Starting phenix.real_space_refine on Wed Sep 17 14:03:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5t_44224/09_2025/9b5t_44224.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5t_44224/09_2025/9b5t_44224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b5t_44224/09_2025/9b5t_44224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5t_44224/09_2025/9b5t_44224.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5t_44224/09_2025/9b5t_44224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5t_44224/09_2025/9b5t_44224.map" } resolution = 3.16 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= 0.072 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 41 5.16 5 C 5703 2.51 5 N 1470 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8935 Number of models: 1 Model: "" Number of chains: 5 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: "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: 2.27, per 1000 atoms: 0.25 Number of scatterers: 8935 At special positions: 0 Unit cell: (85.12, 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 41 16.00 P 3 15.00 Mg 2 11.99 O 1716 8.00 N 1470 7.00 C 5703 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=2.81 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: 0.94 Conformation dependent library (CDL) restraints added in 339.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 9 sheets defined 46.8% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.917A 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: 3.657A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.002A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.088A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.671A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.287A 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: 4.232A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.599A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.636A 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: 4.477A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.913A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.675A 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 removed outlier: 3.572A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.954A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 538 through 553 Processing helix 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 removed outlier: 3.570A pdb=" N THR A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.552A 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: 3.602A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.761A pdb=" N GLN A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 736 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.937A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 4.156A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.646A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.828A 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 'C' and resid 3 through 16 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.821A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.315A 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: 4.382A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.509A 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: 4.382A 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: 6.507A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 460 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.154A 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: 6.505A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.513A 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: 6.505A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.861A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1185 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: 1.80 Time building geometry restraints manager: 1.23 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: 1512 1.27 - 1.41: 2183 1.41 - 1.55: 5376 1.55 - 1.68: 7 1.68 - 1.82: 62 Bond restraints: 9140 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " ideal model delta sigma weight residual 1.453 1.524 -0.071 2.00e-02 2.50e+03 1.28e+01 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 1.02e+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 8.97e-01 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.405 0.011 1.30e-02 5.92e+03 6.65e-01 bond pdb=" CB MET A 35 " pdb=" CG MET A 35 " ideal model delta sigma weight residual 1.520 1.505 0.015 3.00e-02 1.11e+03 2.56e-01 ... (remaining 9135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 12227 1.27 - 2.55: 83 2.55 - 3.82: 69 3.82 - 5.09: 