Starting phenix.real_space_refine on Sat Aug 23 03:58:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5g_44211/08_2025/9b5g_44211.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5g_44211/08_2025/9b5g_44211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b5g_44211/08_2025/9b5g_44211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5g_44211/08_2025/9b5g_44211.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5g_44211/08_2025/9b5g_44211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5g_44211/08_2025/9b5g_44211.map" } resolution = 2.67 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= 0.075 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 2 residue(s): 0.02s 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: 2.44, per 1000 atoms: 0.26 Number of scatterers: 9536 At special positions: 0 Unit cell: (86.184, 98.952, 121.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 2 11.99 O 1836 8.00 N 1575 7.00 C 6078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.91 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 393.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 46.8% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.732A 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 74 through 79 removed outlier: 3.677A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.034A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.351A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.518A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 123 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.663A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.269A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.617A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.614A 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: 4.433A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.512A 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: 3.697A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.863A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.562A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.885A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.542A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.558A pdb=" N VAL A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 679 Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.880A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 835 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.661A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 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: 6.728A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.293A 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: 4.151A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.275A 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: 4.151A 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: 6.567A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.215A 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: 6.377A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.387A 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: 6.377A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.448A 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: 8.900A pdb=" N LEU B 67 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE B 4 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU B 69 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS B 6 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.187A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 460 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: 2.00 Time building geometry restraints manager: 1.24 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: 5640 1.54 - 1.67: 131 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 1.28e+01 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.519 0.012 1.20e-02 6.94e+03 1.06e+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 9.40e-01 bond pdb=" C SER C 94 " pdb=" N PRO C 95 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.48e-01 ... (remaining 9741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 13021 1.37 - 2.74: 104 2.74 - 4.11: 70 4.11 - 5.48: 5 5.48 - 6.85: 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 121.70 128.55 -6.85 1.80e+00 3.09e-01 1.45e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.29 3.24 1.18e+00 7.24e-01 7.58e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.58 4.61 1.76e+00 3.23e-01 6.86e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.07 6.76 2.67e+00 1.40e-01 6.42e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 104.12 6.46 2.79e+00 1.28e-01 5.34e+00 ... (remaining 13199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 5673 17.46 - 34.93: 204 34.93 - 52.39: 43 52.39 - 69.85: 6 69.85 - 87.32: 5 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 -139.70 53.70 1 1.00e+01 1.00e-02 3.92e+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 180.00 164.25 15.75 0 5.00e+00 4.00e-02 9.92e+00 dihedral pdb=" N GLN A 80 " pdb=" CA GLN A 80 " pdb=" CB GLN A 80 " pdb=" CG GLN A 80 " ideal model delta sinusoidal sigma weight residual -180.00 -120.49 -59.51 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1291 0.058 - 0.116: 155 0.116 - 0.174: 22 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 -2.92 0.28 2.00e-01 2.50e+01 1.99e+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 -2.73 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1468 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO C 95 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 75 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO C 76 