Starting phenix.real_space_refine on Sat Aug 23 03:57:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5c_44207/08_2025/9b5c_44207.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5c_44207/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b5c_44207/08_2025/9b5c_44207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5c_44207/08_2025/9b5c_44207.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5c_44207/08_2025/9b5c_44207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5c_44207/08_2025/9b5c_44207.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.070 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9536 Number of models: 1 Model: "" Number of chains: 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: 2.19, per 1000 atoms: 0.23 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: 0.81 Conformation dependent library (CDL) restraints added in 220.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 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: 0.44 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: 1.82 Time building geometry restraints manager: 0.99 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: 5.190 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.590 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.25), 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 ARG 0.003 0.000 ARG B 72 TYR 0.009 0.001 TYR A 544 PHE 0.011 0.001 PHE A 551 TRP 0.007 0.001 TRP A 608 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9746) covalent geometry : angle 0.48262 (13204) SS BOND : bond 0.86891 ( 1) SS BOND : angle 34.75986 ( 2) hydrogen bonds : bond 0.14939 ( 446) hydrogen bonds : angle 5.73527 ( 1248) 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 : 0.383 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: 0.7755 time to fit residues: 119.6974 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 : 0.408 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.0370 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.127865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.087391 restraints weight = 11428.648| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.27 r_work: 0.3011 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9749 Z= 0.123 Angle : 0.477 9.724 13206 Z= 0.252 Chirality : 0.042 0.148 1471 Planarity : 0.004 0.042 1709 Dihedral : 6.158 83.386 1329 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.32 % Allowed : 8.20 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.25), residues: 1200 helix: 1.78 (0.24), residues: 490 sheet: 1.12 (0.37), residues: 180 loop : 0.34 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.015 0.001 TYR A 654 PHE 0.010 0.001 PHE A 360 TRP 0.006 0.001 TRP A 669 HIS 0.001 0.000 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9746) covalent geometry : angle 0.46940 (13204) SS BOND : bond 0.01789 ( 1) SS BOND : angle 7.01947 ( 2) hydrogen bonds : bond 0.04767 ( 446) hydrogen bonds : angle 4.69027 ( 1248) Misc. bond : bond 0.00150 ( 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 146 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.403 Fit side-chains REVERT: A 73 ARG cc_start: 0.7524 (mtp85) cc_final: 0.6787 (mtm-85) REVERT: A 196 MET cc_start: 0.8686 (mmp) cc_final: 0.8374 (mmm) REVERT: A 524 GLU cc_start: 0.8139 (mp0) cc_final: 0.7762 (mp0) REVERT: A 540 GLU cc_start: 0.7952 (tt0) cc_final: 0.7393 (mp0) REVERT: A 626 MET cc_start: 0.7199 (ttt) cc_final: 0.6920 (tmt) REVERT: A 668 MET cc_start: 0.7491 (mmm) cc_final: 0.7279 (mmm) REVERT: A 1004 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8023 (mt-10) REVERT: C 12 ASP cc_start: 0.7846 (t70) cc_final: 0.7525 (t0) REVERT: C 31 PHE cc_start: 0.8472 (m-80) cc_final: 0.8072 (m-10) REVERT: C 143 ARG cc_start: 0.7563 (mtm110) cc_final: 0.7106 (ttm-80) outliers start: 14 outliers final: 6 residues processed: 138 average time/residue: 0.7243 time to fit residues: 106.0540 Evaluate side-chains 130 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 10 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 44 optimal weight: 0.0870 chunk 83 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 chunk 31 optimal weight: 0.4980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.129338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089707 restraints weight = 11407.708| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.21 r_work: 0.3030 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9749 Z= 0.121 