Starting phenix.real_space_refine on Sun Aug 4 03:35:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5n_44218/08_2024/9b5n_44218.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5n_44218/08_2024/9b5n_44218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5n_44218/08_2024/9b5n_44218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5n_44218/08_2024/9b5n_44218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5n_44218/08_2024/9b5n_44218.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5n_44218/08_2024/9b5n_44218.cif" } resolution = 3.12 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= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6074 2.51 5 N 1573 2.21 5 O 1833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9527 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: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} 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: 7.51, per 1000 atoms: 0.79 Number of scatterers: 9527 At special positions: 0 Unit cell: (100.016, 100.016, 119.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 2 11.99 O 1833 8.00 N 1573 7.00 C 6074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.91 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.21 Conformation dependent library (CDL) restraints added in 1.8 seconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 47.3% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.909A 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: 3.709A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.886A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.342A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.485A 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: 3.781A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.521A pdb=" N ASP A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.273A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.672A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.660A 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 399 through 404 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.481A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.541A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.648A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.667A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.901A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.519A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.506A pdb=" N ASN A 597 " --> pdb=" O CYS A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.687A 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: 3.564A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.574A pdb=" N GLN A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 4.016A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.818A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.529A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.567A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 883' Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 98 through 112 removed outlier: 3.649A pdb=" N VAL C 102 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.841A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.408A 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: 4.117A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.117A 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: 6.441A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.148A 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: 6.340A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.518A 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: 6.340A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.141A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 66 " --> pdb=" O HIS C 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 12 through 16 460 hydrogen bonds defined for protein. 