7 5.09 - 6.36: 4 Bond angle restraints: 12390 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 127.63 -5.93 1.80e+00 3.09e-01 1.09e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.08 3.45 1.18e+00 7.24e-01 8.61e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.59 4.60 1.76e+00 3.23e-01 6.83e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.47 6.36 2.67e+00 1.40e-01 5.68e+00 angle pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 111.83 106.21 5.62 2.67e+00 1.40e-01 4.43e+00 ... (remaining 12385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5342 17.43 - 34.85: 159 34.85 - 52.28: 42 52.28 - 69.70: 6 69.70 - 87.13: 3 Dihedral angle restraints: 5552 sinusoidal: 2262 harmonic: 3290 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 -128.05 42.05 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" N GLU A 869 " pdb=" CA GLU A 869 " pdb=" CB GLU A 869 " pdb=" CG GLU A 869 " ideal model delta sinusoidal sigma weight residual -180.00 -120.06 -59.94 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1204 0.055 - 0.110: 132 0.110 - 0.164: 35 0.164 - 0.219: 0 0.219 - 0.274: 3 Chirality restraints: 1374 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 -2.95 0.27 2.00e-01 2.50e+01 1.88e+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 -2.90 0.27 2.00e-01 2.50e+01 1.81e+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 1.29e+00 ... (remaining 1371 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PRO C 95 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 90 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO A 91 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 288 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO A 289 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.014 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 59 2.60 - 3.17: 7537 3.17 - 3.75: 13113 3.75 - 4.32: 18989 4.32 - 4.90: 32186 Nonbonded interactions: 71884 Sorted by model distance: nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.024 2.170 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.031 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.081 2.170 nonbonded pdb="MG MG A1101 " pdb=" O3G ATP A1103 " model vdw 2.137 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2A ATP A1103 " model vdw 2.160 2.170 ... (remaining 71879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.760 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.009 0.780 9143 Z= 0.437 Angle : 0.656 51.842 12392 Z= 0.319 Chirality : 0.041 0.274 1374 Planarity : 0.003 0.031 1604 Dihedral : 9.544 87.130 3425 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.91 % Allowed : 3.93 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.13 (0.26), residues: 1126 helix: 1.70 (0.25), residues: 474 sheet: 0.31 (0.38), residues: 184 loop : 0.06 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.008 0.001 TYR A 732 PHE 0.007 0.001 PHE A 842 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9140) covalent geometry : angle 0.44543 (12390) SS BOND : bond 0.77978 ( 1) SS BOND : angle 37.92647 ( 2) hydrogen bonds : bond 0.15019 ( 419) hydrogen bonds : angle 5.47202 ( 1185) Misc. bond : bond 0.07450 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8598 (mm) cc_final: 0.7964 (mp) REVERT: A 33 LYS cc_start: 0.7988 (tttm) cc_final: 0.7746 (tmmt) REVERT: A 135 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7544 (mttt) REVERT: A 188 ILE cc_start: 0.8489 (mt) cc_final: 0.8250 (mt) REVERT: A 194 VAL cc_start: 0.8255 (t) cc_final: 0.8015 (t) REVERT: A 218 MET cc_start: 0.7340 (mtt) cc_final: 0.6911 (mmm) REVERT: A 236 THR cc_start: 0.8258 (p) cc_final: 0.8022 (t) REVERT: A 274 ASP cc_start: 0.7743 (t70) cc_final: 0.7459 (p0) REVERT: A 311 ARG cc_start: 0.8162 (mtm180) cc_final: 0.7760 (mtm180) REVERT: A 441 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7662 (mm-30) REVERT: A 442 MET cc_start: 0.8601 (tpp) cc_final: 0.8310 (mmm) REVERT: A 567 ASN cc_start: 0.8691 (p0) cc_final: 0.8490 (p0) REVERT: A 596 LYS cc_start: 0.8673 (tmtt) cc_final: 0.8296 (tttt) REVERT: A 675 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: A 784 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8034 (ptpp) REVERT: A 806 THR cc_start: 0.8607 (m) cc_final: 0.8190 (p) REVERT: A 832 MET cc_start: 0.8573 (mtp) cc_final: 0.8297 (mtp) REVERT: A 841 ARG cc_start: 0.7513 (ttm110) cc_final: 0.7295 (mtp-110) REVERT: A 869 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: A 915 LYS cc_start: 0.8119 (mttp) cc_final: 0.7901 (tmtt) REVERT: A 936 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7494 (mtmt) REVERT: A 981 