Starting phenix.real_space_refine on Wed Apr 30 13:28:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5c_44207/04_2025/9b5c_44207.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5c_44207/04_2025/9b5c_44207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5c_44207/04_2025/9b5c_44207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5c_44207/04_2025/9b5c_44207.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5c_44207/04_2025/9b5c_44207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5c_44207/04_2025/9b5c_44207.cif" } resolution = 2.5 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6078 2.51 5 N 1575 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 9536 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 7.12, per 1000 atoms: 0.75 Number of scatterers: 9536 At special positions: 0 Unit cell: (86.184, 98.952, 119.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 2 11.99 O 1836 8.00 N 1575 7.00 C 6078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.90 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 47.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.670A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.697A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.994A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.388A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.514A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.660A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.523A pdb=" N ASN A 222 " --> pdb=" O PRO A 219 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.350A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.608A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.388A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.574A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.582A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 474 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.851A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.839A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.565A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.501A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 582' Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.759A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.580A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.945A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.933A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (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: 3.522A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.681A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 883' Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.753A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.358A 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: 4.152A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.152A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.471A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 429 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N THR A 533 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 431 " --> pdb=" O THR A 533 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908 Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.351A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.351A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.883A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 26 removed outlier: 3.658A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1248 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: 4.06 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1619 1.27 - 1.40: 2292 1.40 - 1.54: 5651 1.54 - 1.67: 120 1.67 - 1.81: 64 Bond restraints: 9746 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " 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 B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.52e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.518 0.013 1.20e-02 6.94e+03 1.12e+00 bond pdb=" CA VAL A1005 " pdb=" CB VAL A1005 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 1.04e+00 bond pdb=" C05 A1AIV D 201 " pdb=" N06 A1AIV D 201 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 9.16e-01 ... (remaining 9741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 13009 1.42 - 2.84: 120 2.84 - 4.26: 66 4.26 - 5.67: 5 5.67 - 7.09: 4 Bond angle restraints: 13204 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 121.70 128.79 -7.09 1.80e+00 3.09e-01 1.55e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.21 3.32 1.18e+00 7.24e-01 