Starting phenix.real_space_refine on Mon May 12 13:39:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5t_44224/05_2025/9b5t_44224.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5t_44224/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5t_44224/05_2025/9b5t_44224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5t_44224/05_2025/9b5t_44224.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5t_44224/05_2025/9b5t_44224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5t_44224/05_2025/9b5t_44224.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.072 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.41, per 1000 atoms: 0.72 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.27 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: 3.92 Time building geometry restraints manager: 2.97 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: 7.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.060 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (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 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS A 818 PHE 0.007 0.001 PHE A 842 TYR 0.008 0.001 TYR A 732 ARG 0.002 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.15019 ( 419) hydrogen bonds : angle 5.47202 ( 1185) SS BOND : bond 0.77978 ( 1) SS BOND : angle 37.92647 ( 2) covalent geometry : bond 0.00266 ( 9140) covalent geometry : angle 0.44543 (12390) 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 : 0.950 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: 0.3194 time to fit residues: 74.6263 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 : 0.959 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.131519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.102436 restraints weight = 12616.069| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.22 r_work: 0.3194 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9143 Z= 0.142 Angle : 0.510 7.096 12392 Z= 0.269 Chirality : 0.042 0.134 1374 Planarity : 0.004 0.041 1604 Dihedral : 6.608 77.051 1256 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.22 % Allowed : 6.45 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1126 helix: 1.57 (0.25), residues: 483 sheet: 0.38 (0.39), residues: 182 loop : 0.02 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 147 PHE 0.008 0.001 PHE A 842 TYR 0.011 0.001 TYR A 732 ARG 0.006 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 419) hydrogen bonds : angle 4.31625 ( 1185) SS BOND : bond 0.00553 ( 1) SS BOND : angle 5.33033 ( 2) covalent geometry : bond 0.00345 ( 9140) covalent geometry : angle 0.50571 (12390) Misc. bond : bond 0.00200 ( 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 133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8968 (t) cc_final: 0.8720 (m) REVERT: A 135 LYS cc_start: 0.8461 (mmmt) cc_final: 0.7944 (mttt) REVERT: A 188 ILE cc_start: 0.8630 (mt) cc_final: 0.8392 (mt) REVERT: A 311 ARG cc_start: 0.8610 (mtm180) cc_final: 0.8406 (mtm180) REVERT: A 675 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: A 710 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7969 (p) REVERT: A 784 LYS cc_start: 0.8448 (ttpp) cc_final: 0.8074 (ptpp) REVERT: A 806 THR cc_start: 0.8704 (m) cc_final: 0.8374 (p) REVERT: A 869 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: A 915 LYS cc_start: 0.8167 (mttp) cc_final: 0.7822 (tmtt) REVERT: A 936 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7672 (mtmt) REVERT: A 997 ASP cc_start: 0.8120 (t0) cc_final: 0.6913 (p0) REVERT: C 90 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7719 (mmm160) REVERT: C 117 ASP cc_start: 0.7519 (t70) cc_final: 0.7227 (t70) outliers start: 22 outliers final: 11 residues processed: 125 average time/residue: 0.2744 time to fit residues: 44.8836 Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.128976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099658 restraints weight = 13032.157| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.38 r_work: 0.3146 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9143 Z= 0.196 Angle : 0.530 6.856 12392 Z= 0.279 Chirality : 0.043 0.140 1374 Planarity : 0.004 0.045 1604 Dihedral : 6.423 64.575 1256 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.52 % Allowed : 7.16 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1126 helix: 1.35 (0.24), residues: 484 sheet: 0.26 (0.38), residues: 180 loop : -0.14 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.003 0.001 HIS A 202 PHE 0.039 0.002 PHE C 62 TYR 0.014 0.002 TYR A 732 ARG 0.005 0.001 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 419) hydrogen bonds : angle 4.31049 ( 1185) SS BOND : bond 0.00582 ( 1) SS BOND : angle 5.35670 ( 2) covalent geometry : bond 0.00489 ( 9140) covalent geometry : angle 0.52582 (12390) Misc. bond : bond 0.00113 ( 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 118 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9012 (t) cc_final: 0.8732 (m) REVERT: A 135 LYS cc_start: 0.8490 (mmmt) cc_final: 0.7853 (mtmt) REVERT: A 218 MET cc_start: 0.7270 (mmm) cc_final: 0.6700 (mmm) REVERT: A 311 ARG cc_start: 0.8634 (mtm180) cc_final: 0.8382 (mtm180) REVERT: A 592 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8257 (tp) REVERT: A 675 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8427 (m-30) REVERT: A 710 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8029 (p) REVERT: A 784 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8062 (ptpp) REVERT: A 869 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: A 915 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7715 (tmtt) REVERT: A 936 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7658 (mtmt) REVERT: A 997 ASP cc_start: 0.8131 (t0) cc_final: 0.6884 (p0) REVERT: C 117 ASP cc_start: 0.7429 (t70) cc_final: 0.7118 (t70) outliers start: 25 outliers final: 11 residues processed: 108 average time/residue: 0.2426 time to fit residues: 35.8430 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 : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 62 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 0.0470 chunk 105 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.131338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102797 restraints weight = 12832.661| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.22 r_work: 0.3184 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9143 Z= 0.104 Angle : 0.465 5.500 12392 Z= 0.244 Chirality : 0.041 0.137 1374 Planarity : 0.004 0.043 1604 Dihedral : 6.109 65.644 1256 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.31 % Allowed : 9.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1126 helix: 1.55 (0.24), residues: 483 sheet: 0.23 (0.38), residues: 190 loop : 0.01 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 917 HIS 0.002 0.000 HIS A 818 PHE 0.017 0.001 PHE C 62 TYR 0.007 0.001 TYR C 127 ARG 0.004 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 419) hydrogen bonds : angle 4.05011 ( 1185) SS BOND : bond 0.00118 ( 1) SS BOND : angle 3.85115 ( 2) covalent geometry : bond 0.00244 ( 9140) covalent geometry : angle 0.46286 (12390) Misc. bond : bond 0.00144 ( 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 111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: A 110 SER cc_start: 0.8936 (t) cc_final: 0.8647 (m) REVERT: A 135 LYS cc_start: 0.8407 (mmmt) cc_final: 0.7717 (mtmt) REVERT: A 218 MET cc_start: 0.7222 (mmm) cc_final: 0.6686 (mmm) REVERT: A 243 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7416 (mmpt) REVERT: A 406 ARG cc_start: 0.7641 (mtm180) cc_final: 0.7308 (mmt-90) REVERT: A 675 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8354 (m-30) REVERT: A 699 GLN cc_start: 0.8635 (mp10) cc_final: 0.8341 (mp10) REVERT: A 710 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8039 (p) REVERT: A 784 LYS cc_start: 0.8579 (ttpp) cc_final: 0.8110 (ptpp) REVERT: A 869 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: A 915 LYS cc_start: 0.8223 (mttp) cc_final: 0.7662 (tmtt) REVERT: A 936 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7659 (mtmt) REVERT: A 997 ASP cc_start: 0.8078 (t0) cc_final: 0.6852 (p0) REVERT: C 117 ASP cc_start: 0.7265 (t70) cc_final: 0.6944 (t70) REVERT: C 143 ARG cc_start: 0.8841 (tmm-80) cc_final: 0.8631 (ttp-110) outliers start: 13 outliers final: 6 residues processed: 105 average time/residue: 0.2647 time to fit residues: 37.3385 Evaluate side-chains 104 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.130029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101721 restraints weight = 12767.955| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.18 r_work: 0.3166 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9143 Z= 0.146 Angle : 0.492 8.809 12392 Z= 0.254 Chirality : 0.042 0.133 1374 Planarity : 0.004 0.044 1604 Dihedral : 5.986 59.530 1256 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.42 % Allowed : 8.67 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1126 helix: 1.49 (0.24), residues: 485 sheet: 0.22 (0.37), residues: 193 loop : 0.05 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 917 HIS 0.002 0.001 HIS A 818 PHE 0.032 0.001 PHE C 62 TYR 0.010 0.001 TYR A 81 ARG 0.006 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 419) hydrogen bonds : angle 4.08030 ( 1185) SS BOND : bond 0.00946 ( 1) SS BOND : angle 4.14745 ( 2) covalent geometry : bond 0.00359 ( 9140) covalent geometry : angle 0.48960 (12390) Misc. bond : bond 0.00062 ( 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 117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8982 (t) cc_final: 0.8686 (m) REVERT: A 135 LYS cc_start: 0.8447 (mmmt) cc_final: 0.7752 (mtmt) REVERT: A 218 MET cc_start: 0.7274 (mmm) cc_final: 0.6682 (mmm) REVERT: A 464 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.7889 (pmt) REVERT: A 592 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8202 (tp) REVERT: A 675 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8373 (m-30) REVERT: A 710 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8030 (p) REVERT: A 784 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8103 (ptpp) REVERT: A 869 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: A 915 LYS cc_start: 0.8248 (mttp) cc_final: 0.7672 (tmtt) REVERT: A 936 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7686 (mtmt) REVERT: A 997 ASP cc_start: 0.8096 (t0) cc_final: 0.6885 (p0) REVERT: C 28 ASP cc_start: 0.7029 (m-30) cc_final: 0.6264 (p0) REVERT: C 117 ASP cc_start: 0.7228 (t70) cc_final: 0.6897 (t70) REVERT: C 143 ARG cc_start: 0.8804 (tmm-80) cc_final: 0.8557 (ttp-110) outliers start: 24 outliers final: 15 residues processed: 107 average time/residue: 0.2416 time to fit residues: 35.3159 Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET 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 343 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 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 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 97 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.129592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101216 restraints weight = 12877.396| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.19 r_work: 0.3173 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9143 Z= 0.143 Angle : 0.494 7.530 12392 Z= 0.255 Chirality : 0.042 0.132 1374 Planarity : 0.004 0.040 1604 Dihedral : 5.940 59.604 1256 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.52 % Allowed : 9.27 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1126 helix: 1.50 (0.24), residues: 485 sheet: 0.18 (0.37), residues: 190 loop : 0.01 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 917 HIS 0.002 0.000 HIS A 818 PHE 0.035 0.001 PHE C 62 TYR 0.011 0.001 TYR A 81 ARG 0.006 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 419) hydrogen bonds : angle 4.06322 ( 1185) SS BOND : bond 0.00698 ( 1) SS BOND : angle 4.16822 ( 2) covalent geometry : bond 0.00352 ( 9140) covalent geometry : angle 0.49078 (12390) Misc. bond : bond 0.00059 ( 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 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8977 (t) cc_final: 0.8684 (m) REVERT: A 135 LYS cc_start: 0.8406 (mmmt) cc_final: 0.7728 (mtmt) REVERT: A 218 MET cc_start: 0.7222 (mmm) cc_final: 0.6634 (mmm) REVERT: A 464 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7908 (pmt) REVERT: A 592 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8125 (tp) REVERT: A 675 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8407 (m-30) REVERT: A 699 GLN cc_start: 0.8617 (mp10) cc_final: 0.8317 (mp10) REVERT: A 710 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8029 (p) REVERT: A 784 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8090 (ptpp) REVERT: A 869 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 915 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7726 (tmtt) REVERT: A 936 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7697 (mtmt) REVERT: A 997 ASP cc_start: 0.8099 (t0) cc_final: 0.6904 (p0) REVERT: C 117 ASP cc_start: 0.7260 (t70) cc_final: 0.6934 (t70) REVERT: C 143 ARG cc_start: 0.8766 (tmm-80) cc_final: 0.8510 (ttp-110) outliers start: 25 outliers final: 17 residues processed: 103 average time/residue: 0.2348 time to fit residues: 33.6196 Evaluate side-chains 111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 464 MET 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 594 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 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 97 LEU 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 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 102 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.129887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.101365 restraints weight = 12935.720| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.23 r_work: 0.3173 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2101 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 : 0.484 6.809 12392 Z= 0.250 Chirality : 0.042 0.132 1374 Planarity : 0.004 0.042 1604 Dihedral : 5.889 59.557 1256 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.52 % Allowed : 9.88 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1126 helix: 1.53 (0.24), residues: 484 sheet: 0.19 (0.38), residues: 190 loop : 0.01 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 917 HIS 0.002 0.000 HIS A 818 PHE 0.010 0.001 PHE A 237 TYR 0.010 0.001 TYR A 81 ARG 0.003 0.000 ARG C 5 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 419) hydrogen bonds : angle 4.04020 ( 1185) SS BOND : bond 0.00217 ( 1) SS BOND : angle 4.09064 ( 2) covalent geometry : bond 0.00327 ( 9140) covalent geometry : angle 0.48124 (12390) Misc. bond : bond 0.00101 ( 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 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8959 (t) cc_final: 0.8691 (m) REVERT: A 218 MET cc_start: 0.7352 (mmm) cc_final: 0.6780 (mmm) REVERT: A 464 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.7944 (pmt) REVERT: A 592 