Starting phenix.real_space_refine on Fri Nov 15 23:32:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3y_27168/11_2024/8d3y_27168.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3y_27168/11_2024/8d3y_27168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3y_27168/11_2024/8d3y_27168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3y_27168/11_2024/8d3y_27168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3y_27168/11_2024/8d3y_27168.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3y_27168/11_2024/8d3y_27168.cif" } resolution = 3.9 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= 0.005 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 S 58 5.16 5 Be 1 3.05 5 C 6340 2.51 5 N 1646 2.21 5 O 1850 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9898 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7341 Classifications: {'peptide': 982} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 41, 'TRANS': 940} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 187 Chain: "B" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2311 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 264} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 246 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Time building chain proxies: 5.61, per 1000 atoms: 0.57 Number of scatterers: 9898 At special positions: 0 Unit cell: (141.48, 122.04, 133.92, 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 58 16.00 F 3 9.00 O 1850 8.00 N 1646 7.00 C 6340 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 45.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 54 through 65 removed outlier: 4.250A pdb=" N ALA A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 removed outlier: 4.267A pdb=" N PHE A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 111 removed outlier: 4.097A pdb=" N LEU A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 143 removed outlier: 3.791A pdb=" N GLY A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.802A pdb=" N GLU A 174 " --> pdb=" O ASN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 removed outlier: 4.052A pdb=" N ARG A 254 " --> pdb=" O THR A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.513A pdb=" N PHE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 320 removed outlier: 3.572A pdb=" N VAL A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 removed outlier: 3.992A pdb=" N VAL A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 360 removed outlier: 4.114A pdb=" N THR A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 360' Processing helix chain 'A' and resid 405 through 419 Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.943A pdb=" N ARG A 435 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 456 through 464 removed outlier: 4.026A pdb=" N MET A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 523 through 537 removed outlier: 3.770A pdb=" N GLU A 534 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 536 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 removed outlier: 3.696A pdb=" N LEU A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 650 removed outlier: 3.594A pdb=" N ALA A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 661 removed outlier: 3.957A pdb=" N LYS A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 657 through 661' Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 684 through 698 removed outlier: 3.711A pdb=" N GLN A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 745 through 771 removed outlier: 3.927A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 786 Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 793 through 803 removed outlier: 3.715A pdb=" N ILE A 797 " --> pdb=" O GLY A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 812 Processing helix chain 'A' and resid 836 through 846 removed outlier: 4.020A pdb=" N GLN A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 865 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 876 through 881 Processing helix chain 'A' and resid 897 through 927 removed outlier: 3.504A pdb=" N ARG A 901 " --> pdb=" O THR A 897 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 959 removed outlier: 4.018A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 980 removed outlier: 3.837A pdb=" N PHE A 979 " --> pdb=" O SER A 976 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 980 " --> pdb=" O TRP A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'B' and resid 33 through 59 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.930A pdb=" N TYR B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 58 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.520A pdb=" N VAL A 161 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N CYS A 239 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU A 241 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS A 201 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A 243 " --> pdb=" O HIS A 199 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 247 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE A 195 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS A 201 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.520A pdb=" N VAL A 161 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N CYS A 239 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU A 241 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS A 201 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A 243 " --> pdb=" O HIS A 199 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 247 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE A 195 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 