7.97e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.69 4.50 1.76e+00 3.23e-01 6.53e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.17 6.66 2.67e+00 1.40e-01 6.23e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 103.94 6.64 2.79e+00 1.28e-01 5.65e+00 ... (remaining 13199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5657 17.59 - 35.19: 218 35.19 - 52.78: 47 52.78 - 70.38: 5 70.38 - 87.97: 4 Dihedral angle restraints: 5931 sinusoidal: 2425 harmonic: 3506 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -141.90 55.90 1 1.00e+01 1.00e-02 4.22e+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 180.00 162.60 17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA TYR A 277 " pdb=" C TYR A 277 " pdb=" N VAL A 278 " pdb=" CA VAL A 278 " ideal model delta harmonic sigma weight residual 180.00 163.27 16.73 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 5928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1284 0.058 - 0.116: 158 0.116 - 0.174: 26 0.174 - 0.232: 1 0.232 - 0.290: 2 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" C5' ATP A1103 " pdb=" O4' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.49 -2.72 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1468 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO C 95 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO C 121 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 75 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO C 76 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.019 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 64 2.61 - 3.18: 8115 3.18 - 3.75: 14053 3.75 - 4.33: 21319 4.33 - 4.90: 35237 Nonbonded interactions: 78788 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.036 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.039 2.170 nonbonded pdb="MG MG A1101 " pdb=" O3G ATP A1103 " model vdw 2.221 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.254 2.170 nonbonded pdb=" N GLU A 489 " pdb=" OE1 GLU A 489 " model vdw 2.260 3.120 ... (remaining 78783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.890 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 0.869 9749 Z= 0.478 Angle : 0.645 46.863 13206 Z= 0.323 Chirality : 0.043 0.290 1471 Planarity : 0.004 0.038 1709 Dihedral : 10.211 87.973 3664 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.66 % Allowed : 2.73 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1200 helix: 1.60 (0.25), residues: 489 sheet: 1.00 (0.36), residues: 184 loop : 0.27 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 608 HIS 0.003 0.001 HIS C 75 PHE 0.011 0.001 PHE A 551 TYR 0.009 0.001 TYR A 544 ARG 0.003 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.14939 ( 446) hydrogen bonds : angle 5.73527 ( 1248) SS BOND : bond 0.86891 ( 1) SS BOND : angle 34.75986 ( 2) covalent geometry : bond 0.00343 ( 9746) covalent geometry : angle 0.48262 (13204) Misc. bond : bond 0.07958 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7406 (mtp85) cc_final: 0.6632 (mmt-90) REVERT: A 135 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7820 (mmmm) REVERT: A 196 MET cc_start: 0.8592 (mmp) cc_final: 0.8211 (mmm) REVERT: A 524 GLU cc_start: 0.7822 (mp0) cc_final: 0.7479 (mp0) REVERT: A 540 GLU cc_start: 0.7558 (tt0) cc_final: 0.7144 (mp0) REVERT: A 668 MET cc_start: 0.7230 (mmm) cc_final: 0.7009 (mmm) REVERT: A 841 ARG cc_start: 0.7444 (mtp180) cc_final: 0.7220 (mtp180) REVERT: A 879 LYS cc_start: 0.8464 (mmmm) cc_final: 0.7799 (mmtt) REVERT: A 1004 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7746 (mt-10) REVERT: A 1011 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8289 (ttmm) REVERT: C 12 ASP cc_start: 0.7747 (t70) cc_final: 0.7504 (t0) REVERT: C 31 PHE cc_start: 0.8630 (m-80) cc_final: 0.8360 (m-10) outliers start: 7 outliers final: 2 residues processed: 146 average time/residue: 1.4608 time to fit residues: 226.5420 Evaluate side-chains 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 0.0000 chunk 108 optimal weight: 1.9990 overall best weight: 0.5044 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.127682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.086287 restraints weight = 11362.857| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.34 r_work: 0.3008 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9749 Z= 0.135 Angle : 0.493 9.444 13206 Z= 0.261 Chirality : 0.043 0.149 1471 Planarity : 0.004 0.042 1709 Dihedral : 6.071 79.590 1329 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.51 % Allowed : 8.11 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1200 