Starting phenix.real_space_refine on Thu May 1 03:48:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5l_44216/05_2025/9b5l_44216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5l_44216/05_2025/9b5l_44216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5l_44216/05_2025/9b5l_44216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5l_44216/05_2025/9b5l_44216.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5l_44216/05_2025/9b5l_44216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5l_44216/05_2025/9b5l_44216.cif" } resolution = 3.3 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= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 43 5.16 5 C 6449 2.51 5 N 1678 2.21 5 O 1946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10117 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "B" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 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: 6.87, per 1000 atoms: 0.68 Number of scatterers: 10117 At special positions: 0 Unit cell: (91.504, 98.952, 120.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 1 15.00 O 1946 8.00 N 1678 7.00 C 6449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.90 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 45.8% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 removed outlier: 3.769A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.769A pdb=" N MET A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.602A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.033A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.215A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.632A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.728A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.276A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.564A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.005A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.567A pdb=" N VAL A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 4.046A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 4.068A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.568A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.872A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 630 removed outlier: 3.579A pdb=" N SER A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 641 removed outlier: 4.076A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.672A pdb=" N VAL A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.772A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.548A pdb=" N GLN A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.889A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.636A pdb=" N LEU A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.678A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 146 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'D' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.948A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR A 385 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.375A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.327A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 460 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 905 through 908 Processing sheet with id=AA6, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.391A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP A 996 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL A 942 " --> pdb=" O ASP A 996 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.391A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.918A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 26 removed outlier: 11.245A pdb=" N GLY C 24 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N PHE C 31 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 26 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 12 through 16 476 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1723 1.27 - 1.40: 2409 1.40 - 1.54: 5972 1.54 - 1.67: 165 1.67 - 1.80: 66 Bond restraints: 10335 Sorted by residual: bond pdb=" C04 A1AIV D 101 " pdb=" C05 A1AIV D 101 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.62e+00 bond pdb=" C4 AMP B 101 " pdb=" C5 AMP B 101 " ideal model delta sigma weight residual 1.490 1.461 0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.131 0.020 2.00e-02 2.50e+03 