Starting phenix.real_space_refine on Thu Jan 16 03:28:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5t_44224/01_2025/9b5t_44224.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5t_44224/01_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_44224/01_2025/9b5t_44224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5t_44224/01_2025/9b5t_44224.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5t_44224/01_2025/9b5t_44224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5t_44224/01_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-5571/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: 6.46, 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: 2.53 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: 1.34 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: 3.47 Time building geometry restraints manager: 2.89 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: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.530 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.550 ------------------------------------------------------------------------------- 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 : 0.003 0.071 9140 Z= 0.180 Angle : 0.445 6.363 12390 Z= 0.222 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 *********************** 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 : 1.194 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: 0.3009 time to fit residues: 69.8231 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 : 1.144 ------------------------------------------------------------------------------- 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 9140 Z= 0.227 Angle : 0.506 5.729 12390 Z= 0.267 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 *********************** 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 : 1.157 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: 0.2852 time to fit residues: 46.8888 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 : 1.127 ------------------------------------------------------------------------------- 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 9140 Z= 0.321 Angle : 0.526 5.380 12390 Z= 0.277 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 *********************** 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 : 1.187 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: 0.2575 time to fit residues: 37.8300 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 : 1.040 ------------------------------------------------------------------------------- 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 9140 Z= 0.162 Angle : 0.463 5.500 12390 Z= 0.242 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 *********************** 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 : 0.909 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: 0.2862 time to fit residues: 40.3150 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 : 1.099 ------------------------------------------------------------------------------- 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 9140 Z= 0.235 Angle : 0.490 8.809 12390 Z= 0.253 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 *********************** 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 : 1.181 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: 0.2460 time to fit residues: 35.8152 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 : 1.070 ------------------------------------------------------------------------------- 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: 0.0000 chunk 20 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.129948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.101311 restraints weight = 12849.593| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.24 r_work: 0.3163 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9140 Z= 0.201 Angle : 0.480 7.556 12390 Z= 0.248 Chirality : 0.041 0.132 1374 Planarity : 0.004 0.042 1604 Dihedral : 5.917 59.718 1256 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.32 % Allowed : 9.48 % 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: 1.01 (0.25), residues: 1126 helix: 1.54 (0.24), residues: 485 sheet: 0.21 (0.38), residues: 190 loop : 0.04 (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 0.029 0.001 PHE C 62 TYR 0.010 0.001 TYR A 81 ARG 0.004 0.000 ARG C 8 *********************** 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: 23 poor density : 91 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8967 (t) cc_final: 0.8689 (m) REVERT: A 135 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7741 (mtmt) REVERT: A 218 MET cc_start: 0.7229 (mmm) cc_final: 0.6645 (mmm) REVERT: A 464 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.7910 (pmt) REVERT: A 592 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8244 (tp) REVERT: A 675 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8391 (m-30) REVERT: A 699 GLN cc_start: 