helix: 1.71 (0.24), residues: 490 sheet: 1.10 (0.37), residues: 180 loop : 0.31 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.001 0.000 HIS A 717 PHE 0.011 0.001 PHE A 237 TYR 0.016 0.001 TYR A 654 ARG 0.005 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 446) hydrogen bonds : angle 4.64965 ( 1248) SS BOND : bond 0.00985 ( 1) SS BOND : angle 6.82609 ( 2) covalent geometry : bond 0.00324 ( 9746) covalent geometry : angle 0.48624 (13204) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.043 Fit side-chains REVERT: A 73 ARG cc_start: 0.7470 (mtp85) cc_final: 0.6732 (mtm-85) REVERT: A 196 MET cc_start: 0.8687 (mmp) cc_final: 0.8398 (mmm) REVERT: A 524 GLU cc_start: 0.8172 (mp0) cc_final: 0.7796 (mp0) REVERT: A 540 GLU cc_start: 0.7961 (tt0) cc_final: 0.7400 (mp0) REVERT: A 626 MET cc_start: 0.7234 (ttt) cc_final: 0.6930 (tmt) REVERT: A 668 MET cc_start: 0.7543 (mmm) cc_final: 0.7331 (mmm) REVERT: A 879 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8274 (mmpt) REVERT: A 1004 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8035 (mt-10) REVERT: C 12 ASP cc_start: 0.7852 (t70) cc_final: 0.7510 (t0) REVERT: C 31 PHE cc_start: 0.8458 (m-80) cc_final: 0.8084 (m-10) REVERT: C 143 ARG cc_start: 0.7563 (mtm110) cc_final: 0.7124 (ttm-80) outliers start: 16 outliers final: 6 residues processed: 138 average time/residue: 1.4954 time to fit residues: 219.9432 Evaluate side-chains 128 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 0.0050 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.127384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.086087 restraints weight = 11578.261| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.35 r_work: 0.2992 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9749 Z= 0.149 Angle : 0.483 7.192 13206 Z= 0.255 Chirality : 0.043 0.150 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.969 74.962 1329 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.41 % Allowed : 9.24 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1200 helix: 1.71 (0.24), residues: 489 sheet: 1.09 (0.36), residues: 180 loop : 0.28 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS C 75 PHE 0.011 0.001 PHE A 237 TYR 0.010 0.001 TYR A 544 ARG 0.004 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 446) hydrogen bonds : angle 4.52865 ( 1248) SS BOND : bond 0.01551 ( 1) SS BOND : angle 5.08690 ( 2) covalent geometry : bond 0.00367 ( 9746) covalent geometry : angle 0.47928 (13204) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7541 (mtp85) cc_final: 0.6819 (mtm-85) REVERT: A 196 MET cc_start: 0.8705 (mmp) cc_final: 0.8398 (mmm) REVERT: A 286 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8387 (mmm) REVERT: A 524 GLU cc_start: 0.8172 (mp0) cc_final: 0.7851 (mp0) REVERT: A 540 GLU cc_start: 0.8034 (tt0) cc_final: 0.7441 (mp0) REVERT: A 879 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8313 (mmmm) REVERT: A 987 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8106 (mttm) REVERT: A 1004 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8079 (mt-10) REVERT: B 71 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8775 (pp) REVERT: C 12 ASP cc_start: 0.7881 (t70) cc_final: 0.7431 (t0) REVERT: C 31 PHE cc_start: 0.8495 (m-80) cc_final: 0.8116 (m-10) REVERT: C 92 GLN cc_start: 0.8071 (mm110) cc_final: 0.7042 (tm-30) REVERT: C 143 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7149 (ttm-80) outliers start: 15 outliers final: 9 residues processed: 132 average time/residue: 2.1394 time to fit residues: 300.7212 Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 chunk 32 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.130509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090484 restraints weight = 11602.180| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.24 r_work: 0.3093 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9749 Z= 0.122 Angle : 0.460 6.252 13206 Z= 0.242 Chirality : 0.042 0.143 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.884 75.324 1329 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.60 % Allowed : 9.71 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1200 helix: 1.75 (0.24), residues: 490 sheet: 1.09 (0.36), residues: 181 loop : 0.30 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.001 0.001 HIS C 32 PHE 0.010 0.001 PHE A 237 TYR 0.009 0.001 TYR A 736 ARG 0.007 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 446) hydrogen bonds : angle 4.39215 ( 1248) SS BOND : bond 0.01024 ( 1) SS BOND : angle 4.56761 ( 2) covalent geometry : bond 0.00294 ( 9746) covalent geometry : angle 0.45641 (13204) Misc. bond : bond 0.00039 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7586 (mtp85) cc_final: 0.6904 (mtm-85) REVERT: A 196 MET cc_start: 0.8723 (mmp) cc_final: 0.8408 (mmm) REVERT: A 524 GLU cc_start: 0.8182 (mp0) cc_final: 0.7823 (mp0) REVERT: A 540 GLU cc_start: 0.8083 (tt0) cc_final: 0.7522 (mp0) REVERT: A 879 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8438 (mmmm) REVERT: A 1004 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8052 (mt-10) REVERT: B 71 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8803 (pp) REVERT: C 31 PHE cc_start: 0.8556 (m-80) cc_final: 0.8193 (m-10) REVERT: C 92 GLN cc_start: 0.8193 (mm110) cc_final: 0.7094 (tm-30) REVERT: C 143 ARG cc_start: 0.7583 (mtm110) cc_final: 0.7144 (ttm-80) outliers start: 17 outliers final: 11 residues processed: 133 average time/residue: 1.9992 time to fit residues: 284.0116 Evaluate side-chains 131 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 86 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.129353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.089260 restraints weight = 11722.076| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.25 r_work: 0.3075 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9749 Z= 0.166 Angle : 0.486 6.646 13206 Z= 0.255 Chirality : 0.043 0.145 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.999 79.487 1329 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.79 % Allowed : 9.99 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1200 helix: 1.70 (0.24), residues: 490 sheet: 1.04 (0.36), residues: 181 loop : 0.27 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS C 75 PHE 0.012 0.002 PHE A 237 TYR 0.010 0.001 TYR A 544 ARG 0.005 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 446) hydrogen bonds : angle 4.46592 ( 1248) SS BOND : bond 0.01103 ( 1) SS BOND : angle 4.89081 ( 2) covalent geometry : bond 0.00414 ( 9746) covalent geometry : angle 0.48272 (13204) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7594 (mtp85) cc_final: 0.6918 (mtm-85) REVERT: A 196 MET cc_start: 0.8715 (mmp) cc_final: 0.8429 (mmm) REVERT: A 333 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: A 524 GLU cc_start: 0.8129 (mp0) cc_final: 0.7760 (mp0) REVERT: A 540 GLU cc_start: 0.8057 (tt0) cc_final: 0.7497 (mp0) REVERT: A 879 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8385 (mmmm) REVERT: A 1004 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8063 (mt-10) REVERT: B 16 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: B 39 ASP cc_start: 0.8335 (m-30) cc_final: 0.7984 (m-30) REVERT: B 71 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8772 (pp) REVERT: C 12 ASP cc_start: 0.7978 (t70) cc_final: 0.7478 (t0) REVERT: C 31 PHE cc_start: 0.8530 (m-80) cc_final: 0.8116 (m-10) REVERT: C 92 GLN cc_start: 0.8118 (mm110) cc_final: 0.6979 (tm-30) REVERT: C 143 ARG cc_start: 0.7555 (mtm110) cc_final: 0.7109 (ttm-80) outliers start: 19 outliers final: 14 residues processed: 132 average time/residue: 1.4277 time to fit residues: 200.4253 Evaluate side-chains 138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 78 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 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 = 0.3629 r_free = 0.3629 target = 0.129617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089441 restraints weight = 11760.781| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.25 r_work: 0.3072 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9749 Z= 0.152 Angle : 0.480 6.362 13206 Z= 0.252 Chirality : 0.043 0.146 1471 Planarity : 0.004 0.047 1709 Dihedral : 6.022 81.683 1329 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.89 % Allowed : 10.08 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.24), residues: 1200 helix: 1.71 (0.24), residues: 490 sheet: 1.08 (0.36), residues: 180 loop : 0.27 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 PHE 0.012 0.001 PHE A 551 TYR 0.010 0.001 TYR A 544 ARG 0.006 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 446) hydrogen bonds : angle 4.43552 ( 1248) SS BOND : bond 0.00936 ( 1) SS BOND : angle 4.76318 ( 2) covalent geometry : bond 0.00377 ( 9746) covalent geometry : angle 0.47662 (13204) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7573 (mtp85) cc_final: 0.6893 (mtm-85) REVERT: A 196 MET cc_start: 0.8699 (mmp) cc_final: 0.8421 (mmm) REVERT: A 524 GLU cc_start: 0.8124 (mp0) cc_final: 0.7752 (mp0) REVERT: A 540 GLU cc_start: 0.8075 (tt0) cc_final: 0.7429 (mp0) REVERT: A 879 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8372 (mmmm) REVERT: B 16 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: B 39 ASP cc_start: 0.8340 (m-30) cc_final: 0.7994 (m-30) REVERT: B 71 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8771 (pp) REVERT: C 12 ASP cc_start: 0.7983 (t70) cc_final: 0.7485 (t0) REVERT: C 31 PHE cc_start: 0.8520 (m-80) cc_final: 0.8120 (m-10) REVERT: C 143 ARG cc_start: 0.7536 (mtm110) cc_final: 0.7100 (ttm-80) outliers start: 20 outliers final: 15 residues processed: 133 average time/residue: 1.5149 time to fit residues: 214.5495 Evaluate side-chains 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.0060 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 53 optimal weight: 0.0970 chunk 21 optimal weight: 0.0570 chunk 81 optimal weight: 0.0670 chunk 73 optimal weight: 0.4980 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.1250 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.132934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093187 restraints weight = 11806.715| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.25 r_work: 0.3137 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9749 Z= 0.083 Angle : 0.427 5.602 13206 Z= 0.224 Chirality : 0.040 0.136 1471 Planarity : 0.004 0.051 1709 Dihedral : 5.752 86.439 1329 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.89 % Allowed : 10.93 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.69 (0.24), residues: 1200 helix: 1.94 (0.24), residues: 488 sheet: 1.19 (0.36), residues: 181 loop : 0.43 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 PHE 0.009 0.001 PHE A 842 TYR 0.008 0.001 TYR A 736 ARG 0.011 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 446) hydrogen bonds : angle 4.13208 ( 1248) SS BOND : bond 0.00509 ( 1) SS BOND : angle 3.48555 ( 2) covalent geometry : bond 0.00179 ( 9746) covalent geometry : angle 0.42473 (13204) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7452 (mtp85) cc_final: 0.6789 (mtm-85) REVERT: A 196 MET cc_start: 0.8660 (mmp) cc_final: 0.8334 (mmm) REVERT: A 524 GLU cc_start: 0.8199 (mp0) cc_final: 0.7833 (mp0) REVERT: A 540 GLU cc_start: 0.8107 (tt0) cc_final: 0.7510 (mp0) REVERT: A 879 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8393 (mmmm) REVERT: B 22 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7302 (p) REVERT: B 39 ASP cc_start: 0.8349 (m-30) cc_final: 0.8019 (m-30) REVERT: C 31 PHE cc_start: 0.8489 (m-80) cc_final: 0.8080 (m-10) REVERT: C 143 ARG cc_start: 0.7546 (mtm110) cc_final: 0.7118 (ttm-80) outliers start: 20 outliers final: 10 residues processed: 135 average time/residue: 1.4063 time to fit residues: 202.4345 Evaluate side-chains 126 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 33 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 70 optimal weight: 0.0040 chunk 46 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.090846 restraints weight = 11748.059| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.27 r_work: 0.3107 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9749 Z= 0.126 Angle : 0.462 6.011 13206 Z= 0.242 Chirality : 0.042 0.139 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.831 85.511 1329 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.41 % Allowed : 11.31 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.24), residues: 1200 helix: 1.91 (0.24), residues: 490 sheet: 1.22 (0.37), residues: 181 loop : 0.45 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS C 32 PHE 0.013 0.001 PHE C 62 TYR 0.016 0.001 TYR A 654 ARG 0.008 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 446) hydrogen bonds : angle 4.22906 ( 1248) SS BOND : bond 0.00778 ( 1) SS BOND : angle 4.14786 ( 2) covalent geometry : bond 0.00305 ( 9746) covalent geometry : angle 0.45947 (13204) Misc. bond : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7565 (mtp85) cc_final: 0.6882 (mtm-85) REVERT: A 524 GLU cc_start: 0.8168 (mp0) cc_final: 0.7796 (mp0) REVERT: A 540 GLU cc_start: 0.8202 (tt0) cc_final: 0.7558 (mp0) REVERT: A 879 LYS cc_start: 0.8664 (mmmm) cc_final: 0.8445 (mmmm) REVERT: B 39 ASP cc_start: 0.8375 (m-30) cc_final: 0.8042 (m-30) REVERT: C 31 PHE cc_start: 0.8499 (m-80) cc_final: 0.8113 (m-10) REVERT: C 143 ARG cc_start: 0.7554 (mtm110) cc_final: 0.7107 (ttm-80) outliers start: 15 outliers final: 10 residues processed: 127 average time/residue: 1.4326 time to fit residues: 193.7463 Evaluate side-chains 125 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 35 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 chunk 15 optimal weight: 0.