9.87e-01 ... (remaining 10330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 13764 1.37 - 2.74: 145 2.74 - 4.11: 76 4.11 - 5.48: 5 5.48 - 6.85: 2 Bond angle restraints: 13992 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 127.77 -6.07 1.80e+00 3.09e-01 1.14e+01 angle pdb=" C5' AMP B 101 " pdb=" O5' AMP B 101 " pdb=" P AMP B 101 " ideal model delta sigma weight residual 120.90 116.54 4.36 1.50e+00 4.44e-01 8.46e+00 angle pdb=" O1P AMP B 101 " pdb=" P AMP B 101 " pdb=" O2P AMP B 101 " ideal model delta sigma weight residual 119.60 112.75 6.85 3.00e+00 1.11e-01 5.21e+00 angle pdb=" C4' AMP B 101 " pdb=" C5' AMP B 101 " pdb=" O5' AMP B 101 " ideal model delta sigma weight residual 111.70 108.67 3.03 1.50e+00 4.44e-01 4.07e+00 angle pdb=" CA TYR A 544 " pdb=" CB TYR A 544 " pdb=" CG TYR A 544 " ideal model delta sigma weight residual 113.90 110.33 3.57 1.80e+00 3.09e-01 3.94e+00 ... (remaining 13987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6005 17.81 - 35.62: 228 35.62 - 53.43: 33 53.43 - 71.24: 11 71.24 - 89.05: 5 Dihedral angle restraints: 6282 sinusoidal: 2561 harmonic: 3721 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -155.12 69.12 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CA ASP D 52 " pdb=" CB ASP D 52 " pdb=" CG ASP D 52 " pdb=" OD1 ASP D 52 " ideal model delta sinusoidal sigma weight residual -30.00 -88.56 58.56 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 163.35 16.65 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 917 0.028 - 0.056: 448 0.056 - 0.083: 100 0.083 - 0.111: 74 0.111 - 0.139: 29 Chirality restraints: 1568 Sorted by residual: chirality pdb=" CA VAL A 852 " pdb=" N VAL A 852 " pdb=" C VAL A 852 " pdb=" CB VAL A 852 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE B 13 " pdb=" N ILE B 13 " pdb=" C ILE B 13 " pdb=" CB ILE B 13 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 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 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1565 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 659 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 660 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 660 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 660 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 756 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO A 757 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 757 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 757 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 17 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO C 18 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " 0.015 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 63 2.53 - 3.12: 7854 3.12 - 3.71: 14744 3.71 - 4.31: 20966 4.31 - 4.90: 36516 Nonbonded interactions: 80143 Sorted by model distance: nonbonded pdb=" OG SER A 395 " pdb=" OD1 ASP A 875 " model vdw 1.933 3.040 nonbonded pdb=" OE2 GLU C 9 " pdb=" OH TYR C 60 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR A 291 " pdb=" OD2 ASP A 387 " model vdw 2.127 3.040 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.149 3.040 nonbonded pdb=" OG SER A 488 " pdb=" OE1 GLU A 489 " model vdw 2.199 3.040 ... (remaining 80138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 1 through 75) selection = (chain 'D' and resid 1 through 75) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.900 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.867 10339 Z= 0.490 Angle : 0.658 51.466 13994 Z= 0.328 Chirality : 0.040 0.139 1568 Planarity : 0.003 0.029 1812 Dihedral : 10.247 89.049 3875 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.42 % Allowed : 4.16 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.42 (0.25), residues: 1273 helix: 1.95 (0.25), residues: 505 sheet: 0.53 (0.36), residues: 213 loop : 0.28 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 141 HIS 0.003 0.001 HIS A 458 PHE 0.011 0.001 PHE A 431 TYR 0.012 0.001 TYR A 544 ARG 0.002 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.14440 ( 472) hydrogen bonds : angle 5.79515 ( 1296) SS BOND : bond 0.86698 ( 1) SS BOND : angle 37.12965 ( 2) covalent geometry : bond 0.00406 (10335) covalent geometry : angle 0.48531 (13992) Misc. bond : bond 0.09534 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8228 (mptt) cc_final: 