348 removed outlier: 5.951A pdb=" N GLY A 721 " --> pdb=" O MET A 738 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU A 740 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA A 723 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 702 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL A 722 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N PHE A 680 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 655 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 383 Processing sheet with id=AA5, first strand: chain 'A' and resid 422 through 423 removed outlier: 3.533A pdb=" N VAL A 422 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 438 " --> pdb=" O VAL A 422 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 466 through 469 removed outlier: 3.717A pdb=" N ALA A 468 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 494 " --> pdb=" O HIS A 483 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A 493 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 577 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS A 547 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N PHE A 575 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR A 549 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N LEU A 573 " --> pdb=" O TYR A 549 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU A 573 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLY A 577 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.625A pdb=" N ILE B 299 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 272 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 301 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR B 270 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 179 removed outlier: 3.691A pdb=" N ILE B 176 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 260 " --> pdb=" O PHE B 230 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1266 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: 3.52 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3224 1.34 - 1.46: 2195 1.46 - 1.58: 4595 1.58 - 1.70: 0 1.70 - 1.81: 85 Bond restraints: 10099 Sorted by residual: bond pdb=" C BFD A 366 " pdb=" O BFD A 366 " ideal model delta sigma weight residual 1.231 1.807 -0.576 2.00e-02 2.50e+03 8.30e+02 bond pdb=" CB BFD A 366 " pdb=" CG BFD A 366 " ideal model delta sigma weight residual 1.529 1.263 0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" OD1 BFD A 366 " pdb="BE BFD A 366 " ideal model delta sigma weight residual 1.737 1.528 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" F1 BFD A 366 " pdb="BE BFD A 366 " ideal model delta sigma weight residual 1.542 1.506 0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" F2 BFD A 366 " pdb="BE BFD A 366 " ideal model delta sigma weight residual 1.535 1.513 0.022 2.00e-02 2.50e+03 1.27e+00 ... (remaining 10094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.21: 13715 11.21 - 22.42: 2 22.42 - 33.62: 1 33.62 - 44.83: 0 44.83 - 56.04: 1 Bond angle restraints: 13719 Sorted by residual: angle pdb=" O BFD A 366 " pdb=" C BFD A 366 " pdb=" N LYS A 367 " ideal model delta sigma weight residual 123.00 66.96 56.04 1.60e+00 3.91e-01 1.23e+03 angle pdb=" CA BFD A 366 " pdb=" C BFD A 366 " pdb=" O BFD A 366 " ideal model delta sigma weight residual 120.80 94.22 26.58 1.70e+00 3.46e-01 2.45e+02 angle pdb=" CA BFD A 366 " pdb=" CB BFD A 366 " pdb=" CG BFD A 366 " ideal model delta sigma weight residual 112.84 131.42 -18.58 3.00e+00 1.11e-01 3.84e+01 angle pdb=" CB BFD A 366 " pdb=" CG BFD A 366 " pdb=" OD2 BFD A 366 " ideal model delta sigma weight residual 118.96 102.03 16.93 3.00e+00 1.11e-01 3.19e+01 angle pdb=" CB MET A 581 " pdb=" CG MET A 581 " pdb=" SD MET A 581 " ideal model delta sigma weight residual 112.70 122.54 -9.84 3.00e+00 1.11e-01 1.08e+01 ... (remaining 13714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5099 17.64 - 35.29: 729 35.29 - 52.93: 188 52.93 - 70.58: 30 70.58 - 88.22: 12 Dihedral angle restraints: 6058 sinusoidal: 2327 harmonic: 3731 Sorted by residual: dihedral pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " pdb=" SG CYS A 49 " pdb=" CB CYS A 49 " ideal model delta sinusoidal sigma weight residual 93.00 165.45 -72.45 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CA ILE A 285 " pdb=" C ILE A 285 " pdb=" N THR A 286 " pdb=" CA THR A 286 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLY B 30 " pdb=" C GLY B 30 " pdb=" N SER B 31 " pdb=" CA SER B 31 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 6055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1174 0.045 - 0.089: 335 0.089 - 0.134: 73 0.134 - 0.178: 2 0.178 - 0.223: 1 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CB ILE A 926 " pdb=" CA ILE A 926 " pdb=" CG1 ILE A 926 " pdb=" CG2 ILE A 926 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB THR A 233 " pdb=" CA THR A 233 " pdb=" OG1 THR A 233 " pdb=" CG2 THR A 233 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA MET B 121 " pdb=" N MET B 121 " pdb=" C MET B 121 " pdb=" CB MET B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1582 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BFD A 366 " 0.222 2.00e-02 2.50e+03 3.06e-01 9.38e+02 pdb=" C BFD A 366 " -0.495 2.00e-02 2.50e+03 pdb=" O BFD A 366 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 367 " 0.285 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 73 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO B 74 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 74 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 74 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 