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.131295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.091409 restraints weight = 11679.816| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.25 r_work: 0.3114 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9749 Z= 0.109 Angle : 0.452 7.414 13206 Z= 0.235 Chirality : 0.041 0.138 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.819 85.974 1329 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.32 % Allowed : 11.40 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1200 helix: 1.90 (0.24), residues: 490 sheet: 1.21 (0.36), residues: 181 loop : 0.47 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 PHE 0.014 0.001 PHE C 62 TYR 0.010 0.001 TYR C 145 ARG 0.008 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 446) hydrogen bonds : angle 4.20223 ( 1248) SS BOND : bond 0.00619 ( 1) SS BOND : angle 4.09801 ( 2) covalent geometry : bond 0.00259 ( 9746) covalent geometry : angle 0.44881 (13204) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7520 (mtp85) cc_final: 0.6817 (mtm-85) REVERT: A 524 GLU cc_start: 0.8152 (mp0) cc_final: 0.7778 (mp0) REVERT: A 540 GLU cc_start: 0.8158 (tt0) cc_final: 0.7517 (mp0) REVERT: A 879 LYS cc_start: 0.8627 (mmmm) cc_final: 0.8404 (mmmm) REVERT: B 39 ASP cc_start: 0.8351 (m-30) cc_final: 0.8016 (m-30) REVERT: C 31 PHE cc_start: 0.8485 (m-80) cc_final: 0.8096 (m-10) REVERT: C 143 ARG cc_start: 0.7531 (mtm110) cc_final: 0.7091 (ttm-80) outliers start: 14 outliers final: 12 residues processed: 125 average time/residue: 1.3768 time to fit residues: 183.4590 Evaluate side-chains 127 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 14 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 85 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.130755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.090644 restraints weight = 11833.040| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.27 r_work: 0.3099 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9749 Z= 0.134 Angle : 0.472 8.679 13206 Z= 0.246 Chirality : 0.042 0.139 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.870 87.094 1329 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.32 % Allowed : 11.40 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1200 helix: 1.86 (0.24), residues: 489 sheet: 1.19 (0.37), residues: 181 loop : 0.43 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS C 32 PHE 0.017 0.001 PHE C 62 TYR 0.011 0.001 TYR C 145 ARG 0.007 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 446) hydrogen bonds : angle 4.25279 ( 1248) SS BOND : bond 0.00968 ( 1) SS BOND : angle 4.35019 ( 2) covalent geometry : bond 0.00330 ( 9746) covalent geometry : angle 0.46940 (13204) Misc. bond : bond 0.00021 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7556 (mtp85) cc_final: 0.6843 (mtm-85) REVERT: A 524 GLU cc_start: 0.8171 (mp0) cc_final: 0.7798 (mp0) REVERT: A 540 GLU cc_start: 0.8197 (tt0) cc_final: 0.7540 (mp0) REVERT: A 879 LYS cc_start: 0.8651 (mmmm) cc_final: 0.8426 (mmmm) REVERT: B 39 ASP cc_start: 0.8369 (m-30) cc_final: 0.8036 (m-30) REVERT: C 31 PHE cc_start: 0.8498 (m-80) cc_final: 0.8118 (m-10) REVERT: C 143 ARG cc_start: 0.7527 (mtm110) cc_final: 0.7084 (ttm-80) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 1.4450 time to fit residues: 187.4265 Evaluate side-chains 126 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.130637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.090730 restraints weight = 11736.743| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.25 r_work: 0.3098 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9749 Z= 0.127 Angle : 0.468 10.277 13206 Z= 0.242 Chirality : 0.042 0.141 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.885 86.967 1329 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.23 % Allowed : 11.59 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.63 (0.24), residues: 1200 helix: 1.85 (0.24), residues: 489 sheet: 1.18 (0.36), residues: 181 loop : 0.43 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 PHE 0.016 0.001 PHE C 62 TYR 0.009 0.001 TYR A 544 ARG 0.006 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 446) hydrogen bonds : angle 4.26588 ( 1248) SS BOND : bond 0.00827 ( 1) SS BOND : angle 4.34154 ( 2) covalent geometry : bond 0.00310 ( 9746) covalent geometry : angle 0.46452 (13204) Misc. bond : bond 0.00032 ( 2) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 8749.98 seconds wall clock time: 152 minutes 24.45 seconds (9144.45 seconds total)