0.7764 (tmtt) REVERT: A 35 MET cc_start: 0.8246 (ttp) cc_final: 0.7978 (ttp) REVERT: A 80 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8281 (tp40) REVERT: A 229 VAL cc_start: 0.9280 (t) cc_final: 0.8925 (p) REVERT: A 464 MET cc_start: 0.8778 (pmt) cc_final: 0.8513 (pmm) REVERT: A 474 ARG cc_start: 0.7667 (ptt-90) cc_final: 0.7382 (ptt180) REVERT: A 587 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8480 (tt0) REVERT: A 623 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6951 (t0) REVERT: A 718 ASN cc_start: 0.8622 (t0) cc_final: 0.8306 (t0) REVERT: A 748 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8537 (pt0) REVERT: A 821 ASP cc_start: 0.9004 (t70) cc_final: 0.8793 (t0) REVERT: A 885 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8601 (m-40) REVERT: B 18 GLU cc_start: 0.8756 (mp0) cc_final: 0.8220 (mp0) REVERT: C 34 GLN cc_start: 0.8767 (tt0) cc_final: 0.7998 (pp30) REVERT: C 66 LYS cc_start: 0.8557 (mttt) cc_final: 0.8283 (mtpt) REVERT: C 72 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8635 (mtp85) REVERT: C 92 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8254 (mm-40) REVERT: C 120 VAL cc_start: 0.8842 (t) cc_final: 0.8571 (m) REVERT: C 137 SER cc_start: 0.9062 (m) cc_final: 0.8775 (p) REVERT: D 31 GLN cc_start: 0.8172 (tt0) cc_final: 0.7599 (tp40) outliers start: 16 outliers final: 7 residues processed: 205 average time/residue: 0.3241 time to fit residues: 87.5606 Evaluate side-chains 132 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.112410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083373 restraints weight = 20932.062| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.16 r_work: 0.3216 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10339 Z= 0.215 Angle : 0.599 9.584 13994 Z= 0.310 Chirality : 0.044 0.141 1568 Planarity : 0.004 0.050 1812 Dihedral : 6.593 89.366 1401 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.01 % Allowed : 7.79 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.21 (0.24), residues: 1273 helix: 1.68 (0.24), residues: 515 sheet: 0.63 (0.37), residues: 212 loop : 0.12 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 141 HIS 0.008 0.001 HIS D 68 PHE 0.013 0.001 PHE A 633 TYR 0.021 0.002 TYR C 145 ARG 0.004 0.001 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 472) hydrogen bonds : angle 4.87916 ( 1296) SS BOND : bond 0.02576 ( 1) SS BOND : angle 7.03595 ( 2) covalent geometry : bond 0.00506 (10335) covalent geometry : angle 0.59268 (13992) Misc. bond : bond 0.00423 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8551 (mptt) cc_final: 0.8050 (tmtt) REVERT: A 35 MET cc_start: 0.8636 (ttp) cc_final: 0.8372 (ttp) REVERT: A 80 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7448 (tp40) REVERT: A 464 MET cc_start: 0.8854 (pmt) cc_final: 0.8502 (pmm) REVERT: A 474 ARG cc_start: 0.8165 (ptt-90) cc_final: 0.7811 (ptt180) REVERT: A 588 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7831 (mmmt) REVERT: A 623 ASN cc_start: 0.7494 (OUTLIER) cc_final: 0.7103 (t0) REVERT: A 717 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.8354 (t-90) REVERT: A 718 ASN cc_start: 0.8430 (t0) cc_final: 0.8095 (t0) REVERT: B 18 GLU cc_start: 0.8794 (mp0) cc_final: 0.8175 (mp0) REVERT: B 21 ASP cc_start: 0.8561 (m-30) cc_final: 0.7595 (m-30) REVERT: B 64 GLU cc_start: 0.9164 (mp0) cc_final: 0.8717 (mp0) REVERT: C 7 ASN cc_start: 0.8748 (t0) cc_final: 0.8496 (t0) REVERT: C 34 GLN cc_start: 0.8892 (tt0) cc_final: 0.8325 (pp30) REVERT: C 38 MET cc_start: 0.8328 (ppp) cc_final: 0.8116 (ppp) REVERT: C 72 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8563 (mtp85) REVERT: C 92 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8298 (mm-40) REVERT: D 31 GLN cc_start: 0.7987 (tt0) cc_final: 0.7417 (tp40) REVERT: D 41 GLN cc_start: 0.8096 (mt0) cc_final: 0.7896 (mt0) REVERT: D 72 ARG cc_start: 0.7700 (tmm160) cc_final: 0.7131 (tmm160) outliers start: 34 outliers final: 25 residues processed: 158 average time/residue: 0.2706 time to fit residues: 58.6382 Evaluate side-chains 142 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 119 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.114291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.084958 restraints weight = 21040.216| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.27 