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8486 (mmmt) REVERT: A 997 ASP cc_start: 0.7946 (t0) cc_final: 0.6729 (p0) REVERT: C 28 ASP cc_start: 0.6894 (m-30) cc_final: 0.6193 (p0) REVERT: C 29 ASP cc_start: 0.7848 (t0) cc_final: 0.7600 (t0) REVERT: C 90 ARG cc_start: 0.7742 (mmm160) cc_final: 0.7483 (mmm160) REVERT: C 116 ASP cc_start: 0.8294 (m-30) cc_final: 0.7934 (m-30) REVERT: C 144 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7983 (tttt) outliers start: 9 outliers final: 1 residues processed: 180 average time/residue: 0.1433 time to fit residues: 32.8970 Evaluate side-chains 110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.130067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.100972 restraints weight = 12732.686| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.21 r_work: 0.3167 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9143 Z= 0.188 Angle : 0.534 7.626 12392 Z= 0.282 Chirality : 0.043 0.141 1374 Planarity : 0.004 0.041 1604 Dihedral : 6.701 74.220 1256 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.32 % Allowed : 6.45 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.98 (0.25), residues: 1126 helix: 1.50 (0.25), residues: 483 sheet: 0.33 (0.39), residues: 182 loop : -0.03 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 73 TYR 0.014 0.001 TYR A 732 PHE 0.009 0.001 PHE A 237 TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 9140) covalent geometry : angle 0.52818 (12390) SS BOND : bond 0.01058 ( 1) SS BOND : angle 5.96289 ( 2) hydrogen bonds : bond 0.04640 ( 419) hydrogen bonds : angle 4.41946 ( 1185) Misc. bond : bond 0.00366 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8999 (t) cc_final: 0.8735 (m) REVERT: A 135 LYS cc_start: 0.8469 (mmmt) cc_final: 0.7868 (mttt) REVERT: A 188 ILE cc_start: 0.8634 (mt) cc_final: 0.8380 (mt) REVERT: A 311 ARG cc_start: 0.8570 (mtm180) cc_final: 0.8314 (mtm180) REVERT: A 442 MET cc_start: 0.8694 (tpp) cc_final: 0.8493 (mmm) REVERT: A 567 ASN cc_start: 0.8865 (p0) cc_final: 0.8647 (p0) REVERT: A 596 LYS cc_start: 0.8671 (tmtt) cc_final: 0.8404 (tttt) REVERT: A 675 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8418 (m-30) REVERT: A 710 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7986 (p) REVERT: A 784 LYS cc_start: 0.8523 (ttpp) cc_final: 0.8083 (ptpp) REVERT: A 806 THR cc_start: 0.8720 (m) cc_final: 0.8313 (p) REVERT: A 869 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: A 915 LYS cc_start: 0.8175 (mttp) cc_final: 0.7789 (tmtt) REVERT: A 936 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7630 (mtmt) REVERT: A 997 ASP cc_start: 0.8104 (t0) cc_final: 0.6846 (p0) REVERT: C 90 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7587 (mmm160) REVERT: C 117 ASP cc_start: 0.7515 (t70) cc_final: 0.7298 (t70) outliers start: 23 outliers final: 12 residues processed: 126 average time/residue: 0.1264 time to fit residues: 20.9355 Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.101573 restraints weight = 12728.239| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.22 r_work: 0.3170 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9143 Z= 0.143 Angle : 0.494 6.764 12392 Z= 0.260 Chirality : 0.042 0.138 1374 Planarity : 0.004 0.044 1604 Dihedral : 6.390 72.345 1256 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.22 % Allowed : 7.56 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.90 (0.25), residues: 1126 helix: 1.48 (0.24), residues: 484 sheet: 0.21 (0.38), residues: 190 loop : -0.08 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 143 TYR 0.010 0.001 TYR A 81 PHE 0.040 0.001 PHE C 62 TRP 0.006 0.001 TRP A 917 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9140) covalent geometry : angle 0.48982 (12390) SS BOND : bond 0.00680 ( 1) SS BOND : angle 5.20643 ( 2) hydrogen bonds : bond 0.03943 ( 419) hydrogen bonds : angle 4.23712 ( 1185) Misc. bond : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8229 (mmm) REVERT: A 110 SER cc_start: 0.8993 (t) cc_final: 0.8710 (m) REVERT: A 135 LYS cc_start: 0.8444 (mmmt) cc_final: 0.7817 (mttt) REVERT: A 218 MET cc_start: 0.7202 (mmm) cc_final: 0.6876 (mmm) REVERT: A 285 MET cc_start: 0.8204 (mmm) cc_final: 0.7965 (mmm) REVERT: A 311 ARG cc_start: 0.8543 (mtm180) cc_final: 0.8281 (mtm180) REVERT: A 442 MET cc_start: 0.8699 (tpp) cc_final: 0.8494 (mmm) REVERT: A 567 ASN cc_start: 0.8879 (p0) cc_final: 0.8643 (p0) REVERT: A 592 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8199 (tp) REVERT: A 675 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8380 (m-30) REVERT: A 710 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.8002 (p) REVERT: A 