Starting phenix.real_space_refine on Thu Feb 15 21:38:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aiq_11802/02_2024/7aiq_11802_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aiq_11802/02_2024/7aiq_11802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aiq_11802/02_2024/7aiq_11802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aiq_11802/02_2024/7aiq_11802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aiq_11802/02_2024/7aiq_11802_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aiq_11802/02_2024/7aiq_11802_updated.pdb" } resolution = 3.72 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= 0.005 sd= 0.039 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 96 5.16 5 C 8769 2.51 5 N 2223 2.21 5 O 2422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B GLU 843": "OE1" <-> "OE2" Residue "B GLU 909": "OE1" <-> "OE2" Residue "B GLU 924": "OE1" <-> "OE2" Residue "B GLU 1051": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13514 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 6695 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 38, 'TRANS': 839} Chain breaks: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 6659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6659 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 37, 'TRANS': 829} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.39, per 1000 atoms: 0.55 Number of scatterers: 13514 At special positions: 0 Unit cell: (107.1, 111.35, 151.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 4 15.00 O 2422 8.00 N 2223 7.00 C 8769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.04 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.04 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 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=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A1101 " - " ASN A 361 " " NAG B1101 " - " ASN B 361 " " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN B 312 " Time building additional restraints: 5.35 Conformation dependent library (CDL) restraints added in 2.3 seconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3210 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 8 sheets defined 54.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 121 through 132 removed outlier: 6.010A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 142 through 176 removed outlier: 6.496A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 193 removed outlier: 4.146A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 226 removed outlier: 3.518A pdb=" N LEU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 268 Processing helix chain 'A' and resid 270 through 300 removed outlier: 5.445A pdb=" N SER A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 420 through 430 Proline residue: A 429 - end of helix Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 447 through 476 Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 505 through 535 removed outlier: 3.654A pdb=" N ILE A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 574 through 601 Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 616 through 633 Processing helix chain 'A' and resid 635 through 660 Processing helix chain 'A' and resid 665 through 681 Processing helix chain 'A' and resid 709 through 719 removed outlier: 3.746A pdb=" N THR A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 755 Processing helix chain 'A' and resid 770 through 779 Processing helix chain 'A' and resid 806 through 819 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 855 through 866 Proline residue: A 862 - end of helix Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 888 through 902 removed outlier: 3.660A pdb=" N HIS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 931 removed outlier: 3.861A pdb=" N GLU A 924 " --> pdb=" O ALA A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1032 removed outlier: 3.604A pdb=" N ARG A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1063 Processing helix chain 'B' and resid 121 through 132 removed outlier: 