0.8620 (mp10) cc_final: 0.8331 (mp10) REVERT: A 710 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8020 (p) REVERT: A 784 LYS cc_start: 0.8559 (ttpp) cc_final: 0.8087 (ptpp) REVERT: A 869 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: A 915 LYS cc_start: 0.8254 (mttp) cc_final: 0.7728 (tmtt) REVERT: A 936 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7731 (mtmt) REVERT: A 997 ASP cc_start: 0.8110 (t0) cc_final: 0.6927 (p0) REVERT: C 117 ASP cc_start: 0.7277 (t70) cc_final: 0.6958 (t70) REVERT: C 143 ARG cc_start: 0.8767 (tmm-80) cc_final: 0.8514 (ttp-110) outliers start: 23 outliers final: 17 residues processed: 103 average time/residue: 0.2431 time to fit residues: 34.4890 Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.129720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.101249 restraints weight = 12947.900| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.22 r_work: 0.3167 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9140 Z= 0.243 Angle : 0.490 6.936 12390 Z= 0.253 Chirality : 0.042 0.131 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.889 59.670 1256 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.62 % Allowed : 9.68 % Favored : 87.70 % 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 669 HIS 0.002 0.000 HIS A 818 PHE 0.013 0.001 PHE C 62 TYR 0.011 0.001 TYR A 81 ARG 0.002 0.000 ARG C 143 *********************** 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 115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8968 (t) cc_final: 0.8698 (m) REVERT: A 218 MET cc_start: 0.7279 (mmm) cc_final: 0.6696 (mmm) REVERT: A 464 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.7947 (pmt) REVERT: A 592 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8305 (tp) REVERT: A 675 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8396 (m-30) REVERT: A 699 GLN cc_start: 0.8613 (mp10) cc_final: 0.8350 (mp10) REVERT: A 710 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8009 (p) REVERT: A 784 LYS cc_start: 0.8522 (ttpp) cc_final: 0.8097 (ptpp) REVERT: A 869 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: A 915 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7753 (tmtt) REVERT: A 936 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7702 (mtmt) REVERT: A 997 ASP cc_start: 0.8130 (t0) cc_final: 0.6989 (p0) REVERT: C 143 ARG cc_start: 0.8704 (tmm-80) cc_final: 0.8446 (ttp-110) outliers start: 26 outliers final: 19 residues processed: 102 average time/residue: 0.2399 time to fit residues: 33.8301 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 : 1.026 ------------------------------------------------------------------------------- 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=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: 0.8980 chunk 84 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 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 = 0.3663 r_free = 0.3663 target = 0.129405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100390 restraints weight = 13121.256| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.30 r_work: 0.3154 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9140 Z= 0.246 Angle : 0.492 7.405 12390 Z= 0.254 Chirality : 0.042 0.132 1374 Planarity : 0.004 0.044 1604 Dihedral : 5.899 59.376 1256 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.82 % Allowed : 9.78 % 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: 0.94 (0.25), residues: 1126 helix: 1.49 (0.24), residues: 485 sheet: 0.16 (0.37), residues: 193 loop : -0.01 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 PHE 0.027 0.001 PHE C 62 TYR 0.011 0.001 TYR A 81 ARG 0.002 0.000 ARG C 143 *********************** 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: 28 poor density : 90 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9009 (t) cc_final: 0.8731 (m) REVERT: A 218 MET cc_start: 0.7321 (mmm) cc_final: 0.6747 (mmm) REVERT: A 464 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8018 (pmt) REVERT: A 592 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8193 (tp) REVERT: A 675 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: A 699 GLN cc_start: 0.8624 (mp10) cc_final: 0.8344 (mp10) REVERT: A 710 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8033 (p) REVERT: A 784 LYS cc_start: 0.8522 (ttpp) cc_final: 0.7872 (mtmm) REVERT: A 869 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: A 915 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7743 (tmtt) REVERT: A 936 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7656 (mtmt) REVERT: A 997 ASP cc_start: 0.8122 (t0) cc_final: 0.6950 (p0) REVERT: C 117 ASP cc_start: 0.7376 (t0) cc_final: 0.6832 (t70) REVERT: C 143 ARG cc_start: 0.8738 (tmm-80) cc_final: 0.8480 (ttp-110) outliers start: 28 outliers final: 18 residues processed: 106 average time/residue: 0.2537 time to fit residues: 37.3274 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 : 0.977 