r_work: 0.3283 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10339 Z= 0.127 Angle : 0.514 8.105 13994 Z= 0.268 Chirality : 0.042 0.140 1568 Planarity : 0.004 0.037 1812 Dihedral : 6.284 86.839 1397 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.30 % Allowed : 9.56 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.25 (0.24), residues: 1273 helix: 1.81 (0.24), residues: 510 sheet: 0.60 (0.36), residues: 211 loop : 0.08 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.007 0.001 HIS D 68 PHE 0.019 0.001 PHE A 633 TYR 0.016 0.001 TYR C 145 ARG 0.002 0.000 ARG A 919 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 472) hydrogen bonds : angle 4.63319 ( 1296) SS BOND : bond 0.00744 ( 1) SS BOND : angle 5.97821 ( 2) covalent geometry : bond 0.00295 (10335) covalent geometry : angle 0.50901 (13992) Misc. bond : bond 0.00175 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8543 (mptt) cc_final: 0.8019 (tmtt) REVERT: A 35 MET cc_start: 0.8592 (ttp) cc_final: 0.8369 (ttp) REVERT: A 51 GLU cc_start: 0.8521 (tp30) cc_final: 0.8219 (tp30) REVERT: A 442 MET cc_start: 0.8671 (tpp) cc_final: 0.8446 (tpp) REVERT: A 474 ARG cc_start: 0.8110 (ptt-90) cc_final: 0.7807 (ptt180) REVERT: A 623 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.7065 (t0) REVERT: A 626 MET cc_start: 0.8001 (ppp) cc_final: 0.7754 (ppp) REVERT: A 653 ASP cc_start: 0.8579 (m-30) cc_final: 0.7630 (m-30) REVERT: A 717 HIS cc_start: 0.8815 (OUTLIER) cc_final: 0.8429 (t-90) REVERT: A 718 ASN cc_start: 0.8439 (t0) cc_final: 0.8089 (t0) REVERT: B 18 GLU cc_start: 0.8796 (mp0) cc_final: 0.8182 (mp0) REVERT: B 21 ASP cc_start: 0.8575 (m-30) cc_final: 0.7611 (m-30) REVERT: B 24 ASP cc_start: 0.8310 (m-30) cc_final: 0.7768 (p0) REVERT: B 64 GLU cc_start: 0.9137 (mp0) cc_final: 0.8747 (mp0) REVERT: C 34 GLN cc_start: 0.8885 (tt0) cc_final: 0.8169 (pp30) REVERT: C 92 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8264 (mm-40) REVERT: D 14 THR cc_start: 0.6484 (OUTLIER) cc_final: 0.6264 (t) REVERT: D 18 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8208 (tm-30) REVERT: D 31 GLN cc_start: 0.7972 (tt0) cc_final: 0.7441 (tp40) REVERT: D 45 PHE cc_start: 0.7714 (t80) cc_final: 0.7455 (t80) outliers start: 26 outliers final: 16 residues processed: 148 average time/residue: 0.2743 time to fit residues: 54.4136 Evaluate side-chains 129 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 64 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 123 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.113045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.083394 restraints weight = 20958.825| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.21 r_work: 0.3252 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10339 Z= 0.177 Angle : 0.546 6.681 13994 Z= 0.282 Chirality : 0.042 0.135 1568 Planarity : 0.004 0.069 1812 Dihedral : 5.913 86.633 1393 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.01 % Allowed : 10.44 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.21 (0.24), residues: 1273 helix: 1.78 (0.24), residues: 509 sheet: 0.62 (0.36), residues: 215 loop : 0.05 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.006 0.001 HIS D 68 PHE 0.025 0.001 PHE A 846 TYR 0.015 0.001 TYR C 145 ARG 0.005 0.000 ARG A 652 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 472) hydrogen bonds : angle 4.64451 ( 1296) SS BOND : bond 0.00992 ( 1) SS BOND : angle 4.85913 ( 2) covalent geometry : bond 0.00420 (10335) covalent geometry : angle 0.54263 (13992) Misc. bond : bond 0.00281 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8563 (mptt) cc_final: 0.8013 (tmtt) REVERT: A 35 MET cc_start: 0.8598 (ttp) cc_final: 0.8358 (ttp) REVERT: A 327 LYS cc_start: 0.8741 (mttm) cc_final: 0.8465 (mttp) REVERT: A 442 MET cc_start: 0.8649 (tpp) cc_final: 0.8429 (tpp) REVERT: A 465 ASP cc_start: 0.8603 (t0) cc_final: 0.8380 (m-30) REVERT: A 474 ARG cc_start: 0.8181 (ptt-90) cc_final: 0.7854 (ptt90) REVERT: A 717 HIS cc_start: 0.8791 (OUTLIER) cc_final: 0.8351 (t-90) REVERT: A 718 ASN cc_start: 0.8419 (t0) cc_final: 0.8070 (t0) REVERT: B 18 GLU cc_start: 0.8842 (mp0) cc_final: 0.8134 (mp0) REVERT: B 21 ASP cc_start: 0.8599 (m-30) cc_final: 0.7528 (m-30) REVERT: B 24 ASP cc_start: 0.8269 (m-30) cc_final: 0.7774 (p0) REVERT: B 64 GLU cc_start: 0.9086 (mp0) cc_final: 