1257 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: 4.06 Time building geometry restraints manager: 4.60 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: 1616 1.27 - 1.40: 2291 1.40 - 1.54: 5675 1.54 - 1.67: 92 1.67 - 1.81: 64 Bond restraints: 9738 Sorted by residual: bond pdb=" C04 A1AIV D 101 " pdb=" C05 A1AIV D 101 " ideal model delta sigma weight residual 1.453 1.526 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.518 0.013 1.20e-02 6.94e+03 1.20e+00 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 9.18e-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 6.94e-01 ... (remaining 9733 not shown) Histogram of bond angle deviations from ideal: 99.65 - 115.53: 6288 115.53 - 131.42: 6895 131.42 - 147.30: 11 147.30 - 163.18: 0 163.18 - 179.07: 1 Bond angle restraints: 13195 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.17 -6.47 1.80e+00 3.09e-01 1.29e+01 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 104.50 7.33 2.67e+00 1.40e-01 7.55e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.36 4.83 1.76e+00 3.23e-01 7.53e+00 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.33 3.20 1.18e+00 7.24e-01 7.41e+00 angle pdb=" C03 A1AIV D 101 " pdb=" C02 A1AIV D 101 " pdb=" N01 A1AIV D 101 " ideal model delta sigma weight residual 111.06 103.08 7.98 3.00e+00 1.11e-01 7.07e+00 ... (remaining 13190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 5713 17.09 - 34.18: 166 34.18 - 51.27: 42 51.27 - 68.36: 6 68.36 - 85.45: 2 Dihedral angle restraints: 5929 sinusoidal: 2424 harmonic: 3505 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 -142.75 56.75 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CA TYR C 60 " pdb=" C TYR C 60 " pdb=" N PRO C 61 " pdb=" CA PRO C 61 " ideal model delta harmonic sigma weight residual 0.00 28.00 -28.00 0 5.00e+00 4.00e-02 3.14e+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 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 5926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1307 0.061 - 0.122: 145 0.122 - 0.183: 16 0.183 - 0.243: 1 0.243 - 0.304: 2 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" C5' ATP A1103 " pdb=" O4' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1468 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 100 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C SER C 100 " -0.036 2.00e-02 2.50e+03 pdb=" O SER C 100 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS C 101 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 103 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C LEU C 103 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU C 103 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU C 104 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 3 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C LEU C 3 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU C 3 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS C 4 " 0.010 2.00e-02 2.50e+03 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 63 2.58 - 3.16: 8029 3.16 - 3.74: 13805 3.74 - 4.32: 20329 4.32 - 4.90: 34667 Nonbonded interactions: 76893 Sorted by model distance: nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.000 3.040 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.033 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.039 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.055 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.067 2.170 ... (remaining 76888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 34.050 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 0.073 9738 Z= 0.226 Angle : 0.466 7.976 13195 Z= 0.238 Chirality : 0.042 0.304 1471 Planarity : 0.004 0.038 1707 Dihedral : 9.091 85.450 3662 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.50 % Favored : 97.25 % Rotamer: Outliers : 0.66 % Allowed : 3.68 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.07 (0.25), residues: 1199 helix: 1.54 (0.25), residues: 482 sheet: 0.09 (0.36), residues: 211 loop : 0.32 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS D 68 PHE 0.010 0.001 PHE A 842 TYR 0.011 0.001 TYR C 60 ARG 0.002 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 181 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8464 (mmp) cc_final: 0.8222 (mmm) REVERT: A 299 SER cc_start: 0.8395 (t) cc_final: 0.8161 (m) REVERT: A 368 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7985 (mm-30) REVERT: A 380 LEU cc_start: 0.8392 (mt) cc_final: 0.8039 (mp) REVERT: A 442 MET cc_start: 0.8989 (tpp) cc_final: 0.8658 (mmm) REVERT: A 723 ASP cc_start: 0.8116 (m-30) cc_final: 0.7791 (m-30) REVERT: A 869 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7853 (mm-30) REVERT: A 919 