430 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 431 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " 0.022 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 859 2.74 - 3.28: 10133 3.28 - 3.82: 15922 3.82 - 4.36: 17798 4.36 - 4.90: 31014 Nonbonded interactions: 75726 Sorted by model distance: nonbonded pdb=" O THR A 607 " pdb=" OG1 THR A 683 " model vdw 2.198 3.040 nonbonded pdb=" OE2 GLU A 33 " pdb=" OH TYR A 45 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A 892 " pdb=" O SER B 62 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLN A 846 " pdb=" OH TYR A 991 " model vdw 2.258 3.040 nonbonded pdb=" O ARG B 150 " pdb=" OH TYR B 242 " model vdw 2.264 3.040 ... (remaining 75721 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 group one per residue 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.140 Find NCS groups from input model: 0.110 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 29.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.007 0.576 10099 Z= 0.371 Angle : 0.814 56.037 13719 Z= 0.443 Chirality : 0.041 0.223 1585 Planarity : 0.008 0.306 1766 Dihedral : 17.343 88.219 3655 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.19 % Allowed : 34.00 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.14 (0.24), residues: 1289 helix: 1.24 (0.24), residues: 517 sheet: -0.56 (0.47), residues: 123 loop : -1.12 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 896 HIS 0.002 0.001 HIS A 909 PHE 0.019 0.001 PHE A 296 TYR 0.010 0.001 TYR G 32 ARG 0.011 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 1.125 Fit side-chains REVERT: A 973 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8311 (pp) outliers start: 2 outliers final: 0 residues processed: 139 average time/residue: 0.1660 time to fit residues: 36.3333 Evaluate side-chains 134 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 973 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 140 GLN A 696 GLN A 895 GLN A 900 GLN B 69 GLN B 82 GLN B 256 GLN G 31 HIS G 35 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10099 Z= 0.196 Angle : 0.554 7.525 13719 Z= 0.285 Chirality : 0.041 0.145 1585 Planarity : 0.004 0.046 1766 Dihedral : 4.152 46.475 1389 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.46 % Allowed : 30.01 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.04 (0.24), residues: 1289 helix: 1.54 (0.24), residues: 524 sheet: -0.57 (0.46), residues: 135 loop : -1.16 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 977 HIS 0.002 0.001 HIS A 610 PHE 0.016 0.001 PHE B 230 TYR 0.013 0.001 TYR A 121 ARG 0.003 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 1.128 Fit side-chains REVERT: A 260 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7463 (mt) REVERT: A 341 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7835 (mtp) REVERT: A 446 LEU cc_start: 0.8656 (tt) cc_final: 0.8368 (mt) REVERT: A 923 ASP cc_start: 0.9014 (t0) cc_final: 0.8791 (t70) REVERT: A 973 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8407 (pp) REVERT: B 229 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.6675 (m-80) REVERT: B 275 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.5922 (pt0) outliers start: 47 outliers final: 24 residues processed: 175 average time/residue: 0.1688 time to fit residues: 45.5598 Evaluate side-chains 162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 79 optimal weight: 0.0050 chunk 32 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 0.0980 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10099 Z= 0.209 Angle : 0.552 7.478 13719 Z= 0.281 Chirality : 0.041 0.143 1585 Planarity : 0.004 0.040 1766 Dihedral : 4.117 41.460 1389 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 5.79 % Allowed : 29.72 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.02 (0.24), residues: 1289 helix: 1.59 (0.24), residues: 522 sheet: -0.78 (0.43), residues: 145 loop : -1.18 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 155 HIS 0.002 0.001 HIS A 909 PHE 0.013 0.001 PHE B 230 TYR 0.013 0.001 TYR A 532 ARG 0.002 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 142 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 260 ILE cc_start: 0.7647 (mt) cc_final: 0.7434 (mt) REVERT: A 283 GLN cc_start: 0.5942 (OUTLIER) cc_final: 0.5462 (mp10) REVERT: A 446 LEU cc_start: 0.8620 (tt) cc_final: 0.8373 (mt) REVERT: A 973 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8406 (pp) REVERT: B 229 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.6732 (m-80) REVERT: B 275 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.5946 (pt0) outliers start: 61 outliers final: 44 residues processed: 184 average time/residue: 0.1726 time to fit residues: 48.4088 Evaluate side-chains 184 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.0000 chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10099 Z= 0.298 Angle : 0.597 7.562 13719 Z= 0.305 Chirality : 0.043 0.142 1585 Planarity : 0.004 0.039 1766 Dihedral : 4.286 30.833 1389 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.06 % Favored : 92.86 % Rotamer: Outliers : 7.60 % Allowed : 28.58 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.20 (0.24), residues: 1289 helix: 1.45 (0.24), residues: 528 sheet: -1.16 (0.40), residues: 155 loop : -1.29 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 977 HIS 0.004 0.001 HIS A 909 PHE 0.017 0.001 PHE B 230 TYR 0.016 0.002 TYR A 532 ARG 0.005 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 138 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 260 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7651 (mt) REVERT: A 446 LEU cc_start: 