASN cc_start: 0.8347 (t0) cc_final: 0.7855 (t0) REVERT: C 136 LEU cc_start: 0.7648 (mm) cc_final: 0.7273 (tt) outliers start: 20 outliers final: 10 residues processed: 129 average time/residue: 1.4443 time to fit residues: 198.2821 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 : 1.036 ------------------------------------------------------------------------------- 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 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 C residue 36 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.125627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.087369 restraints weight = 11917.200| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.31 r_work: 0.2946 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9745 Z= 0.252 Angle : 0.480 6.400 13200 Z= 0.247 Chirality : 0.043 0.142 1471 Planarity : 0.004 0.047 1709 Dihedral : 5.596 84.432 1307 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.07 % Allowed : 10.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1200 helix: 1.72 (0.24), residues: 500 sheet: 1.19 (0.37), residues: 184 loop : 0.21 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.004 0.001 HIS C 32 PHE 0.011 0.001 PHE A 237 TYR 0.024 0.001 TYR C 127 ARG 0.009 0.001 ARG C 5 *********************** 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 128 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7289 (tp30) cc_final: 0.6708 (tp30) REVERT: A 184 MET cc_start: 0.8206 (mtm) cc_final: 0.7443 (mtt) REVERT: A 191 ASP cc_start: 0.7147 (m-30) cc_final: 0.6566 (p0) REVERT: A 196 MET cc_start: 0.8515 (mmp) cc_final: 0.8069 (mmt) REVERT: A 216 LYS cc_start: 0.6953 (mtmm) cc_final: 0.6587 (mtpp) REVERT: A 286 MET cc_start: 0.8396 (mmp) cc_final: 0.7352 (pmt) REVERT: A 455 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8070 (mm-30) REVERT: A 583 GLN cc_start: 0.8194 (mt0) cc_final: 0.7236 (mm110) REVERT: A 614 GLU cc_start: 0.7378 (tp30) cc_final: 0.7045 (tp30) REVERT: A 668 MET cc_start: 0.6346 (mmm) cc_final: 0.5941 (mpt) REVERT: A 699 GLN cc_start: 0.7963 (mp10) cc_final: 0.7417 (mp10) REVERT: A 743 ASP cc_start: 0.6946 (t70) cc_final: 0.6687 (t70) REVERT: A 869 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: A 911 LYS cc_start: 0.7124 (mttt) cc_final: 0.6801 (mttp) REVERT: A 1011 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7130 (tptt) REVERT: B 6 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8059 (mmtm) REVERT: B 34 GLU cc_start: 0.7837 (tp30) cc_final: 0.7572 (mm-30) REVERT: B 71 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8691 (pp) REVERT: C 32 HIS cc_start: 0.7309 (t-90) cc_final: 0.6988 (t70) REVERT: C 63 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7494 (mttm) REVERT: C 66 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7255 (mtmt) REVERT: C 114 ASN cc_start: 0.8385 (t0) cc_final: 0.7899 (t0) REVERT: C 136 LEU cc_start: 0.7655 (mm) cc_final: 0.7272 (tt) outliers start: 22 outliers final: 14 residues processed: 122 average time/residue: 1.4072 time to fit residues: 183.2557 Evaluate side-chains 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 66 LYS 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 33 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 104 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.126251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.088107 restraints weight = 11858.853| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.31 r_work: 0.2954 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9745 Z= 0.195 Angle : 0.462 6.080 13200 Z= 0.238 Chirality : 0.042 0.137 1471 Planarity : 0.004 0.050 1709 Dihedral : 5.126 82.074 1307 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.79 % Allowed : 10.