Angle : 0.463 6.599 13206 Z= 0.243 Chirality : 0.042 0.158 1471 Planarity : 0.004 0.044 1709 Dihedral : 5.853 74.053 1329 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.70 % Allowed : 8.58 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.24), residues: 1200 helix: 1.82 (0.24), residues: 489 sheet: 1.12 (0.37), residues: 181 loop : 0.34 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 5 TYR 0.009 0.001 TYR A 736 PHE 0.010 0.001 PHE C 62 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9746) covalent geometry : angle 0.45907 (13204) SS BOND : bond 0.01967 ( 1) SS BOND : angle 4.66642 ( 2) hydrogen bonds : bond 0.04092 ( 446) hydrogen bonds : angle 4.44178 ( 1248) Misc. bond : bond 0.00036 ( 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 146 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7464 (mtp85) cc_final: 0.6755 (mtm-85) REVERT: A 286 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8330 (mmm) REVERT: A 524 GLU cc_start: 0.8144 (mp0) cc_final: 0.7786 (mp0) REVERT: A 540 GLU cc_start: 0.8005 (tt0) cc_final: 0.7445 (mp0) REVERT: A 668 MET cc_start: 0.7512 (mmm) cc_final: 0.7293 (mmm) REVERT: A 1004 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 71 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8775 (pp) REVERT: C 12 ASP cc_start: 0.7884 (t70) cc_final: 0.7423 (t0) REVERT: C 31 PHE cc_start: 0.8471 (m-80) cc_final: 0.8074 (m-10) REVERT: C 92 GLN cc_start: 0.8044 (mm110) cc_final: 0.7054 (tm-30) REVERT: C 143 ARG cc_start: 0.7578 (mtm110) cc_final: 0.7151 (ttm-80) outliers start: 18 outliers final: 8 residues processed: 134 average time/residue: 0.7277 time to fit residues: 103.5344 Evaluate side-chains 127 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET 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 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 85 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089436 restraints weight = 11816.411| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.25 r_work: 0.3083 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9749 Z= 0.159 Angle : 0.485 6.813 13206 Z= 0.256 Chirality : 0.043 0.145 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.937 74.259 1329 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.60 % Allowed : 9.43 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.24), residues: 1200 helix: 1.74 (0.24), residues: 490 sheet: 1.08 (0.36), residues: 181 loop : 0.30 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 5 TYR 0.011 0.001 TYR A 544 PHE 0.012 0.001 PHE A 551 TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9746) covalent geometry : angle 0.48167 (13204) SS BOND : bond 0.01138 ( 1) SS BOND : angle 4.87356 ( 2) hydrogen bonds : bond 0.04469 ( 446) hydrogen bonds : angle 4.46157 ( 1248) Misc. bond : bond 0.00026 ( 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 140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7600 (mtp85) cc_final: 0.6921 (mtm-85) REVERT: A 524 GLU cc_start: 0.8181 (mp0) cc_final: 0.7824 (mp0) REVERT: A 540 GLU cc_start: 0.8123 (tt0) cc_final: 0.7574 (mp0) REVERT: A 626 MET cc_start: 0.7262 (ttt) cc_final: 0.6998 (tmm) REVERT: A 1004 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8060 (mt-10) REVERT: B 39 ASP cc_start: 0.8364 (m-30) cc_final: 0.8014 (m-30) REVERT: B 71 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8803 (pp) REVERT: C 31 PHE cc_start: 0.8537 (m-80) cc_final: 0.8181 (m-10) REVERT: C 92 GLN cc_start: 0.8202 (mm110) cc_final: 0.7073 (tm-30) REVERT: C 143 ARG cc_start: 0.7603 (mtm110) cc_final: 0.7155 (ttm-80) outliers start: 17 outliers final: 10 residues processed: 132 average time/residue: 0.6983 time to fit residues: 97.8792 Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU 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 22 THR 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 77 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 75 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.129908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.089957 restraints weight = 11693.139| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.24 r_work: 0.3086 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9749 Z= 0.132 Angle : 0.468 6.072 13206 Z= 0.246 Chirality : 0.042 0.144 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.940 78.795 1329 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.51 % Allowed : 9.90 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.24), residues: 