0.8625 (tt) cc_final: 0.8358 (mt) REVERT: A 529 GLN cc_start: 0.8314 (tp-100) cc_final: 0.8036 (tp40) REVERT: A 591 ASP cc_start: 0.7942 (t0) cc_final: 0.7718 (t0) REVERT: A 827 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8864 (ptt-90) REVERT: A 973 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8479 (pp) REVERT: B 187 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8576 (ptpt) REVERT: B 229 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.6660 (m-80) REVERT: B 275 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.5804 (pt0) outliers start: 80 outliers final: 60 residues processed: 195 average time/residue: 0.1705 time to fit residues: 50.7905 Evaluate side-chains 197 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 131 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10099 Z= 0.195 Angle : 0.565 11.015 13719 Z= 0.282 Chirality : 0.041 0.153 1585 Planarity : 0.004 0.039 1766 Dihedral : 4.143 30.209 1389 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.74 % Allowed : 29.91 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.01 (0.24), residues: 1289 helix: 1.61 (0.24), residues: 528 sheet: -0.92 (0.42), residues: 145 loop : -1.21 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 977 HIS 0.002 0.001 HIS A 610 PHE 0.014 0.001 PHE B 230 TYR 0.014 0.001 TYR A 532 ARG 0.002 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 145 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 260 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7643 (mp) REVERT: A 446 LEU cc_start: 0.8662 (tt) cc_final: 0.8424 (mt) REVERT: A 591 ASP cc_start: 0.7956 (t0) cc_final: 0.7670 (t0) REVERT: A 973 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8418 (pp) REVERT: B 229 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.6651 (m-80) REVERT: B 275 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.5789 (pt0) outliers start: 71 outliers final: 52 residues processed: 192 average time/residue: 0.1772 time to fit residues: 52.0819 Evaluate side-chains 195 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 139 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10099 Z= 0.227 Angle : 0.568 9.170 13719 Z= 0.286 Chirality : 0.042 0.173 1585 Planarity : 0.004 0.039 1766 Dihedral : 4.121 30.267 1389 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.52 % Favored : 93.41 % Rotamer: Outliers : 7.12 % Allowed : 30.39 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.01 (0.24), residues: 1289 helix: 1.65 (0.24), residues: 523 sheet: -1.15 (0.40), residues: 155 loop : -1.18 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 155 HIS 0.002 0.001 HIS A 610 PHE 0.014 0.001 PHE B 230 TYR 0.015 0.001 TYR A 532 ARG 0.005 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 142 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: A 260 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7659 (mp) REVERT: A 446 LEU cc_start: 0.8627 (tt) cc_final: 0.8409 (mt) REVERT: A 591 ASP cc_start: 0.8049 (t0) cc_final: 0.7699 (t0) REVERT: A 711 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7082 (t0) REVERT: A 973 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8422 (pp) REVERT: B 229 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.6734 (m-80) REVERT: B 275 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.5885 (pt0) outliers start: 75 outliers final: 61 residues processed: 192 average time/residue: 0.1814 time to fit residues: 52.9961 Evaluate side-chains 203 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 137 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 7.9990 chunk 71 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10099 Z= 0.155 Angle : 0.544 8.503 13719 Z= 0.272 Chirality : 0.041 0.189 1585 Planarity : 0.003 0.039 1766 Dihedral : 3.965 30.146 1389 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 5.70 % Allowed : 31.43 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.15 (0.24), residues: 1289 helix: 1.74 (0.24), residues: 524 sheet: -1.05 (0.43), residues: 133 loop : -1.08 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 896 HIS 0.002 0.000 HIS A 610 PHE 0.013 0.001 PHE B 230 TYR 0.016 0.001 TYR A 532 ARG 0.004 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 146 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: A 260 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7718 (mp) REVERT: A 277 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8507 (mm-30) REVERT: A 591 ASP cc_start: 0.8060 (t0) cc_final: 0.7714 (t0) REVERT: A 973 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8382 (pp) REVERT: B 57 MET cc_start: 0.8310 (tmm) cc_final: 0.8068 (tmm) REVERT: B 229 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.6748 (m-80) REVERT: B 272 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.6993 (tp) REVERT: B 275 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.5979 (pt0) outliers start: 60 outliers final: 46 residues processed: 187 average time/residue: 0.1821 time to fit residues: 51.7509 Evaluate side-chains 190 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10099 Z= 0.257 Angle : 0.589 8.792 13719 Z= 0.296 Chirality : 0.043 0.208 1585 Planarity : 0.004 0.040 1766 Dihedral : 4.096 29.879 1389 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.52 % Favored : 93.41 % Rotamer: Outliers : 6.74 % Allowed : 30.67 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.00 (0.24), residues: 1289 helix: 1.66 (0.24), residues: 528 sheet: -1.25 (0.39), residues: 165 loop : -1.17 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 896 HIS 0.002 0.001 HIS A 909 PHE 0.015 0.001 PHE G 44 TYR 0.016 0.001 TYR A 532 