5.912A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 142 through 176 removed outlier: 6.623A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 193 Processing helix chain 'B' and resid 195 through 226 removed outlier: 3.603A pdb=" N LEU B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 268 Processing helix chain 'B' and resid 270 through 300 removed outlier: 5.652A pdb=" N SER B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 355 through 359 Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 421 through 431 Proline residue: B 429 - end of helix Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 447 through 476 Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'B' and resid 505 through 535 removed outlier: 3.627A pdb=" N ILE B 509 " --> pdb=" O TRP B 505 " (cutoff:3.500A) Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 558 through 571 removed outlier: 4.535A pdb=" N ILE B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 602 Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 616 through 633 Processing helix chain 'B' and resid 635 through 660 Processing helix chain 'B' and resid 665 through 681 Processing helix chain 'B' and resid 710 through 719 Processing helix chain 'B' and resid 739 through 755 Processing helix chain 'B' and resid 770 through 779 removed outlier: 3.622A pdb=" N ALA B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 819 removed outlier: 3.591A pdb=" N ASP B 813 " --> pdb=" O LYS B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 855 through 866 Proline residue: B 862 - end of helix Processing helix chain 'B' and resid 869 through 871 No H-bonds generated for 'chain 'B' and resid 869 through 871' Processing helix chain 'B' and resid 888 through 902 removed outlier: 3.832A pdb=" N HIS B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 925 removed outlier: 5.263A pdb=" N ALA B 920 " --> pdb=" O SER B 916 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR B 921 " --> pdb=" O ASP B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1032 removed outlier: 3.504A pdb=" N MET B1019 " --> pdb=" O ASN B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1063 Processing sheet with id= A, first strand: chain 'A' and resid 306 through 310 Processing sheet with id= B, first strand: chain 'A' and resid 326 through 329 Processing sheet with id= C, first strand: chain 'A' and resid 1039 through 1042 removed outlier: 3.713A pdb=" N VAL A1073 " --> pdb=" O LEU A1041 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL A1070 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A1072 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 726 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE A 761 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N SER A 729 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN A 763 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE A 731 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 765 " --> pdb=" O ILE A 731 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 845 through 848 removed outlier: 5.962A pdb=" N ARG A 875 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 848 " --> pdb=" O ARG A 875 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG A 877 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU A 907 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N THR A 880 " --> pdb=" O GLU A 907 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLU A 909 " --> pdb=" O THR A 880 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 306 through 310 Processing sheet with id= F, first strand: chain 'B' and resid 326 through 329 Processing sheet with id= G, first strand: chain 'B' and resid 1039 through 1042 removed outlier: 3.701A pdb=" N VAL B1073 " --> pdb=" O LEU B1041 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B1070 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B1072 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE B 761 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N SER B 729 " --> pdb=" O PHE B 761 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN B 763 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE B 731 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 765 " --> pdb=" O ILE B 731 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 845 through 848 removed outlier: 6.310A pdb=" N ARG B 875 " --> pdb=" O ILE B 846 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL B 848 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG B 877 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU B 907 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR B 880 " --> pdb=" O GLU B 907 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU B 909 " --> pdb=" O THR B 880 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 666 hydrogen bonds defined for protein. 1992 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: 4.44 Time building geometry restraints manager: 5.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4235 1.35 - 1.47: 3479 1.47 - 1.59: 5957 1.59 - 1.72: 8 1.72 - 1.84: 152 Bond restraints: 13831 Sorted by residual: bond pdb=" C4 ATP B1102 " pdb=" C5 ATP B1102 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.71e+01 bond pdb=" C4 ATP A1102 " pdb=" C5 ATP A1102 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.47e+01 bond pdb=" C5 ATP B1102 " pdb=" C6 ATP B1102 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.08e+01 bond pdb=" O1B ATP B1102 " pdb=" PB ATP B1102 " ideal model delta sigma weight residual 1.477 1.609 -0.132 2.20e-02 2.07e+03 3.58e+01 bond pdb=" O1B ATP A1102 " pdb=" PB ATP A1102 " ideal model delta sigma weight residual 1.477 1.607 -0.130 2.20e-02 2.07e+03 3.48e+01 ... (remaining 13826 not shown) Histogram of bond angle deviations from ideal: 98.83 - 106.21: 391 106.21 - 113.60: 8139 113.60 - 120.98: 6774 120.98 - 128.37: 3402 128.37 - 135.75: 138 Bond angle restraints: 18844 Sorted by residual: angle pdb=" PA ATP A1102 " pdb=" O3A ATP A1102 " pdb=" PB ATP A1102 " ideal model delta sigma weight residual 136.83 122.89 13.94 1.00e+00 1.00e+00 1.94e+02 angle pdb=" PA ATP B1102 " pdb=" O3A ATP B1102 " pdb=" PB ATP B1102 " ideal model delta sigma weight residual 136.83 124.70 12.13 1.00e+00 1.00e+00 1.47e+02 angle pdb=" C5 ATP B1102 " pdb=" C4 ATP B1102 " pdb=" N3 ATP B1102 " ideal model delta sigma weight residual 126.80 118.38 8.42 1.00e+00 1.00e+00 7.08e+01 angle pdb=" C5 ATP A1102 " pdb=" C4 ATP A1102 " pdb=" N3 ATP A1102 " ideal model delta sigma weight residual 126.80 118.45 8.35 1.00e+00 1.00e+00 6.97e+01 angle pdb=" N3 ATP B1102 " pdb=" C4 ATP B1102 " pdb=" N9 ATP B1102 " ideal model delta sigma weight residual 127.04 135.12 -8.08 1.15e+00 7.59e-01 4.95e+01 ... (remaining 18839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.48: 7549 24.48 - 48.97: 596 48.97 - 73.45: 63 73.45 - 97.93: 23 97.93 - 122.41: 25 Dihedral angle restraints: 8256 sinusoidal: 3245 harmonic: 5011 Sorted by residual: dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 353 " pdb=" CB CYS A 353 " ideal model delta sinusoidal sigma weight residual 93.00 138.12 -45.12 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " pdb=" SG CYS B 353 " pdb=" CB CYS B 353 " ideal model delta sinusoidal sigma weight residual 93.00 134.12 -41.12 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C5 NAG C 2 " ideal model delta sinusoidal sigma weight residual -62.96 59.45 -122.41 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 8253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1563 0.051 - 0.103: 541 0.103 - 0.154: 103 0.154 - 0.205: 17 0.205 - 0.257: 5 Chirality restraints: 2229 Sorted by residual: chirality pdb=" CB VAL A 881 " pdb=" CA VAL A 881 " pdb=" CG1 VAL A 881 " pdb=" CG2 VAL A 881 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2226 not shown) Planarity restraints: 2330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 137 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU A 137 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU A 137 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE A 138 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 121 