0.8789 (mp0) REVERT: C 34 GLN cc_start: 0.8904 (tt0) cc_final: 0.8225 (pp30) REVERT: C 38 MET cc_start: 0.8200 (ppp) cc_final: 0.7981 (ppp) REVERT: C 92 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8231 (mm-40) REVERT: D 18 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7946 (tm-30) REVERT: D 31 GLN cc_start: 0.7950 (tt0) cc_final: 0.7396 (tp40) outliers start: 34 outliers final: 21 residues processed: 141 average time/residue: 0.2557 time to fit residues: 49.3091 Evaluate side-chains 134 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 60 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.0070 chunk 105 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.113309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.084219 restraints weight = 20657.148| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.21 r_work: 0.3278 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10339 Z= 0.121 Angle : 0.512 8.061 13994 Z= 0.265 Chirality : 0.041 0.137 1568 Planarity : 0.004 0.039 1812 Dihedral : 5.693 82.771 1391 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.39 % Allowed : 11.59 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.22 (0.24), residues: 1273 helix: 1.77 (0.24), residues: 509 sheet: 0.72 (0.36), residues: 209 loop : 0.01 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS D 68 PHE 0.026 0.001 PHE A 846 TYR 0.016 0.001 TYR A 250 ARG 0.004 0.000 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 472) hydrogen bonds : angle 4.50356 ( 1296) SS BOND : bond 0.00236 ( 1) SS BOND : angle 4.09379 ( 2) covalent geometry : bond 0.00283 (10335) covalent geometry : angle 0.50990 (13992) Misc. bond : bond 0.00084 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8546 (mptt) cc_final: 0.7987 (tmtt) REVERT: A 35 MET cc_start: 0.8576 (ttp) cc_final: 0.8335 (ttp) REVERT: A 465 ASP cc_start: 0.8656 (t0) cc_final: 0.8416 (m-30) REVERT: A 474 ARG cc_start: 0.8175 (ptt-90) cc_final: 0.7793 (ptt90) REVERT: A 717 HIS cc_start: 0.8773 (OUTLIER) cc_final: 0.8385 (t-90) REVERT: A 718 ASN cc_start: 0.8448 (t0) cc_final: 0.8073 (t0) REVERT: B 18 GLU cc_start: 0.8844 (mp0) cc_final: 0.8094 (mp0) REVERT: B 21 ASP cc_start: 0.8586 (m-30) cc_final: 0.7425 (m-30) REVERT: B 24 ASP cc_start: 0.8286 (m-30) cc_final: 0.7788 (p0) REVERT: B 64 GLU cc_start: 0.9121 (mp0) cc_final: 0.8787 (mp0) REVERT: C 34 GLN cc_start: 0.8925 (tt0) cc_final: 0.8171 (pp30) REVERT: C 38 MET cc_start: 0.8253 (ppp) cc_final: 0.7989 (ppp) REVERT: C 92 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8217 (mm-40) REVERT: D 18 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8014 (tm-30) REVERT: D 31 GLN cc_start: 0.7932 (tt0) cc_final: 0.7371 (tp40) REVERT: D 41 GLN cc_start: 0.8102 (mt0) cc_final: 0.7196 (pp30) REVERT: D 43 LEU cc_start: 0.8660 (mt) cc_final: 0.8239 (mt) outliers start: 27 outliers final: 18 residues processed: 132 average time/residue: 0.2564 time to fit residues: 46.5354 Evaluate side-chains 128 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.4980 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.112993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083888 restraints weight = 20880.167| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.23 r_work: 0.3210 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10339 Z= 0.157 Angle : 0.528 6.175 13994 Z= 0.271 Chirality : 0.042 0.132 1568 Planarity : 0.004 0.049 1812 Dihedral : 5.639 79.322 1391 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.39 % Allowed : 11.86 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.19 (0.24), residues: 1273 helix: 1.82 (0.24), residues: 503 sheet: 0.67 (0.36), residues: 209 loop : -0.04 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS D 68 PHE 0.027 0.001 PHE A 846 TYR 0.017 0.001 TYR C 145 ARG 0.011 0.000 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 472) hydrogen bonds : angle 4.52342 ( 1296) SS BOND : bond 0.00390 ( 1) SS BOND : angle 3.86331 ( 2) covalent geometry : bond 0.00371 (10335) covalent geometry : angle 0.52570 (13992) Misc. bond : bond 0.00026 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8531 (mptt) cc_final: 0.7951 (tmtt) REVERT: A 35 MET cc_start: 0.8609 (ttp) cc_final: 0.8394 (ttp) REVERT: A 465 ASP cc_start: 0.8727 (t0) cc_final: 0.8477 (m-30) REVERT: A 474 ARG cc_start: 0.8223 (ptt-90) cc_final: 