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO C 121 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.015 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 56 2.61 - 3.18: 8150 3.18 - 3.75: 14006 3.75 - 4.33: 21197 4.33 - 4.90: 35260 Nonbonded interactions: 78669 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.032 2.170 nonbonded pdb=" OD2 ASP A1002 " pdb=" NH1 ARG C 8 " model vdw 2.142 3.120 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.142 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.167 2.170 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.184 3.040 ... (remaining 78664 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: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.190 Find NCS groups from input model: 0.180 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 0.880 9749 Z= 0.482 Angle : 0.625 45.344 13206 Z= 0.310 Chirality : 0.042 0.290 1471 Planarity : 0.004 0.033 1709 Dihedral : 10.029 87.315 3664 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.94 % Allowed : 2.07 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.24), residues: 1200 helix: 1.77 (0.25), residues: 488 sheet: 0.93 (0.36), residues: 177 loop : 0.36 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.008 0.001 TYR A 736 PHE 0.011 0.001 PHE A 360 TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9746) covalent geometry : angle 0.46659 (13204) SS BOND : bond 0.88004 ( 1) SS BOND : angle 33.81055 ( 2) hydrogen bonds : bond 0.14826 ( 447) hydrogen bonds : angle 5.57030 ( 1248) Misc. bond : bond 0.08011 ( 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 155 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7368 (mmt-90) cc_final: 0.7123 (mmt180) REVERT: A 196 MET cc_start: 0.8690 (mmp) cc_final: 0.8395 (mmm) REVERT: A 235 TYR cc_start: 0.8427 (m-80) cc_final: 0.8132 (m-80) REVERT: A 583 GLN cc_start: 0.8018 (mt0) cc_final: 0.7283 (mm-40) REVERT: A 909 ASN cc_start: 0.7733 (t0) cc_final: 0.7288 (t0) REVERT: A 919 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8338 (pmm-80) REVERT: A 936 LYS cc_start: 0.7933 (ttpp) cc_final: 0.7686 (ttpp) REVERT: A 937 GLU cc_start: 0.7569 (tp30) cc_final: 0.7286 (tp30) REVERT: C 91 ASP cc_start: 0.7471 (p0) cc_final: 0.7109 (p0) outliers start: 10 outliers final: 4 residues processed: 154 average time/residue: 0.7301 time to fit residues: 119.1486 Evaluate side-chains 124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 919 ARG 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: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.121487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.084788 restraints weight = 10938.569| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.86 r_work: 0.2690 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9749 Z= 0.186 Angle : 0.526 9.112 13206 Z= 0.276 Chirality : 0.044 0.153 1471 Planarity : 0.004 0.042 1709 Dihedral : 6.311 82.862 1335 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.98 % Allowed : 7.16 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.24), residues: 1200 helix: 1.58 (0.24), residues: 498 sheet: 1.10 (0.37), residues: 178 loop : 0.30 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 72 TYR 0.012 0.001 TYR A 736 PHE 0.012 0.002 PHE A 237 TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 9746) covalent geometry : angle 0.51910 (13204) SS BOND : bond 0.01845 ( 1) SS BOND : angle 7.02070 ( 2) hydrogen bonds : bond 0.05235 ( 447) hydrogen bonds : angle 4.73054 ( 1248) Misc. bond : bond 0.00384 ( 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: 21 poor density : 125 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7744 (mmt180) REVERT: A 179 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: A 196 MET cc_start: 0.9025 (mmp) cc_final: 0.8784 (mmm) REVERT: A 235 TYR cc_start: 0.8837 (m-80) cc_final: 0.8604 (m-80) REVERT: A 337 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: A 583 GLN cc_start: 0.8583 (mt0) cc_final: 0.8020 (mm-40) REVERT: A 869 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: A 919 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8840 (pmm-80) REVERT: C 91 ASP cc_start: 0.7617 (p0) cc_final: 0.7199 (p0) outliers start: 21 outliers final: 11 residues processed: 138 average time/residue: 0.6639 time to fit residues: 97.6190 Evaluate side-chains 134 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 919 ARG 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 39 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 18 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.122408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.085799 restraints weight = 10865.092| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.83 r_work: 0.2717 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1016 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= 0.142 Angle : 0.488 8.142 13206 Z= 0.255 Chirality : 0.042 0.151 1471 Planarity : 0.004 0.044 1709 Dihedral : 6.201 82.617 1334 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.89 % Allowed : 8.20 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.25), residues: 1200 helix: 1.64 (0.24), residues: 498 sheet: 1.07 (0.37), residues: 178 loop : 0.31 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 5 TYR 0.010 0.001 TYR C 145 PHE 0.011 0.001 PHE A 360 TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9746) covalent geometry : angle 0.48275 (13204) SS BOND : bond 0.02433 ( 1) SS BOND : angle 5.90986 ( 2) hydrogen bonds : bond 0.04506 ( 447) hydrogen bonds : angle 4.53810 ( 1248) Misc. bond : bond 0.00034 ( 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 145 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8269 (ttmm) cc_final: 0.8020 (ttmm) REVERT: A 85 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: A 179 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: A 235 TYR cc_start: 0.8834 (m-80) cc_final: 0.8598 (m-80) REVERT: A 337 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: A 583 GLN cc_start: 0.8580 (mt0) cc_final: 0.7979 (mm-40) REVERT: A 936 LYS cc_start: 0.8514 (ttpp) cc_final: 0.8013 (tmmm) REVERT: C 91 ASP cc_start: 0.7651 (p0) cc_final: 0.7304 (p0) outliers start: 20 outliers final: 10 residues processed: 136 average time/residue: 0.6463 time to fit residues: 93.7684 Evaluate side-chains 133 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 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 C residue 42 ASP 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: 0.3980 chunk 42 optimal weight: 1.9990 chunk 111 optimal weight: 0.0020 chunk 77 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.122842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.086081 restraints weight = 11020.587| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.88 r_work: 0.2719 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 0.055 9749 Z= 0.127 Angle : 0.476 7.876 13206 Z= 0.248 Chirality : 0.042 0.147 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.908 74.889 1330 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.98 % Allowed : 8.95 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.25), residues: 1200 helix: 1.66 (0.24), residues: 499 sheet: 1.10 (0.37), residues: 178 loop : 0.33 (0.28), residues: 523 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 0.011 0.001 PHE A 360 TRP 0.006 0.001 TRP A 608 HIS 0.001 0.000 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9746) covalent geometry : angle 0.47082 (13204) SS BOND : bond 0.01724 ( 1) SS BOND : angle 5.65262 ( 2) hydrogen bonds : bond 0.04192 ( 447) hydrogen bonds : angle 4.45120 ( 1248) Misc. bond : bond 0.00274 ( 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 145 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8274 (ttmm) cc_final: 0.8021 (ttmm) REVERT: A 85 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: A 179 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: A 235 TYR cc_start: 0.8849 (m-80) cc_final: 0.8621 (m-80) REVERT: A 337 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: A 583 GLN cc_start: 0.8555 (mt0) cc_final: 0.8014 (mm110) REVERT: A 835 ASP cc_start: 0.8302 (m-30) cc_final: 0.8055 (t70) REVERT: A 869 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: C 91 ASP cc_start: 0.7677 (p0) cc_final: 0.7328 (p0) outliers start: 21 outliers final: 12 residues processed: 135 average time/residue: 0.6195 time to fit residues: 89.4568 Evaluate side-chains 137 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.085130 restraints weight = 10916.464| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.87 r_work: 0.2704 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9749 Z= 0.170 Angle : 0.496 6.564 13206 Z= 0.258 Chirality : 0.043 0.172 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.974 73.459 1330 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.07 % Allowed : 9.71 % 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 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: 1.39 (0.24), residues: 1200 helix: 1.61 (0.24), residues: 498 sheet: 1.11 (0.37), residues: 178 loop : 0.30 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 5 TYR 0.009 0.001 TYR A 736 PHE 0.011 0.001 PHE A 551 TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 9746) covalent geometry : angle 0.49291 (13204) SS BOND : bond 0.01327 ( 1) SS BOND : angle 4.69134 ( 2) hydrogen bonds : bond 0.04553 ( 447) hydrogen bonds : angle 4.47377 ( 1248) Misc. bond : bond 0.00089 ( 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 143 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8284 (ttmm) cc_final: 0.8035 (ttmm) REVERT: A 85 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: A 179 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: A 235 TYR cc_start: 0.8853 (m-80) cc_final: 0.8619 (m-80) REVERT: A 337 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: A 583 GLN cc_start: 0.8592 (mt0) cc_final: 0.8022 (mm110) REVERT: A 835 ASP cc_start: 0.8292 (m-30) cc_final: 0.8059 (t70) REVERT: A 869 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: B 27 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7513 (mmtm) REVERT: B 31 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: C 91 ASP cc_start: 0.7618 (p0) cc_final: 0.7227 (p0) outliers start: 22 outliers final: 10 residues processed: 133 average time/residue: 0.6207 time to fit residues: 88.2773 Evaluate side-chains 139 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 39 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 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.0030 chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.122766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.086051 restraints weight = 10925.678| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.87 r_work: 0.2718 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1240 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= 0.129 Angle : 0.474 6.443 13206 Z= 0.246 Chirality : 0.042 0.157 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.910 74.380 1330 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.17 % Allowed : 9.71 % Favored : 88.12 % 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: 1.45 (0.25), residues: 1200 helix: 1.63 (0.24), residues: 499 sheet: 1.09 (0.37), residues: 180 loop : 0.37 (0.28), residues: 521 