784 LYS cc_start: 0.8531 (ttpp) cc_final: 0.8058 (ptpp) REVERT: A 806 THR cc_start: 0.8716 (m) cc_final: 0.8292 (p) REVERT: A 869 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: A 915 LYS cc_start: 0.8190 (mttp) cc_final: 0.7678 (tmtt) REVERT: A 936 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7672 (mttt) REVERT: A 997 ASP cc_start: 0.8098 (t0) cc_final: 0.6849 (p0) REVERT: C 117 ASP cc_start: 0.7409 (t70) cc_final: 0.7092 (t70) outliers start: 22 outliers final: 12 residues processed: 107 average time/residue: 0.1189 time to fit residues: 17.1483 Evaluate side-chains 109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.129677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100330 restraints weight = 13048.092| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.40 r_work: 0.3144 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9143 Z= 0.154 Angle : 0.490 5.922 12392 Z= 0.257 Chirality : 0.042 0.134 1374 Planarity : 0.004 0.044 1604 Dihedral : 6.173 59.783 1256 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.22 % Allowed : 8.47 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.91 (0.25), residues: 1126 helix: 1.48 (0.24), residues: 484 sheet: 0.18 (0.37), residues: 190 loop : -0.06 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 143 TYR 0.011 0.001 TYR A 81 PHE 0.014 0.001 PHE C 62 TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9140) covalent geometry : angle 0.48682 (12390) SS BOND : bond 0.00595 ( 1) SS BOND : angle 4.70133 ( 2) hydrogen bonds : bond 0.03883 ( 419) hydrogen bonds : angle 4.17684 ( 1185) Misc. bond : bond 0.00042 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8209 (mmm) REVERT: A 110 SER cc_start: 0.8998 (t) cc_final: 0.8715 (m) REVERT: A 135 LYS cc_start: 0.8468 (mmmt) cc_final: 0.7825 (mtmt) REVERT: A 243 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7468 (mmpt) REVERT: A 311 ARG cc_start: 0.8585 (mtm180) cc_final: 0.8295 (mtm180) REVERT: A 406 ARG cc_start: 0.7679 (mtm180) cc_final: 0.7322 (mmt-90) REVERT: A 567 ASN cc_start: 0.8951 (p0) cc_final: 0.8731 (p0) REVERT: A 592 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8253 (tp) REVERT: A 675 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8434 (m-30) REVERT: A 699 GLN cc_start: 0.8626 (mp10) cc_final: 0.8325 (mp10) REVERT: A 710 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8031 (p) REVERT: A 784 LYS cc_start: 0.8558 (ttpp) cc_final: 0.8072 (ptpp) REVERT: A 869 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: A 915 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7697 (tmtt) REVERT: A 936 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7632 (mttt) REVERT: A 997 ASP cc_start: 0.8113 (t0) cc_final: 0.6858 (p0) REVERT: C 117 ASP cc_start: 0.7318 (t70) cc_final: 0.7006 (t70) REVERT: C 143 ARG cc_start: 0.8894 (tmm-80) cc_final: 0.8683 (ttp-110) outliers start: 22 outliers final: 12 residues processed: 107 average time/residue: 0.1252 time to fit residues: 17.7636 Evaluate side-chains 110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 0.0470 chunk 110 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 48 optimal weight: 0.0170 chunk 64 optimal weight: 0.7980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.131813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103269 restraints weight = 12809.087| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.23 r_work: 0.3191 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9143 Z= 0.098 Angle : 0.467 9.222 12392 Z= 0.241 Chirality : 0.040 0.135 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.946 60.514 1256 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.81 % Allowed : 9.38 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.09 (0.26), residues: 1126 helix: 1.61 (0.24), residues: 484 sheet: 0.28 (0.38), residues: 190 loop : 0.06 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 143 TYR 0.007 0.001 TYR A 933 PHE 0.032 0.001 PHE C 62 TRP 0.006 0.001 TRP A 917 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9140) covalent geometry : angle 0.46449 (12390) SS BOND : bond 0.00578 ( 1) SS BOND : angle 3.83388 ( 2) hydrogen bonds : bond 0.03297 ( 419) hydrogen bonds : angle 4.01229 ( 1185) Misc. bond : bond 0.00053 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8189 (mmm) REVERT: A 110 SER cc_start: 0.8930 (t) cc_final: 0.8652 (m) REVERT: A 135 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7702 (mtmt) REVERT: A 406 ARG cc_start: 0.7588 (mtm180) cc_final: 0.7311 (mmt-90) REVERT: A 567 ASN cc_start: 0.8867 (p0) cc_final: 0.8636 (p0) REVERT: A 592 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8196 (tp) REVERT: A 675 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8401 (m-30) REVERT: A 699 GLN cc_start: 0.8618 (mp10) cc_final: 0.8325 (mp10) REVERT: A 710 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.8027 (p) REVERT: A 784 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8054 (ptpp) REVERT: A 869 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: A 915 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7662 (tmtt) REVERT: A 936 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7693 (mtmt) REVERT: A 997 ASP cc_start: 0.8098 (t0) cc_final: 0.6895 (p0) REVERT: C 117 ASP cc_start: 0.7238 (t70) cc_final: 0.6920 (t70) REVERT: C 143 ARG cc_start: 0.8774 (tmm-80) cc_final: 0.8541 (ttp-110) outliers start: 18 outliers final: 10 residues processed: 105 average time/residue: 0.1194 time to fit residues: 16.7812 Evaluate side-chains 106 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 88 optimal weight: 0.0020 chunk 43 optimal weight: 0.9990 chunk 109 optimal weight: 0.0770 chunk 40 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5348 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.131388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102702 restraints weight = 12883.243| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.24 r_work: 0.3198 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9143 Z= 0.111 Angle : 0.471 7.949 12392 Z= 0.242 Chirality : 0.041 0.132 1374 Planarity : 0.004 0.039 1604 Dihedral : 5.893 59.281 1256 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.12 % Allowed : 9.48 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.11 (0.26), residues: 1126 helix: 1.62 (0.24), residues: 485 sheet: 0.28 (0.38), residues: 190 loop : 0.09 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 8 TYR 0.008 0.001 TYR A 81 PHE 0.012 0.001 PHE C 62 TRP 0.006 0.001 TRP A 917 HIS 0.003 0.000 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9140) covalent geometry : angle 0.46842 (12390) SS BOND : bond 0.00562 ( 1) SS BOND : angle 3.80929 ( 2) hydrogen bonds : bond 0.03337 ( 419) hydrogen bonds : angle 3.97770 ( 1185) Misc. bond : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8142 (mmm) REVERT: A 110 SER cc_start: 0.8956 (t) cc_final: 0.8675 (m) REVERT: A 135 LYS cc_start: 0.8358 (mmmt) cc_final: 0.7674 (mtmt) REVERT: A 567 ASN cc_start: 0.8872 (p0) cc_final: 0.8640 (p0) REVERT: A 592 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8168 (tp) REVERT: A 675 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8357 (m-30) REVERT: A 710 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.8036 (p) REVERT: A 784 LYS cc_start: 0.8579 (ttpp) cc_final: 0.8100 (ptpp) REVERT: A 869 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: A 915 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7663 (tmtt) REVERT: A 936 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7668 (mtmt) REVERT: A 997 ASP cc_start: 0.8082 (t0) cc_final: 0.6874 (p0) REVERT: C 101 LYS cc_start: 0.7689 (mtmt) cc_final: 0.7304 (mtmt) REVERT: C 117 ASP cc_start: 0.7215 (t70) cc_final: 0.6884 (t70) REVERT: C 143 ARG cc_start: 0.8758 (tmm-80) cc_final: 0.8512 (ttp-110) outliers start: 21 outliers final: 13 residues processed: 101 average time/residue: 0.1118 time to fit residues: 15.2869 Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 86 optimal weight: 0.0770 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.130653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102070 restraints weight = 12935.517| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.24 r_work: 0.3173 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9143 Z= 0.120 Angle : 0.475 7.149 12392 Z= 0.244 Chirality : 0.041 0.132 1374 Planarity : 0.004 0.042 1604 Dihedral : 5.861 59.387 1256 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.32 % Allowed : 9.78 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.10 (0.26), residues: 1126 helix: 1.62 (0.24), residues: 484 sheet: 0.26 (0.38), residues: 190 loop : 0.09 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 8 TYR 0.009 0.001 TYR A 81 PHE 0.032 0.001 PHE C 62 TRP 0.005 0.001 TRP A 917 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9140) covalent geometry : angle 0.47262 (12390) SS BOND : bond 0.00401 ( 1) SS BOND : angle 3.84093 ( 2) hydrogen bonds : bond 0.03397 ( 419) hydrogen bonds : angle 3.98060 ( 1185) Misc. bond : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8163 (mmm) REVERT: A 110 SER cc_start: 0.8963 (t) cc_final: 0.8687 (m) REVERT: A 567 ASN cc_start: 0.8870 (p0) cc_final: 0.8665 (p0) REVERT: A 592 