0.7816 (ptt90) REVERT: A 717 HIS cc_start: 0.8800 (OUTLIER) cc_final: 0.8432 (t-90) REVERT: A 718 ASN cc_start: 0.8445 (t0) cc_final: 0.8066 (t0) REVERT: B 18 GLU cc_start: 0.8876 (mp0) cc_final: 0.8084 (mp0) REVERT: B 21 ASP cc_start: 0.8577 (m-30) cc_final: 0.7293 (m-30) REVERT: B 24 ASP cc_start: 0.8323 (m-30) cc_final: 0.7806 (p0) REVERT: B 64 GLU cc_start: 0.9174 (mp0) cc_final: 0.8777 (mp0) REVERT: C 34 GLN cc_start: 0.8956 (tt0) cc_final: 0.8141 (pp30) REVERT: C 38 MET cc_start: 0.8269 (ppp) cc_final: 0.7970 (ppp) REVERT: C 92 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8209 (mm-40) REVERT: C 144 LYS cc_start: 0.8722 (tttp) cc_final: 0.8298 (tttm) REVERT: D 18 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8169 (tm-30) REVERT: D 31 GLN cc_start: 0.7950 (tt0) cc_final: 0.7404 (tp40) outliers start: 27 outliers final: 23 residues processed: 133 average time/residue: 0.2795 time to fit residues: 51.1612 Evaluate side-chains 136 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 39 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 94 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.113725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084839 restraints weight = 20816.283| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.22 r_work: 0.3231 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10339 Z= 0.117 Angle : 0.512 7.781 13994 Z= 0.262 Chirality : 0.041 0.145 1568 Planarity : 0.004 0.049 1812 Dihedral : 5.578 79.367 1391 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.12 % Allowed : 13.10 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.24 (0.24), residues: 1273 helix: 1.87 (0.24), residues: 503 sheet: 0.70 (0.38), residues: 196 loop : -0.00 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.004 0.001 HIS D 68 PHE 0.027 0.001 PHE A 846 TYR 0.018 0.001 TYR C 145 ARG 0.012 0.000 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 472) hydrogen bonds : angle 4.45406 ( 1296) SS BOND : bond 0.00734 ( 1) SS BOND : angle 3.64653 ( 2) covalent geometry : bond 0.00274 (10335) covalent geometry : angle 0.51000 (13992) Misc. bond : bond 0.00009 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8526 (mptt) cc_final: 0.7944 (tmtt) REVERT: A 35 MET cc_start: 0.8576 (ttp) cc_final: 0.8356 (ttp) REVERT: A 327 LYS cc_start: 0.8911 (mtmm) cc_final: 0.8491 (mtmm) REVERT: A 465 ASP cc_start: 0.8711 (t0) cc_final: 0.8470 (m-30) REVERT: A 474 ARG cc_start: 0.8202 (ptt-90) cc_final: 0.7784 (ptt90) REVERT: A 717 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8408 (t-90) REVERT: A 718 ASN cc_start: 0.8418 (t0) cc_final: 0.8054 (t0) REVERT: B 18 GLU cc_start: 0.8864 (mp0) cc_final: 0.8079 (mp0) REVERT: B 21 ASP cc_start: 0.8556 (m-30) cc_final: 0.7317 (m-30) REVERT: B 24 ASP cc_start: 0.8286 (m-30) cc_final: 0.7803 (p0) REVERT: B 64 GLU cc_start: 0.9152 (mp0) cc_final: 0.8776 (mp0) REVERT: C 34 GLN cc_start: 0.8928 (tt0) cc_final: 0.8151 (pp30) REVERT: C 38 MET cc_start: 0.8253 (ppp) cc_final: 0.7947 (ppp) REVERT: C 92 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8214 (mm-40) REVERT: C 144 LYS cc_start: 0.8739 (tttp) cc_final: 0.8262 (tttm) REVERT: D 18 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 31 GLN cc_start: 0.7907 (tt0) cc_final: 0.7339 (tp40) REVERT: D 41 GLN cc_start: 0.8161 (mt0) cc_final: 0.7303 (pp30) outliers start: 24 outliers final: 22 residues processed: 130 average time/residue: 0.2630 time to fit residues: 46.6368 Evaluate side-chains 134 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 46 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.113808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.084989 restraints weight = 20907.817| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.20 r_work: 0.3228 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10339 Z= 0.127 Angle : 0.517 9.208 13994 Z= 0.263 Chirality : 0.042 0.181 1568 Planarity : 0.004 0.051 1812 Dihedral : 5.474 79.428 1388 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.30 % Allowed : 12.92 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.27 (0.24), residues: 1273 helix: 1.94 (0.24), residues: 497 sheet: 0.72 (0.37), residues: 202 loop : -0.03 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS D 68 PHE 0.028 0.001 PHE A 846 TYR 0.019 0.001 TYR C 145 ARG 0.013 0.000 