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.129677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100721 restraints weight = 12933.505| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.29 r_work: 0.3164 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9140 Z= 0.223 Angle : 0.489 7.817 12390 Z= 0.253 Chirality : 0.042 0.131 1374 Planarity : 0.004 0.044 1604 Dihedral : 5.900 59.362 1256 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.62 % Allowed : 9.68 % Favored : 87.70 % 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: 0.92 (0.25), residues: 1126 helix: 1.49 (0.24), residues: 484 sheet: 0.14 (0.37), residues: 190 loop : -0.03 (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 0.012 0.001 PHE C 62 TYR 0.010 0.001 TYR A 81 ARG 0.006 0.000 ARG C 8 *********************** 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 118 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8996 (t) cc_final: 0.8705 (m) REVERT: A 218 MET cc_start: 0.7253 (mmm) cc_final: 0.6652 (mmm) REVERT: A 464 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7909 (pmt) REVERT: A 592 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8175 (tp) REVERT: A 675 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8393 (m-30) REVERT: A 699 GLN cc_start: 0.8594 (mp10) cc_final: 0.8319 (mp10) REVERT: A 710 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8035 (p) REVERT: A 784 LYS cc_start: 0.8527 (ttpp) cc_final: 0.7876 (mtmm) REVERT: A 869 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: A 915 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7736 (tmtt) REVERT: A 936 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7644 (mtmt) REVERT: A 997 ASP cc_start: 0.8109 (t0) cc_final: 0.6935 (p0) REVERT: C 117 ASP cc_start: 0.7464 (t0) cc_final: 0.6847 (t70) REVERT: C 143 ARG cc_start: 0.8737 (tmm-80) cc_final: 0.8478 (ttp-110) outliers start: 26 outliers final: 18 residues processed: 105 average time/residue: 0.2365 time to fit residues: 34.6779 Evaluate side-chains 115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 10 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.130195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101645 restraints weight = 12904.844| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.21 r_work: 0.3178 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9140 Z= 0.213 Angle : 0.492 8.325 12390 Z= 0.255 Chirality : 0.042 0.163 1374 Planarity : 0.004 0.044 1604 Dihedral : 5.909 59.363 1256 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.84 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: 0.94 (0.25), residues: 1126 helix: 1.52 (0.24), residues: 485 sheet: 0.16 (0.37), residues: 190 loop : -0.03 (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 0.024 0.001 PHE C 62 TYR 0.010 0.001 TYR A 81 ARG 0.007 0.000 ARG C 8 ********************** 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 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 SER cc_start: 0.8980 (t) cc_final: 0.8680 (m) REVERT: A 218 MET cc_start: 0.7229 (mmm) cc_final: 0.6605 (mmm) REVERT: A 464 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7887 (pmt) REVERT: A 592 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8132 (tp) REVERT: A 675 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8393 (m-30) REVERT: A 699 GLN cc_start: 0.8581 (mp10) cc_final: 0.8299 (mp10) REVERT: A 710 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8026 (p) REVERT: A 784 LYS cc_start: 0.8530 (ttpp) cc_final: 0.7880 (mtmm) REVERT: A 869 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: A 915 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7715 (tmtt) REVERT: A 936 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7620 (mtmt) REVERT: A 997 ASP cc_start: 0.8089 (t0) cc_final: 0.6906 (p0) REVERT: C 117 ASP cc_start: 0.7509 (t0) cc_final: 0.6820 (t70) outliers start: 27 outliers final: 18 residues processed: 103 average time/residue: 0.2368 time to fit residues: 33.9564 Evaluate side-chains 111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 106 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101411 restraints weight = 12997.168| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.23 r_work: 0.3173 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9140 Z= 0.219 Angle : 0.496 8.211 12390 Z= 0.257 Chirality : 0.042 0.141 1374 Planarity : 0.004 0.044 1604 Dihedral : 5.935 59.392 1256 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.52 % Allowed : 10.08 % 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: 0.94 (0.25), residues: 1126 helix: 1.51 (0.24), residues: 485 sheet: 0.15 (0.37), residues: 193 loop : -0.03 (0.30), residues: 448 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 0.009 0.001 PHE A 237 TYR 0.010 0.001 TYR A 81 ARG 0.008 0.000 ARG C 8 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 4709.11 seconds wall clock time: 84 minutes 22.98 seconds (5062.98 seconds total)