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8227 (tp) REVERT: A 675 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8415 (m-30) REVERT: A 699 GLN cc_start: 0.8617 (mp10) cc_final: 0.8354 (mp10) REVERT: A 710 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.7999 (p) REVERT: A 784 LYS cc_start: 0.8501 (ttpp) cc_final: 0.8067 (ptpp) REVERT: A 869 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: A 915 LYS cc_start: 0.8214 (mttp) cc_final: 0.7751 (tmtt) REVERT: A 936 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7699 (mtmt) REVERT: A 997 ASP cc_start: 0.8126 (t0) cc_final: 0.6991 (p0) REVERT: C 117 ASP cc_start: 0.7265 (t70) cc_final: 0.6966 (t70) REVERT: C 143 ARG cc_start: 0.8700 (tmm-80) cc_final: 0.8446 (ttp-110) outliers start: 25 outliers final: 17 residues processed: 102 average time/residue: 0.2218 time to fit residues: 31.3262 Evaluate side-chains 111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 464 MET 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 594 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 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 67 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.129712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100554 restraints weight = 13115.816| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.32 r_work: 0.3158 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9143 Z= 0.142 Angle : 0.489 7.503 12392 Z= 0.253 Chirality : 0.042 0.131 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.880 59.469 1256 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.72 % Allowed : 9.68 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1126 helix: 1.52 (0.24), residues: 484 sheet: 0.17 (0.37), residues: 193 loop : 0.01 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 917 HIS 0.002 0.000 HIS A 818 PHE 0.030 0.001 PHE C 62 TYR 0.010 0.001 TYR A 81 ARG 0.002 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 419) hydrogen bonds : angle 4.05216 ( 1185) SS BOND : bond 0.00657 ( 1) SS BOND : angle 4.09608 ( 2) covalent geometry : bond 0.00351 ( 9140) covalent geometry : angle 0.48671 (12390) Misc. bond : bond 0.00088 ( 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 118 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8998 (t) cc_final: 0.8711 (m) REVERT: A 218 MET cc_start: 0.7321 (mmm) cc_final: 0.6744 (mmm) REVERT: A 464 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.7905 (pmt) REVERT: A 592 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8173 (tp) REVERT: A 675 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8426 (m-30) REVERT: A 699 GLN cc_start: 0.8618 (mp10) cc_final: 0.8334 (mp10) REVERT: A 710 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8036 (p) REVERT: A 784 LYS cc_start: 0.8524 (ttpp) cc_final: 0.7874 (mtmm) REVERT: A 869 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: A 915 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7724 (tmtt) REVERT: A 936 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7655 (mtmt) REVERT: A 997 ASP cc_start: 0.8113 (t0) cc_final: 0.6934 (p0) REVERT: C 117 ASP cc_start: 0.7288 (t70) cc_final: 0.6960 (t70) outliers start: 27 outliers final: 19 residues processed: 105 average time/residue: 0.2389 time to fit residues: 34.7276 Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 464 MET 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 594 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 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 97 LEU 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 44 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101767 restraints weight = 12932.734| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.20 r_work: 0.3180 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2167 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= 0.131 Angle : 0.487 7.853 12392 Z= 0.251 Chirality : 0.041 0.131 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.878 59.489 1256 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.82 % Allowed : 9.38 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1126 helix: 1.54 (0.24), residues: 484 sheet: 0.16 (0.37), residues: 190 loop : -0.01 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 917 HIS 0.002 0.000 HIS A 818 PHE 0.010 0.001 PHE C 62 TYR 0.010 0.001 TYR A 81 ARG 0.007 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 419) hydrogen bonds : angle 4.09734 ( 1185) SS BOND : bond 0.00594 ( 1) SS BOND : angle 4.00534 ( 2) covalent geometry : bond 0.00321 ( 9140) covalent geometry : angle 0.48400 (12390) Misc. bond : bond 0.00085 ( 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 119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8973 (t) cc_final: 0.8674 (m) REVERT: A 218 MET cc_start: 0.7230 (mmm) cc_final: 0.6629 (mmm) REVERT: A 464 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7871 (pmt) REVERT: A 592 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8120 (tp) REVERT: A 600 ASN cc_start: 0.8986 (p0) cc_final: 