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 472) hydrogen bonds : angle 4.45545 ( 1296) SS BOND : bond 0.00363 ( 1) SS BOND : angle 3.51389 ( 2) covalent geometry : bond 0.00300 (10335) covalent geometry : angle 0.51495 (13992) Misc. bond : bond 0.00041 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8516 (mptt) cc_final: 0.7946 (tmtt) REVERT: A 35 MET cc_start: 0.8576 (ttp) cc_final: 0.8359 (ttp) REVERT: A 465 ASP cc_start: 0.8683 (t0) cc_final: 0.8443 (m-30) REVERT: A 474 ARG cc_start: 0.8213 (ptt-90) cc_final: 0.7803 (ptt90) REVERT: A 717 HIS cc_start: 0.8796 (OUTLIER) cc_final: 0.8406 (t-90) REVERT: A 718 ASN cc_start: 0.8409 (t0) cc_final: 0.8066 (t0) REVERT: B 18 GLU cc_start: 0.8856 (mp0) cc_final: 0.8074 (mp0) REVERT: B 21 ASP cc_start: 0.8548 (m-30) cc_final: 0.7310 (m-30) REVERT: B 24 ASP cc_start: 0.8267 (m-30) cc_final: 0.7805 (p0) REVERT: B 31 GLN cc_start: 0.8820 (tt0) cc_final: 0.8566 (tt0) REVERT: B 62 GLN cc_start: 0.8279 (mm110) cc_final: 0.7958 (mm110) REVERT: B 64 GLU cc_start: 0.9148 (mp0) cc_final: 0.8790 (mp0) REVERT: C 34 GLN cc_start: 0.8927 (tt0) cc_final: 0.8224 (tm-30) REVERT: C 38 MET cc_start: 0.8259 (ppp) cc_final: 0.7934 (ppp) REVERT: C 92 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8217 (mm-40) REVERT: C 144 LYS cc_start: 0.8770 (tttp) cc_final: 0.8294 (tttm) REVERT: D 18 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 31 GLN cc_start: 0.7924 (tt0) cc_final: 0.7357 (tp40) REVERT: D 41 GLN cc_start: 0.8182 (mt0) cc_final: 0.7121 (pp30) outliers start: 26 outliers final: 23 residues processed: 131 average time/residue: 0.3022 time to fit residues: 54.8493 Evaluate side-chains 137 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 39 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 111 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 68 optimal weight: 0.0010 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 58 optimal weight: 0.0010 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.114954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.085933 restraints weight = 20906.293| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.22 r_work: 0.3248 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10339 Z= 0.105 Angle : 0.523 9.450 13994 Z= 0.265 Chirality : 0.041 0.191 1568 Planarity : 0.004 0.055 1812 Dihedral : 5.445 80.146 1388 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.04 % Allowed : 13.19 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.32 (0.25), residues: 1273 helix: 1.98 (0.24), residues: 497 sheet: 0.77 (0.37), residues: 202 loop : -0.00 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.000 HIS D 68 PHE 0.030 0.001 PHE A 846 TYR 0.020 0.001 TYR C 145 ARG 0.013 0.000 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.02969 ( 472) hydrogen bonds : angle 4.41807 ( 1296) SS BOND : bond 0.00431 ( 1) SS BOND : angle 3.43014 ( 2) covalent geometry : bond 0.00242 (10335) covalent geometry : angle 0.52098 (13992) Misc. bond : bond 0.00018 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8509 (mptt) cc_final: 0.7941 (tmtt) REVERT: A 35 MET cc_start: 0.8554 (ttp) cc_final: 0.8354 (ttp) REVERT: A 327 LYS cc_start: 0.8891 (mtmm) cc_final: 0.8620 (mttp) REVERT: A 465 ASP cc_start: 0.8635 (t0) cc_final: 0.8414 (m-30) REVERT: A 474 ARG cc_start: 0.8172 (ptt-90) cc_final: 0.7774 (ptt90) REVERT: A 717 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8394 (t-90) REVERT: A 718 ASN cc_start: 0.8435 (t0) cc_final: 0.8069 (t0) REVERT: B 18 GLU cc_start: 0.8848 (mp0) cc_final: 0.8059 (mp0) REVERT: B 21 ASP cc_start: 0.8553 (m-30) cc_final: 0.7309 (m-30) REVERT: B 24 ASP cc_start: 0.8242 (m-30) cc_final: 0.7793 (p0) REVERT: B 31 GLN cc_start: 0.8797 (tt0) cc_final: 0.8500 (tt0) REVERT: B 62 GLN cc_start: 0.8257 (mm110) cc_final: 0.7936 (mm110) REVERT: B 64 GLU cc_start: 0.9148 (mp0) cc_final: 0.8788 (mp0) REVERT: B 74 ARG cc_start: 0.8297 (ptm-80) cc_final: 0.7997 (ptm160) REVERT: C 34 GLN cc_start: 0.8930 (tt0) cc_final: 0.8210 (tm-30) REVERT: C 38 MET cc_start: 0.8207 (ppp) cc_final: 0.7863 (ppp) REVERT: C 92 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8178 (mm-40) REVERT: C 144 LYS cc_start: 0.8773 (tttp) cc_final: 0.8458 (tttm) REVERT: D 18 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8195 (tm-30) REVERT: D 31 GLN cc_start: 