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 0.011 0.001 PHE A 360 TRP 0.006 0.001 TRP A 608 HIS 0.001 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9746) covalent geometry : angle 0.47144 (13204) SS BOND : bond 0.01042 ( 1) SS BOND : angle 4.34227 ( 2) hydrogen bonds : bond 0.04113 ( 447) hydrogen bonds : angle 4.39378 ( 1248) Misc. bond : bond 0.00063 ( 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 150 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8277 (ttmm) cc_final: 0.8034 (ttmm) REVERT: A 85 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: A 135 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7847 (mmmm) REVERT: A 179 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: A 235 TYR cc_start: 0.8857 (m-80) cc_final: 0.8625 (m-80) REVERT: A 337 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.7038 (tt0) REVERT: A 583 GLN cc_start: 0.8526 (mt0) cc_final: 0.7988 (mm110) REVERT: A 835 ASP cc_start: 0.8289 (m-30) cc_final: 0.8063 (t70) REVERT: A 869 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8198 (mm-30) REVERT: B 31 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: C 91 ASP cc_start: 0.7608 (p0) cc_final: 0.7213 (p0) outliers start: 23 outliers final: 12 residues processed: 141 average time/residue: 0.5531 time to fit residues: 83.3427 Evaluate side-chains 141 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU 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: 0.5980 chunk 60 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 109 optimal weight: 0.0970 chunk 24 optimal weight: 0.0670 chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 36 optimal weight: 0.0270 overall best weight: 0.2774 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.124306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.087659 restraints weight = 10942.807| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.86 r_work: 0.2744 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9749 Z= 0.100 Angle : 0.459 5.435 13206 Z= 0.239 Chirality : 0.041 0.174 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.825 74.085 1330 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.17 % Allowed : 10.08 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.25), residues: 1200 helix: 1.73 (0.24), residues: 499 sheet: 1.21 (0.37), residues: 178 loop : 0.36 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 5 TYR 0.007 0.001 TYR A 736 PHE 0.010 0.001 PHE A 360 TRP 0.004 0.001 TRP A 669 HIS 0.001 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9746) covalent geometry : angle 0.45658 (13204) SS BOND : bond 0.00635 ( 1) SS BOND : angle 3.87591 ( 2) hydrogen bonds : bond 0.03596 ( 447) hydrogen bonds : angle 4.25599 ( 1248) Misc. bond : bond 0.00048 ( 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 144 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7978 (ttmm) REVERT: A 85 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: A 179 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: A 235 TYR cc_start: 0.8855 (m-80) cc_final: 0.8611 (m-80) REVERT: A 337 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6976 (tt0) REVERT: A 583 GLN cc_start: 0.8521 (mt0) cc_final: 0.7997 (mm110) REVERT: A 835 ASP cc_start: 0.8260 (m-30) cc_final: 0.8031 (t70) REVERT: A 936 LYS cc_start: 0.8585 (ttpp) cc_final: 0.8355 (tmmm) REVERT: A 995 CYS cc_start: 0.8408 (p) cc_final: 0.8181 (m) REVERT: C 91 ASP cc_start: 0.7607 (p0) cc_final: 0.7173 (p0) outliers start: 23 outliers final: 12 residues processed: 135 average time/residue: 0.5890 time to fit residues: 85.1686 Evaluate side-chains 138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 113 optimal weight: 0.0000 chunk 110 optimal weight: 0.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.123331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.086691 restraints weight = 10842.137| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.85 r_work: 0.2731 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1348 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= 0.132 Angle : 0.480 5.624 13206 Z= 0.249 Chirality : 0.042 0.195 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.794 73.196 1330 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.70 % Allowed : 10.84 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.64 (0.24), residues: 498 sheet: 1.24 (0.37), residues: 178 loop : 0.32 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 5 TYR 0.008 0.001 TYR A 736 PHE 0.011 0.001 PHE A 360 TRP 0.006 0.001 TRP A 608 HIS 0.002 0.000 HIS C 55 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9746) covalent geometry : angle 0.47759 (13204) SS BOND : bond 0.00995 ( 1) SS BOND : angle 4.23818 ( 2) hydrogen bonds : bond 0.03903 ( 447) hydrogen bonds : angle 4.36348 ( 1248) Misc. bond : bond 0.00027 ( 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 137 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8246 (ttmm) cc_final: 0.8002 (ttmm) REVERT: A 85 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: A 179 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: A 235 TYR cc_start: 0.8850 (m-80) cc_final: 0.8607 (m-80) REVERT: A 337 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6986 (tt0) REVERT: A 583 GLN cc_start: 0.8529 (mt0) cc_final: 0.7995 (mm110) REVERT: A 835 ASP cc_start: 0.8239 (m-30) cc_final: 0.8009 (t70) REVERT: C 91 ASP cc_start: 0.7612 (p0) cc_final: 0.7176 (p0) outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 0.5890 time to fit residues: 82.4439 Evaluate side-chains 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 0.0030 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 32 optimal weight: 0.0030 