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C LEU B 121 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU B 121 " -0.014 2.00e-02 2.50e+03 pdb=" N MET B 122 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 408 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO B 409 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.028 5.00e-02 4.00e+02 ... (remaining 2327 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1929 2.74 - 3.28: 13450 3.28 - 3.82: 21392 3.82 - 4.36: 23255 4.36 - 4.90: 41758 Nonbonded interactions: 101784 Sorted by model distance: nonbonded pdb=" OG1 THR A 314 " pdb=" O VAL A 391 " model vdw 2.202 2.440 nonbonded pdb=" NE2 GLN A 152 " pdb=" OH TYR A 384 " model vdw 2.227 2.520 nonbonded pdb=" OG SER B 430 " pdb=" OH TYR B 466 " model vdw 2.245 2.440 nonbonded pdb=" O GLY A 479 " pdb=" NH2 ARG A 483 " model vdw 2.245 2.520 nonbonded pdb=" O SER B 780 " pdb=" OG SER B 780 " model vdw 2.254 2.440 ... (remaining 101779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 116 through 881 or resid 887 through 926 or resid 1014 thr \ ough 1081 or resid 1101 through 1102)) selection = (chain 'B' and (resid 116 through 233 or resid 244 through 347 or (resid 348 and \ (name N or name CA or name C or name O or name CB )) or resid 349 through 912 o \ r (resid 913 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 14 through 1019 or (resid 1020 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1021 through 1081 or resid 1101 through 1102)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.100 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: 6.240 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 37.380 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.132 13831 Z= 0.575 Angle : 1.014 13.940 18844 Z= 0.559 Chirality : 0.053 0.257 2229 Planarity : 0.005 0.050 2326 Dihedral : 18.348 122.414 5028 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.20 % Allowed : 20.95 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.45 (0.19), residues: 1731 helix: 0.32 (0.16), residues: 953 sheet: -1.90 (0.41), residues: 136 loop : -2.74 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 795 HIS 0.011 0.002 HIS B 853 PHE 0.026 0.003 PHE B 541 TYR 0.021 0.002 TYR A 356 ARG 0.005 0.001 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 307 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8251 (mtp) cc_final: 0.7775 (tmm) REVERT: A 144 MET cc_start: 0.8485 (ttp) cc_final: 0.8037 (ptm) REVERT: A 186 TYR cc_start: 0.8882 (t80) cc_final: 0.8591 (t80) REVERT: A 188 MET cc_start: 0.7584 (mtm) cc_final: 0.7211 (ttt) REVERT: A 313 ARG cc_start: 0.6922 (mtm180) cc_final: 0.6262 (mtm-85) REVERT: A 358 MET cc_start: 0.9423 (mpp) cc_final: 0.9108 (mpp) REVERT: A 391 VAL cc_start: 0.8254 (t) cc_final: 0.7669 (t) REVERT: A 630 MET cc_start: 0.8819 (ttp) cc_final: 0.8449 (ttp) REVERT: A 658 GLU cc_start: 0.8283 (tt0) cc_final: 0.7922 (mm-30) REVERT: A 752 MET cc_start: 0.9315 (tpp) cc_final: 0.8882 (tpp) REVERT: A 859 MET cc_start: 0.9326 (mtp) cc_final: 0.8793 (mmp) REVERT: A 878 ILE cc_start: 0.8829 (mt) cc_final: 0.8614 (mm) REVERT: A 1074 ARG cc_start: 0.8646 (ttt90) cc_final: 0.8376 (ttt90) REVERT: A 1078 ARG cc_start: 0.8653 (mtm110) cc_final: 0.8316 (ptm160) REVERT: B 118 MET cc_start: 0.8444 (ptm) cc_final: 0.7770 (ptm) REVERT: B 122 MET cc_start: 0.8997 (mtp) cc_final: 0.8205 (tmm) REVERT: B 385 LEU cc_start: 0.9527 (mt) cc_final: 0.9058 (mt) REVERT: B 419 SER cc_start: 0.8544 (t) cc_final: 0.7926 (p) REVERT: B 563 LEU cc_start: 0.8774 (mp) cc_final: 0.8524 (tt) REVERT: B 596 CYS cc_start: 0.8318 (m) cc_final: 0.8034 (t) REVERT: B 630 MET cc_start: 0.9050 (ttp) cc_final: 0.8621 (ttm) REVERT: B 659 LYS cc_start: 0.9087 (tttt) cc_final: 0.8728 (ttmm) REVERT: B 696 VAL cc_start: 0.9062 (t) cc_final: 0.8849 (m) REVERT: B 746 GLU cc_start: 0.8805 (tt0) cc_final: 0.8264 (tp30) REVERT: B 750 LYS cc_start: 0.9389 (mttt) cc_final: 0.8569 (mttp) REVERT: B 752 MET cc_start: 0.8794 (tpp) cc_final: 0.8564 (tpp) REVERT: B 791 VAL cc_start: 0.9485 (t) cc_final: 