0.7893 (tt0) cc_final: 0.7650 (tp40) REVERT: D 41 GLN cc_start: 0.8174 (mt0) cc_final: 0.7292 (pp30) REVERT: D 51 GLU cc_start: 0.6992 (pm20) cc_final: 0.6787 (pm20) outliers start: 23 outliers final: 20 residues processed: 128 average time/residue: 0.2767 time to fit residues: 48.1267 Evaluate side-chains 135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.113321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.084451 restraints weight = 20873.938| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.21 r_work: 0.3240 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10339 Z= 0.148 Angle : 0.538 8.629 13994 Z= 0.274 Chirality : 0.042 0.147 1568 Planarity : 0.004 0.056 1812 Dihedral : 5.430 76.879 1388 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.86 % Allowed : 13.63 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 (0.25), residues: 1273 helix: 1.98 (0.24), residues: 497 sheet: 0.78 (0.37), residues: 208 loop : 0.02 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS D 68 PHE 0.031 0.001 PHE A 846 TYR 0.018 0.001 TYR C 145 ARG 0.014 0.000 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 472) hydrogen bonds : angle 4.46902 ( 1296) SS BOND : bond 0.00780 ( 1) SS BOND : angle 3.60198 ( 2) covalent geometry : bond 0.00353 (10335) covalent geometry : angle 0.53646 (13992) Misc. bond : bond 0.00080 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8554 (mptt) cc_final: 0.7987 (tmtt) REVERT: A 327 LYS cc_start: 0.8914 (mtmm) cc_final: 0.8653 (mttp) REVERT: A 465 ASP cc_start: 0.8670 (t0) cc_final: 0.8425 (m-30) REVERT: A 474 ARG cc_start: 0.8229 (ptt-90) cc_final: 0.7811 (ptt90) REVERT: A 717 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8426 (t-90) REVERT: A 718 ASN cc_start: 0.8408 (t0) cc_final: 0.8066 (t0) REVERT: A 850 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8001 (tmtt) REVERT: B 18 GLU cc_start: 0.8852 (mp0) cc_final: 0.8041 (mp0) REVERT: B 21 ASP cc_start: 0.8558 (m-30) cc_final: 0.7289 (m-30) REVERT: B 24 ASP cc_start: 0.8266 (m-30) cc_final: 0.7821 (p0) REVERT: B 31 GLN cc_start: 0.8779 (tt0) cc_final: 0.8518 (tt0) REVERT: B 62 GLN cc_start: 0.8291 (mm110) cc_final: 0.7980 (mm110) REVERT: B 64 GLU cc_start: 0.9173 (mp0) cc_final: 0.8805 (mp0) REVERT: C 34 GLN cc_start: 0.8906 (tt0) cc_final: 0.8187 (tm-30) REVERT: C 38 MET cc_start: 0.8124 (ppp) cc_final: 0.7812 (ppp) REVERT: C 92 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8210 (mm-40) REVERT: C 144 LYS cc_start: 0.8788 (tttp) cc_final: 0.8473 (tttm) REVERT: D 18 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8101 (tm-30) REVERT: D 31 GLN cc_start: 0.7821 (tt0) cc_final: 0.7599 (tp40) REVERT: D 41 GLN cc_start: 0.8166 (mt0) cc_final: 0.7293 (pp30) outliers start: 21 outliers final: 20 residues processed: 124 average time/residue: 0.3169 time to fit residues: 54.4114 Evaluate side-chains 132 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 717 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 chunk 3 optimal weight: 0.0040 chunk 80 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 78 optimal weight: 0.0170 overall best weight: 0.1430 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.115969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.087238 restraints weight = 20773.950| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.25 r_work: 0.3289 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10339 Z= 0.097 Angle : 0.520 10.399 13994 Z= 0.262 Chirality : 0.041 0.132 1568 Planarity : 0.004 0.054 1812 Dihedral : 5.337 80.865 1388 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.68 % Allowed : 13.98 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.41 (0.25), residues: 1273 helix: 2.02 (0.24), residues: 497 sheet: 0.85 (0.38), residues: 203 loop : 0.06 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.003 0.001 HIS D 68 PHE 0.029 0.001 PHE A 846 TYR 0.018 0.001 TYR C 145 ARG 0.013 0.000 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.02709 ( 472) hydrogen bonds : angle 4.33584 ( 1296) SS BOND : bond 0.00320 ( 1) SS BOND : angle 3.24384 ( 2) covalent geometry : bond 0.00216 (10335) covalent geometry : angle 0.51885 (13992) Misc. bond : bond 0.00045 ( 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: 4746.46 seconds wall clock time: 83 minutes 12.98 seconds (4992.98 seconds total)