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8530 (ptp-170) REVERT: A 1011 LYS cc_start: 0.8423 (ttmm) cc_final: 0.8073 (tppt) REVERT: C 72 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.8126 (mmm-85) outliers start: 7 outliers final: 3 residues processed: 185 average time/residue: 0.3014 time to fit residues: 71.6645 Evaluate side-chains 138 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9738 Z= 0.246 Angle : 0.526 6.317 13195 Z= 0.277 Chirality : 0.043 0.185 1471 Planarity : 0.004 0.042 1707 Dihedral : 6.446 85.529 1339 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.41 % Rotamer: Outliers : 1.79 % Allowed : 7.07 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.23 (0.25), residues: 1199 helix: 1.75 (0.24), residues: 489 sheet: 0.35 (0.37), residues: 211 loop : 0.22 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 93 HIS 0.004 0.001 HIS D 68 PHE 0.012 0.001 PHE A 842 TYR 0.009 0.001 TYR A 235 ARG 0.005 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: A 201 ARG cc_start: 0.6888 (mtp-110) cc_final: 0.6521 (mtp-110) REVERT: A 299 SER cc_start: 0.8441 (t) cc_final: 0.8149 (m) REVERT: A 368 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8088 (mm-30) REVERT: A 380 LEU cc_start: 0.8503 (mt) cc_final: 0.8145 (mp) REVERT: A 442 MET cc_start: 0.9010 (tpp) cc_final: 0.8626 (mmm) REVERT: A 919 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8264 (ptp-170) REVERT: A 1011 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8060 (tppt) REVERT: C 72 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8175 (mmm-85) REVERT: C 97 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6806 (pt) REVERT: C 104 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7590 (pp) REVERT: C 135 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7634 (mm-30) outliers start: 19 outliers final: 8 residues processed: 142 average time/residue: 0.2788 time to fit residues: 52.6096 Evaluate side-chains 131 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9738 Z= 0.287 Angle : 0.518 6.929 13195 Z= 0.270 Chirality : 0.043 0.138 1471 Planarity : 0.004 0.046 1707 Dihedral : 6.391 89.250 1333 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.34 % Favored : 97.58 % Rotamer: Outliers : 1.89 % Allowed : 8.67 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.09 (0.25), residues: 1199 helix: 1.60 (0.24), residues: 489 sheet: 0.23 (0.37), residues: 215 loop : 0.20 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS A 458 PHE 0.012 0.001 PHE A 842 TYR 0.013 0.001 TYR D 59 ARG 0.005 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: A 299 SER cc_start: 0.8488 (t) cc_final: 0.8204 (m) REVERT: A 368 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8121 (mm-30) REVERT: A 380 LEU cc_start: 0.8597 (mt) cc_final: 0.8246 (mp) REVERT: A 442 MET cc_start: 0.9055 (tpp) cc_final: 0.8533 (mpp) REVERT: A 869 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: A 919 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8351 (ptp-170) REVERT: A 937 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 1011 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8161 (tppt) REVERT: C 38 MET cc_start: 0.7575 (mmp) cc_final: 0.6836 (mmt) REVERT: C 72 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8228 (mmm-85) REVERT: C 97 LEU cc_start: 0.7178 (pt) cc_final: 0.6735 (pt) REVERT: C 104 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7506 (pp) outliers start: 20 outliers final: 11 residues processed: 135 average time/residue: 0.2775 time to fit residues: 49.7678 Evaluate side-chains 127 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9738 Z= 0.307 Angle : 0.522 8.488 13195 Z= 0.272 Chirality : 0.043 0.165 1471 Planarity : 0.004 0.046 1707 Dihedral : 6.018 60.865 1332 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 2.54 % Allowed : 8.58 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1199 helix: 1.47 (0.24), residues: 495 sheet: 0.13 (0.36), residues: 215 loop : 0.18 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 458 PHE 0.011 0.001 PHE A 842 TYR 0.013 0.001 TYR D 59 ARG 0.005 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: A 299 SER cc_start: 0.8502 (t) cc_final: 0.8214 (m) REVERT: A 380 LEU cc_start: 0.8647 (mt) cc_final: 0.8308 (mp) REVERT: A 442 MET