0.9196 (m) REVERT: B 813 ASP cc_start: 0.9114 (m-30) cc_final: 0.8845 (t0) REVERT: B 857 MET cc_start: 0.8982 (ptm) cc_final: 0.8624 (pmm) REVERT: B 874 CYS cc_start: 0.8415 (m) cc_final: 0.6985 (t) REVERT: B 1055 ASN cc_start: 0.9231 (m110) cc_final: 0.8759 (t0) outliers start: 17 outliers final: 9 residues processed: 321 average time/residue: 0.2377 time to fit residues: 111.2675 Evaluate side-chains 174 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 699 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 344 HIS A 655 GLN A 717 GLN A 732 GLN A 751 ASN B 130 GLN B 152 GLN B 250 ASN B 344 HIS B 655 GLN B 717 GLN B 732 GLN B 747 GLN B 751 ASN B 763 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13831 Z= 0.234 Angle : 0.659 9.206 18844 Z= 0.326 Chirality : 0.043 0.231 2229 Planarity : 0.004 0.048 2326 Dihedral : 13.059 106.995 2121 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.74 % Allowed : 22.01 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.20), residues: 1731 helix: 1.45 (0.17), residues: 947 sheet: -0.89 (0.43), residues: 133 loop : -2.39 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 799 HIS 0.006 0.001 HIS A 845 PHE 0.017 0.002 PHE B1059 TYR 0.011 0.001 TYR B1056 ARG 0.006 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 203 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8236 (mtp) cc_final: 0.7798 (tmm) REVERT: A 147 THR cc_start: 0.8238 (t) cc_final: 0.7966 (t) REVERT: A 186 TYR cc_start: 0.8825 (t80) cc_final: 0.8515 (t80) REVERT: A 188 MET cc_start: 0.7527 (mtm) cc_final: 0.7115 (ttt) REVERT: A 358 MET cc_start: 0.9461 (mpp) cc_final: 0.9153 (mpp) REVERT: A 501 TRP cc_start: 0.7692 (t60) cc_final: 0.7448 (t60) REVERT: A 631 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8402 (t80) REVERT: A 658 GLU cc_start: 0.8366 (tt0) cc_final: 0.7875 (mm-30) REVERT: A 752 MET cc_start: 0.9317 (tpp) cc_final: 0.8866 (tpp) REVERT: A 793 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8577 (pp) REVERT: A 859 MET cc_start: 0.9294 (mtp) cc_final: 0.8764 (mmp) REVERT: A 864 LEU cc_start: 0.9272 (mt) cc_final: 0.9053 (mp) REVERT: A 1042 ASN cc_start: 0.7722 (p0) cc_final: 0.7350 (p0) REVERT: A 1043 MET cc_start: 0.9095 (ptt) cc_final: 0.8771 (pmm) REVERT: A 1073 VAL cc_start: 0.9409 (OUTLIER) cc_final: 0.9105 (m) REVERT: A 1078 ARG cc_start: 0.8623 (mtm110) cc_final: 0.8274 (ptm160) REVERT: B 118 MET cc_start: 0.8366 (ptm) cc_final: 0.8164 (ptm) REVERT: B 353 CYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8310 (m) REVERT: B 380 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8702 (tt) REVERT: B 419 SER cc_start: 0.8657 (t) cc_final: 0.8380 (p) REVERT: B 542 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8311 (pp) REVERT: B 563 LEU cc_start: 0.8662 (mp) cc_final: 0.8409 (tt) REVERT: B 566 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8529 (tm-30) REVERT: B 576 MET cc_start: 0.8358 (mtp) cc_final: 0.8019 (mtp) REVERT: B 587 MET cc_start: 0.8950 (tpt) cc_final: 0.8574 (tpt) REVERT: B 623 MET cc_start: 0.9325 (tmm) cc_final: 0.8716 (tmm) REVERT: B 630 MET cc_start: 0.8839 (ttp) cc_final: 0.8580 (ttm) REVERT: B 659 LYS cc_start: 0.9053 (tttt) cc_final: 0.8718 (ttmm) REVERT: B 693 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8117 (mm110) REVERT: B 712 LEU cc_start: 0.8715 (mt) cc_final: 0.8427 (mt) REVERT: B 750 LYS cc_start: 0.9368 (mttt) cc_final: 0.9025 (mtmm) REVERT: B 813 ASP cc_start: 0.9084 (m-30) cc_final: 0.8813 (t0) REVERT: B 857 MET cc_start: 0.8899 (ptm) cc_final: 0.8603 (pmm) REVERT: B 874 CYS cc_start: 0.8539 (m) cc_final: 0.7251 (t) REVERT: B 1055 ASN cc_start: 0.9188 (m110) cc_final: 0.8731 (t0) outliers start: 67 outliers final: 32 residues processed: 258 average time/residue: 0.1994 time to fit residues: 81.4973 Evaluate side-chains 209 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 171 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 106 optimal weight: 0.4980 chunk 43 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN B 615 HIS B 763 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 