ARG 0.005 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 142 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 254 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8755 (mtm-85) REVERT: A 257 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7302 (tmm) REVERT: A 260 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7687 (mp) REVERT: A 263 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7160 (mp) REVERT: A 591 ASP cc_start: 0.8107 (t0) cc_final: 0.7747 (t0) REVERT: A 697 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7923 (ptp-110) REVERT: A 711 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7114 (t0) REVERT: A 973 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8433 (pp) REVERT: B 229 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.6810 (m-80) REVERT: B 268 MET cc_start: 0.7764 (mpp) cc_final: 0.7275 (mtm) REVERT: B 272 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7025 (tp) REVERT: B 275 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5835 (pt0) outliers start: 71 outliers final: 54 residues processed: 188 average time/residue: 0.1833 time to fit residues: 51.6469 Evaluate side-chains 202 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 138 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.0670 chunk 119 optimal weight: 10.0000 chunk 69 optimal weight: 0.0980 chunk 50 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 10099 Z= 0.149 Angle : 0.560 8.110 13719 Z= 0.278 Chirality : 0.041 0.224 1585 Planarity : 0.004 0.039 1766 Dihedral : 3.913 29.620 1389 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 5.03 % Allowed : 32.86 % Favored : 62.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.20 (0.24), residues: 1289 helix: 1.76 (0.24), residues: 529 sheet: -0.98 (0.43), residues: 141 loop : -1.05 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 896 HIS 0.002 0.000 HIS A 909 PHE 0.019 0.001 PHE G 44 TYR 0.018 0.001 TYR A 532 ARG 0.004 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 140 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7276 (tmm) REVERT: A 260 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7843 (mp) REVERT: A 591 ASP cc_start: 0.8120 (t0) cc_final: 0.7798 (t0) REVERT: A 711 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7022 (t0) REVERT: A 973 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8356 (pp) REVERT: B 229 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: B 268 MET cc_start: 0.7759 (mpp) cc_final: 0.7326 (mtm) REVERT: B 272 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6870 (tp) REVERT: B 275 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.5969 (pt0) outliers start: 53 outliers final: 39 residues processed: 176 average time/residue: 0.2072 time to fit residues: 55.9993 Evaluate side-chains 182 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 118 optimal weight: 0.0030 chunk 102 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 0.0060 overall best weight: 0.5208 ------------------------------------------------------------------------------- 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: 0.7918 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 10099 Z= 0.149 Angle : 0.558 8.675 13719 Z= 0.276 Chirality : 0.041 0.211 1585 Planarity : 0.004 0.041 1766 Dihedral : 3.834 30.445 1389 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.34 % Rotamer: Outliers : 4.56 % Allowed : 33.71 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.26 (0.24), residues: 1289 helix: 1.76 (0.24), residues: 530 sheet: -1.11 (0.44), residues: 134 loop : -0.94 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 977 HIS 0.001 0.000 HIS G 31 PHE 0.018 0.001 PHE G 44 TYR 0.018 0.001 TYR A 532 ARG 0.004 0.000 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7236 (tmm) REVERT: A 260 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7912 (mp) REVERT: A 591 ASP cc_start: 0.8115 (t0) cc_final: 0.7775 (t0) REVERT: A 638 LEU cc_start: 0.6646 (pt) cc_final: 0.6250 (tp) REVERT: A 697 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7962 (ttp-110) REVERT: A 711 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7024 (t0) REVERT: A 973 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8349 (pp) REVERT: B 229 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: B 268 MET cc_start: 0.7756 (mpp) cc_final: 0.7348 (mtm) REVERT: B 272 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6706 (tp) REVERT: B 275 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.5983 (pt0) outliers start: 48 outliers final: 37 residues processed: 172 average time/residue: 0.1758 time to fit residues: 46.4865 Evaluate side-chains 179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112657 restraints weight = 16784.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113423 restraints weight = 10140.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114111 restraints weight = 7727.583| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10099 Z= 0.149 Angle : 0.560 10.006 13719 Z= 0.275 Chirality : 0.041 0.219 1585 Planarity : 0.004 0.041 1766 Dihedral : 3.744 29.624 1389 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 4.65 % Allowed : 33.71 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.28 (0.24), residues: 1289 helix: 1.80 (0.24), residues: 534 sheet: -1.03 (0.43), residues: 146 loop : -0.98 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 977 HIS 0.002 0.000 HIS A 909 PHE 0.017 0.001 PHE G 44 TYR 0.019 0.001 TYR A 532 ARG 0.004 0.000 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2052.88 seconds wall clock time: 38 minutes 9.26 seconds (2289.26 seconds total)