1200 helix: 1.77 (0.24), residues: 490 sheet: 1.08 (0.36), residues: 181 loop : 0.31 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 5 TYR 0.009 0.001 TYR A 544 PHE 0.012 0.001 PHE C 62 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9746) covalent geometry : angle 0.46458 (13204) SS BOND : bond 0.00946 ( 1) SS BOND : angle 4.50996 ( 2) hydrogen bonds : bond 0.04173 ( 446) hydrogen bonds : angle 4.39261 ( 1248) Misc. bond : bond 0.00017 ( 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 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7512 (mtp85) cc_final: 0.6816 (mtm-85) REVERT: A 524 GLU cc_start: 0.8132 (mp0) cc_final: 0.7764 (mp0) REVERT: A 540 GLU cc_start: 0.8059 (tt0) cc_final: 0.7488 (mp0) REVERT: A 626 MET cc_start: 0.7343 (ttt) cc_final: 0.7033 (tmm) REVERT: A 1004 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8051 (mt-10) REVERT: B 16 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: B 39 ASP cc_start: 0.8333 (m-30) cc_final: 0.7984 (m-30) REVERT: B 71 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8772 (pp) REVERT: C 31 PHE cc_start: 0.8511 (m-80) cc_final: 0.8091 (m-10) REVERT: C 92 GLN cc_start: 0.8118 (mm110) cc_final: 0.7010 (tm-30) REVERT: C 143 ARG cc_start: 0.7576 (mtm110) cc_final: 0.7109 (ttm-80) outliers start: 16 outliers final: 11 residues processed: 130 average time/residue: 0.7045 time to fit residues: 97.4500 Evaluate side-chains 130 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.128673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.088543 restraints weight = 11750.828| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.24 r_work: 0.3059 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9749 Z= 0.195 Angle : 0.511 7.038 13206 Z= 0.268 Chirality : 0.044 0.155 1471 Planarity : 0.004 0.047 1709 Dihedral : 6.103 81.239 1329 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.79 % Allowed : 9.90 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.24), residues: 1200 helix: 1.65 (0.24), residues: 490 sheet: 1.05 (0.36), residues: 180 loop : 0.24 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 72 TYR 0.011 0.002 TYR A 544 PHE 0.014 0.002 PHE A 551 TRP 0.008 0.001 TRP A 608 HIS 0.003 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 9746) covalent geometry : angle 0.50661 (13204) SS BOND : bond 0.01207 ( 1) SS BOND : angle 5.19752 ( 2) hydrogen bonds : bond 0.04789 ( 446) hydrogen bonds : angle 4.52385 ( 1248) Misc. bond : bond 0.00045 ( 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 139 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7659 (mtp85) cc_final: 0.6994 (mtm-85) REVERT: A 333 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: A 524 GLU cc_start: 0.8166 (mp0) cc_final: 0.7803 (mp0) REVERT: A 540 GLU cc_start: 0.8118 (tt0) cc_final: 0.7572 (mp0) REVERT: B 16 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: B 39 ASP cc_start: 0.8368 (m-30) cc_final: 0.8029 (m-30) REVERT: B 71 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8802 (pp) REVERT: C 12 ASP cc_start: 0.7987 (t70) cc_final: 0.7488 (t0) REVERT: C 31 PHE cc_start: 0.8554 (m-80) cc_final: 0.8177 (m-10) REVERT: C 92 GLN cc_start: 0.8153 (mm110) cc_final: 0.7007 (tm-30) REVERT: C 143 ARG cc_start: 0.7598 (mtm110) cc_final: 0.7137 (ttm-80) outliers start: 19 outliers final: 13 residues processed: 130 average time/residue: 0.6760 time to fit residues: 93.2327 Evaluate side-chains 134 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 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 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 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 85 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 109 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.129872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.089854 restraints weight = 11782.144| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.25 r_work: 0.3091 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9749 Z= 0.126 Angle : 0.469 6.134 13206 Z= 0.245 Chirality : 0.042 0.143 1471 Planarity : 0.004 0.046 1709 Dihedral : 6.033 83.518 1329 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.98 % Allowed : 10.37 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.24), residues: 1200 helix: 1.74 (0.24), residues: 490 sheet: 1.07 (0.36), residues: 181 loop : 0.30 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 8 TYR 0.009 0.001 TYR A 736 PHE 0.011 0.001 