cc_start: 0.9069 (tpp) cc_final: 0.8506 (mpp) REVERT: A 526 PHE cc_start: 0.9495 (OUTLIER) cc_final: 0.9281 (m-80) REVERT: A 739 LYS cc_start: 0.8433 (tptp) cc_final: 0.7843 (ptpt) REVERT: A 869 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: A 919 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8575 (ptp-170) REVERT: A 937 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: A 1011 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8154 (tppt) REVERT: C 97 LEU cc_start: 0.7112 (pt) cc_final: 0.6700 (pt) REVERT: C 131 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8277 (mmm160) outliers start: 27 outliers final: 17 residues processed: 140 average time/residue: 0.2795 time to fit residues: 52.1215 Evaluate side-chains 132 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 79 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 103 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9738 Z= 0.164 Angle : 0.486 7.914 13195 Z= 0.251 Chirality : 0.041 0.155 1471 Planarity : 0.004 0.044 1707 Dihedral : 5.810 61.734 1332 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.75 % Favored : 98.17 % Rotamer: Outliers : 2.17 % Allowed : 9.52 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.15 (0.25), residues: 1199 helix: 1.57 (0.24), residues: 501 sheet: 0.28 (0.36), residues: 214 loop : 0.28 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 93 HIS 0.001 0.000 HIS C 75 PHE 0.009 0.001 PHE A 842 TYR 0.018 0.001 TYR A 235 ARG 0.006 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: A 299 SER cc_start: 0.8482 (t) cc_final: 0.8192 (m) REVERT: A 380 LEU cc_start: 0.8602 (mt) cc_final: 0.8350 (mp) REVERT: A 442 MET cc_start: 0.8972 (tpp) cc_final: 0.8651 (mmm) REVERT: A 526 PHE cc_start: 0.9461 (OUTLIER) cc_final: 0.9238 (m-80) REVERT: A 626 MET cc_start: 0.7993 (ttm) cc_final: 0.7761 (ttt) REVERT: A 739 LYS cc_start: 0.8392 (tptp) cc_final: 0.7827 (ptpt) REVERT: A 869 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: A 919 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8308 (ptp-170) REVERT: A 1011 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8144 (tppt) REVERT: C 38 MET cc_start: 0.7714 (mmp) cc_final: 0.6958 (mmt) REVERT: C 104 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7547 (pp) outliers start: 23 outliers final: 14 residues processed: 137 average time/residue: 0.2790 time to fit residues: 50.9610 Evaluate side-chains 134 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 0.0060 chunk 67 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 9 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9738 Z= 0.155 Angle : 0.488 8.635 13195 Z= 0.250 Chirality : 0.041 0.150 1471 Planarity : 0.004 0.044 1707 Dihedral : 5.633 59.293 1332 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.92 % Favored : 98.00 % Rotamer: Outliers : 2.26 % Allowed : 10.37 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.25), residues: 1199 helix: 1.72 (0.24), residues: 495 sheet: 0.32 (0.36), residues: 213 loop : 0.26 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 93 HIS 0.001 0.000 HIS A 818 PHE 0.008 0.001 PHE A 633 TYR 0.016 0.001 TYR A 235 ARG 0.013 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: A 218 MET cc_start: 0.6619 (mmm) cc_final: 0.5577 (mmt) REVERT: A 299 SER cc_start: 0.8513 (t) cc_final: 0.8222 (m) REVERT: A 380 LEU cc_start: 0.8569 (mt) cc_final: 0.8238 (mp) REVERT: A 442 MET cc_start: 0.8995 (tpp) cc_final: 0.8659 (mmm) REVERT: A 526 PHE cc_start: 0.9475 (OUTLIER) cc_final: 0.9250 (m-80) REVERT: A 626 MET cc_start: 0.7930 (ttm) cc_final: 0.7706 (ttt) REVERT: A 739 LYS cc_start: 0.8379 (tptp) cc_final: 0.7818 (ptpt) REVERT: A 869 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7792 (mm-30) REVERT: A 919 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8305 (ptp-170) REVERT: A 1011 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8130 (tppt) REVERT: C 38 MET cc_start: 0.7578 (mmp) cc_final: 0.6834 (mmt) REVERT: C 104 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7549 (pp) REVERT: C 131 ARG cc_start: 0.8487 (mmm-85) cc_final: 0.8191 (mmm160) REVERT: C 135 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7787 (mm-30) outliers start: 24 outliers final: 17 residues processed: 137 average time/residue: 0.2872 