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8194 (tp) REVERT: A 675 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8371 (m-30) REVERT: A 699 GLN cc_start: 0.8629 (mp10) cc_final: 0.8333 (mp10) REVERT: A 710 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8039 (p) REVERT: A 784 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8100 (ptpp) REVERT: A 869 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8108 (mm-30) REVERT: A 915 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7676 (tmtt) REVERT: A 936 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7703 (mtmt) REVERT: A 997 ASP cc_start: 0.8090 (t0) cc_final: 0.6889 (p0) REVERT: C 117 ASP cc_start: 0.7226 (t70) cc_final: 0.6898 (t70) REVERT: C 143 ARG cc_start: 0.8756 (tmm-80) cc_final: 0.8509 (ttp-110) outliers start: 23 outliers final: 15 residues processed: 101 average time/residue: 0.1106 time to fit residues: 15.2968 Evaluate side-chains 111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 75 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.130464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.102056 restraints weight = 12950.292| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.23 r_work: 0.3177 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9143 Z= 0.133 Angle : 0.486 7.344 12392 Z= 0.250 Chirality : 0.041 0.129 1374 Planarity : 0.004 0.042 1604 Dihedral : 5.849 59.948 1256 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.42 % Allowed : 10.28 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.06 (0.26), residues: 1126 helix: 1.57 (0.24), residues: 485 sheet: 0.24 (0.38), residues: 190 loop : 0.08 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.009 0.001 TYR A 81 PHE 0.025 0.001 PHE C 62 TRP 0.006 0.001 TRP A 917 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9140) covalent geometry : angle 0.48371 (12390) SS BOND : bond 0.00476 ( 1) SS BOND : angle 3.99209 ( 2) hydrogen bonds : bond 0.03497 ( 419) hydrogen bonds : angle 4.01828 ( 1185) Misc. bond : bond 0.00039 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8096 (mmm) REVERT: A 110 SER cc_start: 0.8978 (t) cc_final: 0.8687 (m) REVERT: A 567 ASN cc_start: 0.8888 (p0) cc_final: 0.8667 (p0) REVERT: A 592 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8163 (tp) REVERT: A 675 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8354 (m-30) REVERT: A 699 GLN cc_start: 0.8599 (mp10) cc_final: 0.8292 (mp10) REVERT: A 710 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8041 (p) REVERT: A 784 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8092 (ptpp) REVERT: A 869 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8112 (mm-30) REVERT: A 915 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7702 (ttpp) REVERT: A 936 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7647 (mtmt) REVERT: A 997 ASP cc_start: 0.8065 (t0) cc_final: 0.6857 (p0) REVERT: C 117 ASP cc_start: 0.7260 (t70) cc_final: 0.6922 (t70) REVERT: C 143 ARG cc_start: 0.8764 (tmm-80) cc_final: 0.8511 (ttp-110) outliers start: 24 outliers final: 16 residues processed: 104 average time/residue: 0.1092 time to fit residues: 15.6749 Evaluate side-chains 113 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 0.0070 chunk 39 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.131055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102766 restraints weight = 12899.425| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.22 r_work: 0.3190 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9143 Z= 0.113 Angle : 0.475 7.992 12392 Z= 0.244 Chirality : 0.041 0.131 1374 Planarity : 0.004 0.042 1604 Dihedral : 5.796 58.814 1256 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.22 % Allowed : 10.48 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.13 (0.26), residues: 1126 helix: 1.66 (0.24), residues: 484 sheet: 0.25 (0.37), residues: 190 loop : 0.10 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 5 TYR 0.008 0.001 TYR A 920 PHE 0.009 0.001 PHE A 985 TRP 0.005 0.001 TRP A 917 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9140) covalent geometry : angle 0.47241 (12390) SS BOND : bond 0.00626 ( 1) SS BOND : angle 3.75338 ( 2) hydrogen bonds : bond 0.03317 ( 419) hydrogen bonds : angle 3.96433 ( 1185) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8097 (mmm) REVERT: A 110 SER cc_start: 0.8960 (t) cc_final: 0.8672 (m) REVERT: A 567 ASN cc_start: 0.8859 (p0) cc_final: 0.8636 (p0) REVERT: A 592 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8162 (tp) REVERT: A 675 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8352 (m-30) REVERT: A 699 GLN cc_start: 0.8607 (mp10) cc_final: 