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1200 helix: 1.74 (0.24), residues: 500 sheet: 1.16 (0.38), residues: 179 loop : 0.19 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.004 0.001 HIS C 32 PHE 0.010 0.001 PHE A 360 TYR 0.025 0.001 TYR C 127 ARG 0.012 0.001 ARG C 143 *********************** 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 125 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7048 (tp30) cc_final: 0.6510 (tp30) REVERT: A 184 MET cc_start: 0.8194 (mtm) cc_final: 0.7439 (mtt) REVERT: A 191 ASP cc_start: 0.7153 (m-30) cc_final: 0.6573 (p0) REVERT: A 196 MET cc_start: 0.8514 (mmp) cc_final: 0.8074 (mmt) REVERT: A 216 LYS cc_start: 0.6951 (mtmm) cc_final: 0.6585 (mtpp) REVERT: A 286 MET cc_start: 0.8182 (mmp) cc_final: 0.7203 (pmt) REVERT: A 455 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8083 (mm-30) REVERT: A 583 GLN cc_start: 0.8200 (mt0) cc_final: 0.7234 (mm110) REVERT: A 614 GLU cc_start: 0.7412 (tp30) cc_final: 0.7081 (tp30) REVERT: A 668 MET cc_start: 0.6305 (mmm) cc_final: 0.5919 (mpt) REVERT: A 699 GLN cc_start: 0.7967 (mp10) cc_final: 0.7440 (mp10) REVERT: A 743 ASP cc_start: 0.6941 (t70) cc_final: 0.6598 (t70) REVERT: A 869 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: A 911 LYS cc_start: 0.7125 (mttt) cc_final: 0.6803 (mttp) REVERT: A 1011 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7118 (tptt) REVERT: B 6 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8194 (mmtm) REVERT: B 71 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8688 (pp) REVERT: C 32 HIS cc_start: 0.7309 (t-90) cc_final: 0.6935 (t70) REVERT: C 63 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7495 (mttm) REVERT: C 66 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7288 (mtmt) REVERT: C 114 ASN cc_start: 0.8379 (t0) cc_final: 0.7862 (t0) REVERT: C 136 LEU cc_start: 0.7651 (mm) cc_final: 0.7269 (tt) outliers start: 19 outliers final: 12 residues processed: 119 average time/residue: 1.4268 time to fit residues: 181.4492 Evaluate side-chains 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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 66 LYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.0570 chunk 15 optimal weight: 0.0980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.126564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.088557 restraints weight = 11794.034| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.27 r_work: 0.2964 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9745 Z= 0.178 Angle : 0.458 5.801 13200 Z= 0.236 Chirality : 0.041 0.142 1471 Planarity : 0.004 0.046 1709 Dihedral : 4.873 80.477 1307 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.89 % Allowed : 10.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1200 helix: 1.76 (0.24), residues: 500 sheet: 1.17 (0.38), residues: 179 loop : 0.19 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.004 0.001 HIS C 32 PHE 0.010 0.001 PHE A 360 TYR 0.025 0.001 TYR C 127 ARG 0.010 0.000 ARG C 143 *********************** 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 126 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7022 (tp30) cc_final: 0.6483 (tp30) REVERT: A 184 MET cc_start: 0.8159 (mtm) cc_final: 0.7402 (mtt) REVERT: A 191 ASP cc_start: 0.7142 (m-30) cc_final: 0.6561 (p0) REVERT: A 196 MET cc_start: 0.8497 (mmp) cc_final: 0.8058 (mmt) REVERT: A 216 LYS cc_start: 0.6868 (mtmm) cc_final: 0.6495 (mtpp) REVERT: A 286 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7180 (pmt) REVERT: A 455 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8062 (mm-30) REVERT: A 583 GLN cc_start: 0.8193 (mt0) cc_final: 0.7227 (mm110) REVERT: A 614 GLU cc_start: 0.7349 (tp30) cc_final: 0.7013 (tp30) REVERT: A 668 MET cc_start: 0.6268 (mmm) cc_final: 0.5882 (mpt) REVERT: A 699 GLN cc_start: 0.7951 (mp10) cc_final: 0.7420 (mp10) REVERT: A 743 ASP cc_start: 0.6938 (t70) cc_final: 0.6673 (t70) REVERT: A 869 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: A 911 LYS cc_start: 0.7113 (mttt) cc_final: 0.6790 (mttp) REVERT: A 1011 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7091 (tptt) REVERT: B 6 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8164 (mmtm) REVERT: B 57 SER cc_start: 0.8288 (t) cc_final: 0.7992 (p) REVERT: B 71 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8677 (pp) REVERT: C 32 HIS cc_start: 0.7293 (t-90) cc_final: 0.6936 (t70) REVERT: C 63 LYS cc_start: 0.7936 (mtpp) cc_final: 0.7477 (mttm) REVERT: C 66 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7220 (mtmt) REVERT: C 79 ASN cc_start: 0.7682 (p0) cc_final: 0.7430 (p0) REVERT: C 114 ASN cc_start: 0.8364 (t0) cc_final: 0.7848 (t0) REVERT: C 136 LEU cc_start: 0.7625 (mm) cc_final: 0.7243 (tt) outliers start: 20 outliers final: 12 residues processed: 120 average time/residue: 1.4017 time to fit residues: 179.4433 Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 