time to fit residues: 52.3872 Evaluate side-chains 139 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 84 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 0.0670 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9738 Z= 0.162 Angle : 0.492 7.070 13195 Z= 0.253 Chirality : 0.041 0.149 1471 Planarity : 0.003 0.043 1707 Dihedral : 5.503 57.724 1332 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.25 % Favored : 97.66 % Rotamer: Outliers : 2.26 % Allowed : 9.99 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.29 (0.25), residues: 1199 helix: 1.77 (0.24), residues: 495 sheet: 0.34 (0.36), residues: 213 loop : 0.28 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.003 0.000 HIS A 305 PHE 0.008 0.001 PHE A 633 TYR 0.015 0.001 TYR D 59 ARG 0.007 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: A 218 MET cc_start: 0.6671 (mmm) cc_final: 0.6368 (mmm) REVERT: A 299 SER cc_start: 0.8557 (t) cc_final: 0.8253 (m) REVERT: A 442 MET cc_start: 0.8990 (tpp) cc_final: 0.8656 (mmm) REVERT: A 526 PHE cc_start: 0.9474 (OUTLIER) cc_final: 0.9250 (m-80) REVERT: A 626 MET cc_start: 0.7944 (ttm) cc_final: 0.7703 (ttt) REVERT: A 739 LYS cc_start: 0.8347 (tptp) cc_final: 0.7746 (ptpt) REVERT: A 869 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: A 919 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8354 (ptp-170) REVERT: A 944 MET cc_start: 0.8024 (ttp) cc_final: 0.7548 (ttp) REVERT: A 1011 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8113 (tppt) REVERT: C 38 MET cc_start: 0.7529 (mmp) cc_final: 0.6777 (mmt) REVERT: D 59 TYR cc_start: 0.5004 (m-10) cc_final: 0.4542 (m-10) outliers start: 24 outliers final: 17 residues processed: 137 average time/residue: 0.2743 time to fit residues: 50.6622 Evaluate side-chains 141 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 109 optimal weight: 0.0970 chunk 100 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9738 Z= 0.195 Angle : 0.502 7.861 13195 Z= 0.259 Chirality : 0.041 0.145 1471 Planarity : 0.004 0.041 1707 Dihedral : 5.553 57.633 1332 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.25 % Favored : 97.66 % Rotamer: Outliers : 2.64 % Allowed : 10.08 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.25), residues: 1199 helix: 1.77 (0.24), residues: 495 sheet: 0.29 (0.36), residues: 213 loop : 0.23 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.009 0.001 PHE A 842 TYR 0.021 0.001 TYR D 59 ARG 0.006 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: A 205 GLU cc_start: 0.7975 (pm20) cc_final: 0.7706 (pm20) REVERT: A 218 MET cc_start: 0.6567 (mmm) cc_final: 0.6250 (mmm) REVERT: A 299 SER cc_start: 0.8563 (t) cc_final: 0.8266 (m) REVERT: A 442 MET cc_start: 0.9008 (tpp) cc_final: 0.8666 (mmm) REVERT: A 526 PHE cc_start: 0.9478 (OUTLIER) cc_final: 0.9260 (m-80) REVERT: A 626 MET cc_start: 0.7947 (ttm) cc_final: 0.7703 (ttt) REVERT: A 739 LYS cc_start: 0.8343 (tptp) cc_final: 0.7701 (ptpt) REVERT: A 869 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: A 919 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8334 (ptp-170) REVERT: A 937 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: A 944 MET cc_start: 0.8050 (ttp) cc_final: 0.7695 (ttp) REVERT: A 1011 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8139 (tppt) REVERT: C 38 MET cc_start: 0.7516 (mmp) cc_final: 0.6761 (mmt) outliers start: 28 outliers final: 22 residues processed: 140 average time/residue: 0.2671 time to fit residues: 50.1250 Evaluate side-chains 144 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.3980 chunk 109 optimal weight: 0.5980 chunk 64 optimal weight: 0.0670 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 chunk 113 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9738 Z= 0.164 Angle : 0.513 8.502 13195 Z= 0.264 Chirality : 0.041 0.168 1471 Planarity : 0.003 0.041 1707 Dihedral : 5.525 57.719 1332 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.17 % Favored : 97.75 % Rotamer: Outliers : 2.64 % Allowed : 10.65 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.29 (0.25), residues: 1199 helix: 1.82 (0.24), residues: 494 sheet: 0.34 (0.36), residues: 213 loop : 0.21 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS D 68 PHE 0.008 0.001 PHE A 633 TYR 0.020 0.001 TYR D 59 ARG 0.007 