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 overall best weight: 0.4200 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.123879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.087172 restraints weight = 10934.691| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.87 r_work: 0.2736 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1372 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= 0.115 Angle : 0.473 6.294 13206 Z= 0.245 Chirality : 0.042 0.315 1471 Planarity : 0.004 0.045 1709 Dihedral : 5.763 72.320 1330 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.79 % Allowed : 10.46 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.24), residues: 1200 helix: 1.65 (0.24), residues: 498 sheet: 1.25 (0.37), residues: 178 loop : 0.33 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 72 TYR 0.008 0.001 TYR A 736 PHE 0.011 0.001 PHE A 360 TRP 0.005 0.001 TRP A 608 HIS 0.001 0.000 HIS C 55 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9746) covalent geometry : angle 0.47074 (13204) SS BOND : bond 0.00730 ( 1) SS BOND : angle 3.99067 ( 2) hydrogen bonds : bond 0.03750 ( 447) hydrogen bonds : angle 4.33225 ( 1248) Misc. bond : bond 0.00094 ( 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 138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.417 Fit side-chains REVERT: A 33 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7985 (ttmm) REVERT: A 85 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: A 135 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7844 (mmmm) REVERT: A 179 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: A 235 TYR cc_start: 0.8844 (m-80) cc_final: 0.8599 (m-80) REVERT: A 337 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: A 583 GLN cc_start: 0.8535 (mt0) cc_final: 0.7992 (mm110) REVERT: A 835 ASP cc_start: 0.8223 (m-30) cc_final: 0.7996 (t70) REVERT: C 91 ASP cc_start: 0.7620 (p0) cc_final: 0.7180 (p0) outliers start: 19 outliers final: 12 residues processed: 133 average time/residue: 0.5559 time to fit residues: 79.4996 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 : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 713 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 39 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.9980 chunk 74 optimal weight: 0.0870 chunk 112 optimal weight: 0.7980 chunk 39 optimal weight: 0.0070 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 chunk 108 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.088015 restraints weight = 10882.739| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.88 r_work: 0.2749 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1429 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= 0.100 Angle : 0.487 12.837 13206 Z= 0.250 Chirality : 0.042 0.323 1471 Planarity : 0.004 0.051 1709 Dihedral : 5.592 77.049 1329 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.70 % Allowed : 10.84 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.69 (0.24), residues: 498 sheet: 1.29 (0.37), residues: 178 loop : 0.35 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 645 TYR 0.007 0.001 TYR A 736 PHE 0.010 0.001 PHE A 360 TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS C 55 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9746) covalent geometry : angle 0.48673 (13204) SS BOND : bond 0.02283 ( 1) SS BOND : angle 1.25028 ( 2) hydrogen bonds : bond 0.03506 ( 447) hydrogen bonds : angle 4.29083 ( 1248) Misc. bond : bond 0.00196 ( 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 137 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.299 Fit side-chains REVERT: A 33 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7974 (ttmm) REVERT: A 85 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: A 179 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: A 235 TYR cc_start: 0.8890 (m-80) cc_final: 0.8641 (m-80) REVERT: A 337 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: A 583 GLN cc_start: 0.8534 (mt0) cc_final: 0.7995 (mm110) REVERT: A 713 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8708 (p) REVERT: A 835 ASP cc_start: 0.8193 (m-30) cc_final: 0.7976 (t70) outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 0.5261 time to fit residues: 74.1009 Evaluate side-chains 135 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 713 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 39 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 76 optimal weight: 0.5980 chunk 116 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.124714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.087428 restraints weight = 10966.246| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.94 r_work: 0.2775 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9749 Z= 0.148 Angle : 0.514 11.695 13206 Z= 0.265 Chirality : 0.044 0.334 1471 Planarity : 0.004 0.056 1709 Dihedral : 5.669 74.182 1329 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.60 % Allowed : 11.03 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.24), residues: 1200 helix: 1.59 (0.24), residues: 498 sheet: 1.27 (0.37), residues: 178 loop : 0.33 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 645 TYR 0.009 0.001 TYR A 544 PHE 0.011 0.001 PHE A 360 TRP 0.006 0.001 TRP A 608 HIS 0.001 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9746) covalent geometry : angle 0.51339 (13204) SS BOND : bond 0.02180 ( 1) SS BOND : angle 2.03044 ( 2) hydrogen bonds : bond 0.04068 ( 447) hydrogen bonds : angle 4.37544 ( 1248) Misc. bond : bond 0.00057 ( 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: 3619.05 seconds wall clock time: 62 minutes 5.85 seconds (3725.85 seconds total)