189 THR 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 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 14 optimal weight: 0.8980 chunk 116 optimal weight: 0.0870 chunk 85 optimal weight: 0.0770 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 0.0070 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- 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 = 0.129140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.091177 restraints weight = 11964.285| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.27 r_work: 0.2983 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9745 Z= 0.139 Angle : 0.441 5.494 13200 Z= 0.227 Chirality : 0.041 0.140 1471 Planarity : 0.004 0.045 1709 Dihedral : 4.551 76.705 1307 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1200 helix: 1.81 (0.24), residues: 500 sheet: 1.13 (0.37), residues: 187 loop : 0.18 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.004 0.001 HIS C 32 PHE 0.009 0.001 PHE A 360 TYR 0.025 0.001 TYR C 127 ARG 0.009 0.000 ARG C 143 ********************** 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 124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7015 (tp30) cc_final: 0.6468 (tp30) REVERT: A 184 MET cc_start: 0.8126 (mtm) cc_final: 0.7534 (mtt) REVERT: A 191 ASP cc_start: 0.7145 (m-30) cc_final: 0.6568 (p0) REVERT: A 196 MET cc_start: 0.8486 (mmp) cc_final: 0.8234 (mmt) REVERT: A 216 LYS cc_start: 0.6905 (mtmm) cc_final: 0.6546 (mtpp) REVERT: A 286 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7274 (pmt) REVERT: A 455 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8119 (mm-30) REVERT: A 583 GLN cc_start: 0.8201 (mt0) cc_final: 0.7232 (mm110) REVERT: A 614 GLU cc_start: 0.7360 (tp30) cc_final: 0.7016 (tp30) REVERT: A 668 MET cc_start: 0.6300 (mmm) cc_final: 0.5936 (mpt) REVERT: A 699 GLN cc_start: 0.7992 (mp10) cc_final: 0.7466 (mp10) REVERT: A 743 ASP cc_start: 0.6925 (t70) cc_final: 0.6663 (t70) REVERT: A 869 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: A 911 LYS cc_start: 0.7042 (mttt) cc_final: 0.6703 (mttp) REVERT: A 1011 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7074 (tptt) REVERT: B 6 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8087 (mmtm) REVERT: B 19 SER cc_start: 0.8294 (p) cc_final: 0.8086 (t) REVERT: B 34 GLU cc_start: 0.7714 (tp30) cc_final: 0.7359 (mm-30) REVERT: B 57 SER cc_start: 0.8295 (t) cc_final: 0.8035 (p) REVERT: B 71 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8678 (pp) REVERT: C 32 HIS cc_start: 0.7284 (t-90) cc_final: 0.6927 (t70) REVERT: C 63 LYS cc_start: 0.7946 (mtpp) cc_final: 0.7422 (mttm) REVERT: C 79 ASN cc_start: 0.7668 (p0) cc_final: 0.7405 (p0) REVERT: C 114 ASN cc_start: 0.8384 (t0) cc_final: 0.7877 (t0) REVERT: C 136 LEU cc_start: 0.7638 (mm) cc_final: 0.7254 (tt) outliers start: 15 outliers final: 10 residues processed: 121 average time/residue: 1.4045 time to fit residues: 181.5491 Evaluate side-chains 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 335 ASP Chi-restraints excluded: chain A residue 461 VAL 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 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 117 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 29 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 96 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 overall best weight: 0.3258 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.128913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.090985 restraints weight = 11845.275| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.27 r_work: 0.2983 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9745 Z= 0.150 Angle : 0.443 5.495 13200 Z= 0.228 Chirality : 0.041 0.142 1471 Planarity : 0.004 0.045 1709 Dihedral : 4.509 74.541 1307 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.41 % Allowed : 11.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.25), residues: 1200 helix: 1.84 (0.24), residues: 500 sheet: 1.21 (0.38), residues: 179 loop : 0.24 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.004 0.001 HIS C 32 PHE 0.009 0.001 PHE A 360 TYR 0.025 0.001 TYR C 127 ARG 0.008 0.000 ARG C 143 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 7661.19 seconds wall clock time: 135 minutes 58.18 seconds (8158.18 seconds total)