PHE A 237 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9746) covalent geometry : angle 0.46505 (13204) SS BOND : bond 0.00893 ( 1) SS BOND : angle 4.65566 ( 2) hydrogen bonds : bond 0.04096 ( 446) hydrogen bonds : angle 4.38253 ( 1248) Misc. bond : bond 0.00026 ( 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 143 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7543 (mtp85) cc_final: 0.6860 (mtm-85) REVERT: A 524 GLU cc_start: 0.8177 (mp0) cc_final: 0.7812 (mp0) REVERT: A 540 GLU cc_start: 0.8101 (tt0) cc_final: 0.7463 (mp0) REVERT: B 16 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: B 39 ASP cc_start: 0.8362 (m-30) cc_final: 0.8033 (m-30) REVERT: B 71 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8778 (pp) REVERT: C 12 ASP cc_start: 0.8007 (t70) cc_final: 0.7518 (t0) REVERT: C 31 PHE cc_start: 0.8520 (m-80) cc_final: 0.8073 (m-10) REVERT: C 72 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7987 (mmm-85) REVERT: C 143 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7110 (ttm-80) outliers start: 21 outliers final: 14 residues processed: 135 average time/residue: 0.6328 time to fit residues: 90.8459 Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 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 A residue 1004 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 96 optimal weight: 0.0770 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.130084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.089936 restraints weight = 11649.638| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.24 r_work: 0.3089 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1152 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= 0.130 Angle : 0.469 5.951 13206 Z= 0.246 Chirality : 0.042 0.143 1471 Planarity : 0.004 0.046 1709 Dihedral : 6.014 85.125 1329 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.89 % Allowed : 10.84 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.24), residues: 1200 helix: 1.79 (0.24), residues: 489 sheet: 1.08 (0.36), residues: 181 loop : 0.32 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 72 TYR 0.008 0.001 TYR A 544 PHE 0.013 0.001 PHE C 62 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9746) covalent geometry : angle 0.46591 (13204) SS BOND : bond 0.00759 ( 1) SS BOND : angle 4.56538 ( 2) hydrogen bonds : bond 0.04046 ( 446) hydrogen bonds : angle 4.35773 ( 1248) Misc. bond : bond 0.00036 ( 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 138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7540 (mtp85) cc_final: 0.6875 (mtm-85) REVERT: A 524 GLU cc_start: 0.8165 (mp0) cc_final: 0.7797 (mp0) REVERT: A 540 GLU cc_start: 0.8113 (tt0) cc_final: 0.7493 (mp0) REVERT: B 16 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: B 39 ASP cc_start: 0.8356 (m-30) cc_final: 0.8024 (m-30) REVERT: B 71 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8795 (pp) REVERT: C 12 ASP cc_start: 0.7996 (t70) cc_final: 0.7497 (t0) REVERT: C 31 PHE cc_start: 0.8523 (m-80) cc_final: 0.8086 (m-10) REVERT: C 72 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.8009 (mmm-85) REVERT: C 143 ARG cc_start: 0.7590 (mtm110) cc_final: 0.7139 (ttm-80) outliers start: 20 outliers final: 14 residues processed: 131 average time/residue: 0.6390 time to fit residues: 88.8626 Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 273 LYS Chi-restraints excluded: chain A residue 330 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 101 optimal weight: 0.0470 chunk 61 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 52 optimal weight: 0.0970 overall best weight: 0.3276 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.130985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.090976 restraints weight = 11747.830| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.25 r_work: 0.3109 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9749 Z= 0.103 Angle : 0.452 6.441 13206 Z= 0.236 Chirality : 0.041 0.140 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.921 85.363 1329 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.41 % Allowed : 11.40 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.24), residues: 1200 helix: 1.85 (0.24), residues: 489 sheet: 1.12 (0.36), residues: 181 loop : 0.37 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 72 TYR 0.008 0.001 TYR A 736 PHE 0.014 0.001 PHE C 62 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9746) covalent geometry : angle 0.44837 (13204) SS BOND : bond 0.00544 ( 1) SS BOND : angle 4.39924 ( 2) hydrogen bonds : bond 0.03646 ( 446) hydrogen bonds : angle 4.26909 ( 1248) Misc. bond : bond 0.00030 ( 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: 15 poor density : 115 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7521 (mtp85) cc_final: 0.6853 (mtm-85) REVERT: A 524 GLU cc_start: 0.8200 (mp0) cc_final: 0.7839 (mp0) REVERT: A 540 GLU cc_start: 0.8157 (tt0) cc_final: 0.7515 (mp0) REVERT: B 16 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: B 39 ASP cc_start: 0.8362 (m-30) cc_final: 0.8035 (m-30) REVERT: B 71 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8788 (pp) REVERT: C 31 PHE cc_start: 0.8489 (m-80) cc_final: 0.8051 (m-10) REVERT: C 143 ARG cc_start: 0.7531 (mtm110) cc_final: 0.7094 (ttm-80) outliers start: 15 outliers final: 13 residues processed: 124 average time/residue: 0.6834 time to fit residues: 90.0240 Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 273 LYS Chi-restraints excluded: chain A residue 330 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 39 optimal weight: 0.0470 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 60 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 = 0.130876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.090845 restraints weight = 11676.575| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.24 r_work: 0.3109 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9749 Z= 0.114 Angle : 0.463 8.304 13206 Z= 0.242 Chirality : 0.042 0.140 1471 Planarity : 0.004 0.051 1709 Dihedral : 5.897 85.153 1329 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.51 % Allowed : 11.78 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.24), residues: 1200 helix: 1.87 (0.24), residues: 489 sheet: 1.11 (0.36), residues: 181 loop : 0.39 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 72 TYR 0.010 0.001 TYR C 145 PHE 0.014 0.001 PHE C 62 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9746) covalent geometry : angle 0.46001 (13204) SS BOND : bond 0.00636 ( 1) SS BOND : angle 4.35535 ( 2) hydrogen bonds : bond 0.03727 ( 446) hydrogen bonds : angle 4.26778 ( 1248) Misc. bond : bond 0.00028 ( 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 130 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7525 (mtp85) cc_final: 0.6854 (mtm-85) REVERT: A 524 GLU cc_start: 0.8132 (mp0) cc_final: 0.7764 (mp0) REVERT: A 540 GLU cc_start: 0.8141 (tt0) cc_final: 0.7514 (mp0) REVERT: B 16 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: B 39 ASP cc_start: 0.8346 (m-30) cc_final: 0.8017 (m-30) REVERT: B 71 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8791 (pp) REVERT: C 31 PHE cc_start: 0.8481 (m-80) cc_final: 0.8115 (m-10) REVERT: C 72 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7995 (mmm-85) REVERT: C 143 ARG cc_start: 0.7538 (mtm110) cc_final: 0.7094 (ttm-80) outliers start: 16 outliers final: 13 residues processed: 125 average time/residue: 0.7095 time to fit residues: 94.1570 Evaluate side-chains 128 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 273 LYS Chi-restraints excluded: chain A residue 330 SER 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 20 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 116 optimal weight: 0.1980 chunk 32 optimal weight: 0.0570 chunk 65 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.130837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.090890 restraints weight = 11706.797| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.27 r_work: 0.3105 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 0.029 9749 Z= 0.116 Angle : 0.464 9.625 13206 Z= 0.241 Chirality : 0.042 0.140 1471 Planarity : 0.004 0.046 1709 Dihedral : 5.892 85.079 1329 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.60 % Allowed : 11.59 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.24), residues: 1200 helix: 1.85 (0.24), residues: 489 sheet: 1.11 (0.36), residues: 181 loop : 0.39 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 72 TYR 0.010 0.001 TYR C 145 PHE 0.023 0.001 PHE C 62 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9746) covalent geometry : angle 0.46117 (13204) SS BOND : bond 0.00724 ( 1) SS BOND : angle 4.36860 ( 2) hydrogen bonds : bond 0.03745 ( 446) hydrogen bonds : angle 4.27179 ( 1248) Misc. bond : bond 0.00029 ( 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: 4190.36 seconds wall clock time: 71 minutes 44.61 seconds (4304.61 seconds total)