0.8305 (mp10) REVERT: A 710 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8039 (p) REVERT: A 784 LYS cc_start: 0.8536 (ttpp) cc_final: 0.8044 (ptpp) REVERT: A 869 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8098 (mm-30) REVERT: A 915 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7653 (tmtt) REVERT: A 936 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7632 (mtmt) REVERT: A 997 ASP cc_start: 0.8064 (t0) cc_final: 0.6878 (p0) REVERT: C 101 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7320 (mtmt) REVERT: C 143 ARG cc_start: 0.8750 (tmm-80) cc_final: 0.8498 (ttp-110) outliers start: 22 outliers final: 15 residues processed: 103 average time/residue: 0.0943 time to fit residues: 13.6745 Evaluate side-chains 113 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 109 optimal weight: 0.0040 chunk 86 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 102 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.131634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103311 restraints weight = 12760.649| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.22 r_work: 0.3203 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9143 Z= 0.102 Angle : 0.476 8.336 12392 Z= 0.244 Chirality : 0.041 0.147 1374 Planarity : 0.004 0.042 1604 Dihedral : 5.845 58.762 1256 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.32 % Allowed : 10.48 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.17 (0.26), residues: 1126 helix: 1.67 (0.24), residues: 485 sheet: 0.27 (0.37), residues: 190 loop : 0.14 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 8 TYR 0.007 0.001 TYR A 933 PHE 0.026 0.001 PHE C 62 TRP 0.006 0.001 TRP A 917 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9140) covalent geometry : angle 0.47413 (12390) SS BOND : bond 0.00488 ( 1) SS BOND : angle 3.53514 ( 2) hydrogen bonds : bond 0.03234 ( 419) hydrogen bonds : angle 3.92665 ( 1185) Misc. bond : bond 0.00070 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8212 (mmm) REVERT: A 110 SER cc_start: 0.8937 (t) cc_final: 0.8683 (m) REVERT: A 567 ASN cc_start: 0.8838 (p0) cc_final: 0.8603 (p0) REVERT: A 600 ASN cc_start: 0.8920 (p0) cc_final: 0.8705 (p0) REVERT: A 627 TYR cc_start: 0.8071 (t80) cc_final: 0.7603 (t80) REVERT: A 675 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: A 699 GLN cc_start: 0.8607 (mp10) cc_final: 0.8359 (mp10) REVERT: A 710 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8013 (p) REVERT: A 784 LYS cc_start: 0.8469 (ttpp) cc_final: 0.8042 (ptpp) REVERT: A 869 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8094 (mm-30) REVERT: A 915 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7696 (ttpp) REVERT: A 936 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7687 (mtmt) REVERT: A 997 ASP cc_start: 0.8107 (t0) cc_final: 0.7028 (p0) REVERT: C 66 LYS cc_start: 0.8417 (mtpp) cc_final: 0.7869 (tttm) REVERT: C 90 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7730 (mmm160) REVERT: C 117 ASP cc_start: 0.7302 (t0) cc_final: 0.6869 (t70) outliers start: 23 outliers final: 16 residues processed: 107 average time/residue: 0.1078 time to fit residues: 15.9032 Evaluate side-chains 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 0.0270 chunk 87 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 0.0040 chunk 101 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.0000 chunk 62 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.3654 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.132096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103416 restraints weight = 12710.039| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.29 r_work: 0.3207 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9143 Z= 0.097 Angle : 0.482 11.055 12392 Z= 0.244 Chirality : 0.040 0.134 1374 Planarity : 0.004 0.042 1604 Dihedral : 5.764 58.430 1256 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.22 % Allowed : 10.69 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.25 (0.26), residues: 1126 helix: 1.73 (0.24), residues: 486 sheet: 0.36 (0.38), residues: 181 loop : 0.16 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 8 TYR 0.007 0.001 TYR A 933 PHE 0.009 0.001 PHE A 237 TRP 0.006 0.001 TRP A 917 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9140) covalent geometry : angle 0.48017 (12390) SS BOND : bond 0.00434 ( 1) SS BOND : angle 3.34634 ( 2) hydrogen bonds : bond 0.03110 ( 419) hydrogen bonds : angle 3.88128 ( 1185) Misc. bond : bond 0.00067 ( 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: 2341.83 seconds wall clock time: 40 minutes 29.88 seconds (2429.88 seconds total)