13831 Z= 0.330 Angle : 0.684 13.899 18844 Z= 0.333 Chirality : 0.043 0.210 2229 Planarity : 0.004 0.047 2326 Dihedral : 12.021 105.789 2104 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.09 % Allowed : 23.14 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.20), residues: 1731 helix: 1.73 (0.17), residues: 943 sheet: -0.65 (0.43), residues: 133 loop : -2.06 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 143 HIS 0.006 0.001 HIS A 788 PHE 0.018 0.002 PHE A 541 TYR 0.011 0.001 TYR A 227 ARG 0.005 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 162 time to evaluate : 1.615 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8241 (mtp) cc_final: 0.7759 (tmm) REVERT: A 188 MET cc_start: 0.7451 (mtm) cc_final: 0.7108 (ttt) REVERT: A 536 ASP cc_start: 0.8388 (t70) cc_final: 0.8010 (t0) REVERT: A 658 GLU cc_start: 0.8375 (tt0) cc_final: 0.7924 (tp30) REVERT: A 752 MET cc_start: 0.9314 (tpp) cc_final: 0.8854 (tpp) REVERT: A 792 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8887 (m) REVERT: A 859 MET cc_start: 0.9308 (mtp) cc_final: 0.8802 (mmp) REVERT: A 1041 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7537 (pt) REVERT: A 1043 MET cc_start: 0.9142 (ptt) cc_final: 0.8686 (pmm) REVERT: A 1073 VAL cc_start: 0.9449 (OUTLIER) cc_final: 0.9153 (m) REVERT: A 1078 ARG cc_start: 0.8714 (mtm110) cc_final: 0.8339 (ptm160) REVERT: B 118 MET cc_start: 0.8321 (ptm) cc_final: 0.8080 (ptm) REVERT: B 258 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8299 (t80) REVERT: B 416 ILE cc_start: 0.9401 (tt) cc_final: 0.9067 (mm) REVERT: B 542 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8375 (pp) REVERT: B 563 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8448 (tt) REVERT: B 576 MET cc_start: 0.8315 (mtp) cc_final: 0.7960 (mtp) REVERT: B 587 MET cc_start: 0.8858 (tpt) cc_final: 0.8508 (tpt) REVERT: B 630 MET cc_start: 0.8649 (ttp) cc_final: 0.8345 (ttm) REVERT: B 659 LYS cc_start: 0.9067 (tttt) cc_final: 0.8737 (ttmm) REVERT: B 750 LYS cc_start: 0.9372 (mttt) cc_final: 0.9069 (mtmm) REVERT: B 813 ASP cc_start: 0.9069 (m-30) cc_final: 0.8814 (t0) REVERT: B 857 MET cc_start: 0.8793 (ptm) cc_final: 0.8557 (pmm) REVERT: B 874 CYS cc_start: 0.8708 (m) cc_final: 0.7335 (t) REVERT: B 900 TYR cc_start: 0.8989 (m-80) cc_final: 0.8517 (m-80) REVERT: B 1055 ASN cc_start: 0.9205 (m110) cc_final: 0.8737 (t0) outliers start: 86 outliers final: 57 residues processed: 233 average time/residue: 0.1979 time to fit residues: 73.4282 Evaluate side-chains 213 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 150 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13831 Z= 0.260 Angle : 0.637 12.069 18844 Z= 0.307 Chirality : 0.042 0.188 2229 Planarity : 0.003 0.038 2326 Dihedral : 11.148 104.258 2103 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.80 % Allowed : 24.27 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.20), residues: 1731 helix: 1.95 (0.17), residues: 934 sheet: -0.39 (0.43), residues: 132 loop : -1.81 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 143 HIS 0.007 0.001 HIS B 853 PHE 0.022 0.001 PHE A 541 TYR 0.011 0.001 TYR B 649 ARG 0.003 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 160 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8270 (mtp) cc_final: 0.7775 (tmm) REVERT: A 186 TYR cc_start: 0.8916 (t80) cc_final: 0.8614 (t80) REVERT: A 188 MET cc_start: 0.7388 (mtm) cc_final: 0.7054 (ttm) REVERT: A 536 ASP cc_start: 0.8728 (t70) cc_final: 0.8363 (t0) REVERT: A 658 GLU cc_start: 0.8378 (tt0) cc_final: 0.7909 (tp30) REVERT: A 752 MET cc_start: 0.9324 (tpp) cc_final: 0.8844 (tpp) REVERT: A 792 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8896 (m) REVERT: A 806 ARG cc_start: 0.8776 (mmt90) cc_final: 0.8262 (mmp80) REVERT: A 859 MET cc_start: 0.9296 (mtp) cc_final: 0.8821 (mmp) REVERT: A 1042 ASN cc_start: 0.7970 (p0) cc_final: 0.7438 (p0) REVERT: A 1043 MET cc_start: 0.9165 (ptt) cc_final: 0.8713 (pmm) REVERT: A 1073 VAL cc_start: 0.9518 (OUTLIER) cc_final: 0.9091 (m) REVERT: A 1078 ARG cc_start: 