0.8694 (p0) REVERT: A 675 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8393 (m-30) REVERT: A 699 GLN cc_start: 0.8607 (mp10) cc_final: 0.8316 (mp10) REVERT: A 710 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8027 (p) REVERT: A 784 LYS cc_start: 0.8528 (ttpp) cc_final: 0.7881 (mtmm) REVERT: A 869 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: A 915 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7707 (tmtt) REVERT: A 936 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7607 (mtmt) REVERT: A 997 ASP cc_start: 0.8096 (t0) cc_final: 0.6919 (p0) REVERT: C 117 ASP cc_start: 0.7255 (t70) cc_final: 0.6924 (t70) REVERT: C 143 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8196 (ttm110) outliers start: 28 outliers final: 19 residues processed: 106 average time/residue: 0.2171 time to fit residues: 32.1212 Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 464 MET 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 594 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 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 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 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.130235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.101735 restraints weight = 12896.761| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.23 r_work: 0.3174 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2175 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= 0.124 Angle : 0.490 8.263 12392 Z= 0.254 Chirality : 0.041 0.155 1374 Planarity : 0.004 0.046 1604 Dihedral : 5.882 59.551 1256 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.62 % Allowed : 9.78 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1126 helix: 1.55 (0.24), residues: 485 sheet: 0.17 (0.37), residues: 190 loop : 0.00 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 917 HIS 0.002 0.000 HIS A 818 PHE 0.030 0.001 PHE C 62 TYR 0.009 0.001 TYR A 81 ARG 0.006 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 419) hydrogen bonds : angle 4.06631 ( 1185) SS BOND : bond 0.00535 ( 1) SS BOND : angle 3.95671 ( 2) covalent geometry : bond 0.00302 ( 9140) covalent geometry : angle 0.48716 (12390) Misc. bond : bond 0.00065 ( 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 115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 SER cc_start: 0.8962 (t) cc_final: 0.8691 (m) REVERT: A 218 MET cc_start: 0.7283 (mmm) cc_final: 0.6659 (mmm) REVERT: A 464 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.7908 (pmt) REVERT: A 592 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8230 (tp) REVERT: A 600 ASN cc_start: 0.8935 (p0) cc_final: 0.8664 (p0) REVERT: A 675 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8383 (m-30) REVERT: A 699 GLN cc_start: 0.8581 (mp10) cc_final: 0.8355 (mp10) REVERT: A 710 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.8005 (p) REVERT: A 784 LYS cc_start: 0.8476 (ttpp) cc_final: 0.7852 (mtmm) REVERT: A 869 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: A 915 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7762 (tmtt) REVERT: A 936 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7696 (mtmt) REVERT: A 997 ASP cc_start: 0.8124 (t0) cc_final: 0.7001 (p0) REVERT: C 117 ASP cc_start: 0.7262 (t70) cc_final: 0.6957 (t70) REVERT: C 143 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8206 (ttm110) outliers start: 26 outliers final: 19 residues processed: 103 average time/residue: 0.2574 time to fit residues: 37.0991 Evaluate side-chains 113 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 464 MET 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 594 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 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 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 10 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.0020 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.130478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.101856 restraints weight = 12973.924| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.22 r_work: 0.3182 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9143 Z= 0.127 Angle : 0.491 8.179 12392 Z= 0.253 Chirality : 0.041 0.138 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.871 59.811 1256 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.62 % Allowed : 9.98 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1126 helix: 1.56 (0.24), residues: 485 sheet: 0.16 (0.37), residues: 190 loop : -0.00 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 917 HIS 0.003 0.001 HIS A 574 PHE 0.009 0.001 PHE A 237 TYR 0.009 0.001 TYR A 81 ARG 0.007 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 419) hydrogen bonds : angle 4.04003 ( 1185) SS BOND : bond 0.00556 ( 1) SS BOND : angle 3.91881 ( 2) covalent geometry : bond 0.00308 ( 9140) covalent geometry : angle 0.48851 (12390) 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: 4885.77 seconds wall clock time: 85 minutes 14.01 seconds (5114.01 seconds total)