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: A 205 GLU cc_start: 0.7979 (pm20) cc_final: 0.7703 (pm20) REVERT: A 218 MET cc_start: 0.6531 (mmm) cc_final: 0.6226 (mmm) REVERT: A 299 SER cc_start: 0.8528 (t) cc_final: 0.8228 (m) REVERT: A 442 MET cc_start: 0.8986 (tpp) cc_final: 0.8655 (mmm) REVERT: A 526 PHE cc_start: 0.9475 (OUTLIER) cc_final: 0.9253 (m-80) REVERT: A 626 MET cc_start: 0.7960 (ttm) cc_final: 0.7729 (ttt) REVERT: A 699 GLN cc_start: 0.8081 (mp10) cc_final: 0.7856 (mp10) REVERT: A 739 LYS cc_start: 0.8338 (tptp) cc_final: 0.7705 (ptpt) REVERT: A 869 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7794 (mm-30) REVERT: A 937 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: A 944 MET cc_start: 0.8029 (ttp) cc_final: 0.7720 (ttp) REVERT: A 1011 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8111 (tppt) REVERT: C 38 MET cc_start: 0.7484 (mmp) cc_final: 0.6696 (mmt) REVERT: C 135 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7260 (mm-30) REVERT: D 51 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6506 (pm20) outliers start: 28 outliers final: 21 residues processed: 143 average time/residue: 0.2513 time to fit residues: 48.1087 Evaluate side-chains 142 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 118 optimal weight: 0.5980 chunk 109 optimal weight: 0.2980 chunk 94 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.0970 chunk 74 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9738 Z= 0.150 Angle : 0.498 8.884 13195 Z= 0.257 Chirality : 0.041 0.153 1471 Planarity : 0.004 0.042 1707 Dihedral : 5.332 57.944 1328 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.17 % Favored : 97.75 % Rotamer: Outliers : 2.26 % Allowed : 10.74 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.33 (0.25), residues: 1199 helix: 1.86 (0.24), residues: 494 sheet: 0.38 (0.36), residues: 213 loop : 0.21 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.001 0.000 HIS D 68 PHE 0.008 0.001 PHE A 633 TYR 0.017 0.001 TYR A 235 ARG 0.007 0.000 ARG C 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: A 205 GLU cc_start: 0.7986 (pm20) cc_final: 0.7716 (pm20) REVERT: A 218 MET cc_start: 0.6505 (mmm) cc_final: 0.6206 (mmm) REVERT: A 299 SER cc_start: 0.8548 (t) cc_final: 0.8256 (m) REVERT: A 442 MET cc_start: 0.8977 (tpp) cc_final: 0.8661 (mmm) REVERT: A 526 PHE cc_start: 0.9476 (OUTLIER) cc_final: 0.9253 (m-80) REVERT: A 626 MET cc_start: 0.7907 (ttm) cc_final: 0.7655 (ttt) REVERT: A 699 GLN cc_start: 0.8101 (mp10) cc_final: 0.7875 (mp10) REVERT: A 739 LYS cc_start: 0.8325 (tptp) cc_final: 0.7694 (ptpt) REVERT: A 869 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7796 (mm-30) REVERT: A 937 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: A 944 MET cc_start: 0.8003 (ttp) cc_final: 0.7767 (ttp) REVERT: A 1011 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8107 (tppt) REVERT: C 38 MET cc_start: 0.7461 (mmp) cc_final: 0.6649 (mmt) REVERT: C 104 LEU cc_start: 0.7880 (mm) cc_final: 0.7382 (pp) REVERT: C 135 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7239 (mm-30) REVERT: C 143 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7208 (mtm110) outliers start: 24 outliers final: 16 residues processed: 139 average time/residue: 0.3219 time to fit residues: 61.5833 Evaluate side-chains 137 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.133590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.084633 restraints weight = 13663.631| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.99 r_work: 0.2967 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9738 Z= 0.215 Angle : 0.522 9.748 13195 Z= 0.267 Chirality : 0.041 0.148 1471 Planarity : 0.004 0.053 1707 Dihedral : 5.387 57.823 1328 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.25 % Favored : 97.66 % Rotamer: Outliers : 2.17 % Allowed : 10.93 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 1.25 (0.25), residues: 1199 helix: 1.81 (0.24), residues: 493 sheet: 0.35 (0.36), residues: 213 loop : 0.15 (0.30), residues: 493 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 0.009 0.001 PHE A 842 TYR 0.019 0.001 TYR A 119 ARG 0.020 0.001 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: 2401.44 seconds wall clock time: 43 minutes 11.06 seconds (2591.06 seconds total)