0.8765 (mtm110) cc_final: 0.8407 (ptm160) REVERT: B 118 MET cc_start: 0.8215 (ptm) cc_final: 0.7975 (ptm) REVERT: B 258 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8192 (t80) REVERT: B 416 ILE cc_start: 0.9434 (tt) cc_final: 0.9127 (mm) REVERT: B 542 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8365 (pp) REVERT: B 576 MET cc_start: 0.8316 (mtp) cc_final: 0.7970 (mtp) REVERT: B 587 MET cc_start: 0.8804 (tpt) cc_final: 0.8557 (tpt) REVERT: B 659 LYS cc_start: 0.9018 (tttt) cc_final: 0.8700 (ttmm) REVERT: B 750 LYS cc_start: 0.9366 (mttt) cc_final: 0.9046 (mtmm) REVERT: B 813 ASP cc_start: 0.9068 (m-30) cc_final: 0.8812 (t0) REVERT: B 857 MET cc_start: 0.8823 (ptm) cc_final: 0.8527 (pmm) REVERT: B 874 CYS cc_start: 0.8776 (m) cc_final: 0.7331 (t) REVERT: B 1055 ASN cc_start: 0.9180 (m110) cc_final: 0.8729 (t0) outliers start: 82 outliers final: 59 residues processed: 228 average time/residue: 0.2011 time to fit residues: 72.3584 Evaluate side-chains 213 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 150 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 853 HIS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.7567 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13831 Z= 0.182 Angle : 0.569 8.457 18844 Z= 0.274 Chirality : 0.040 0.177 2229 Planarity : 0.003 0.037 2326 Dihedral : 9.701 99.799 2101 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.60 % Allowed : 26.68 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.21), residues: 1731 helix: 2.19 (0.17), residues: 940 sheet: -0.22 (0.46), residues: 122 loop : -1.61 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 501 HIS 0.003 0.001 HIS B 853 PHE 0.022 0.001 PHE B1059 TYR 0.011 0.001 TYR B 649 ARG 0.003 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 172 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8190 (mtp) cc_final: 0.7666 (tmm) REVERT: A 186 TYR cc_start: 0.8945 (t80) cc_final: 0.8657 (t80) REVERT: A 188 MET cc_start: 0.7262 (mtm) cc_final: 0.6964 (ttm) REVERT: A 380 LEU cc_start: 0.9113 (tt) cc_final: 0.8879 (pp) REVERT: A 536 ASP cc_start: 0.8755 (t70) cc_final: 0.8325 (t0) REVERT: A 658 GLU cc_start: 0.8345 (tt0) cc_final: 0.7883 (tp30) REVERT: A 752 MET cc_start: 0.9306 (tpp) cc_final: 0.8828 (tpp) REVERT: A 792 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8861 (m) REVERT: A 859 MET cc_start: 0.9293 (mtp) cc_final: 0.8794 (mmp) REVERT: A 1041 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7324 (pt) REVERT: A 1042 ASN cc_start: 0.7978 (p0) cc_final: 0.7505 (p0) REVERT: A 1043 MET cc_start: 0.9147 (ptt) cc_final: 0.8763 (pmm) REVERT: A 1078 ARG cc_start: 0.8784 (mtm110) cc_final: 0.8444 (ptm160) REVERT: B 118 MET cc_start: 0.8056 (ptm) cc_final: 0.7799 (ptm) REVERT: B 258 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8174 (t80) REVERT: B 416 ILE cc_start: 0.9418 (tt) cc_final: 0.9125 (mm) REVERT: B 542 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8280 (pp) REVERT: B 576 MET cc_start: 0.8257 (mtp) cc_final: 0.7896 (mtp) REVERT: B 587 MET cc_start: 0.8862 (tpt) cc_final: 0.8586 (tpt) REVERT: B 630 MET cc_start: 0.8830 (ttm) cc_final: 0.8500 (ttm) REVERT: B 659 LYS cc_start: 0.8970 (tttt) cc_final: 0.8619 (ttmm) REVERT: B 750 LYS cc_start: 0.9340 (mttt) cc_final: 0.9030 (mtmm) REVERT: B 781 CYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8282 (m) REVERT: B 813 ASP cc_start: 0.9043 (m-30) cc_final: 0.8810 (t0) REVERT: B 857 MET cc_start: 0.8799 (ptm) cc_final: 0.8502 (pmm) REVERT: B 874 CYS cc_start: 0.8764 (m) cc_final: 0.7278 (t) REVERT: B 1055 ASN cc_start: 0.9177 (m110) cc_final: 0.8708 (t0) outliers start: 65 outliers final: 45 residues processed: 225 average time/residue: 0.1980 time to fit residues: 70.3048 Evaluate side-chains 205 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 155 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 853 HIS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 0.0040 chunk 41 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13831 Z= 0.211 Angle : 0.580 8.168 18844 Z= 0.281 Chirality : 0.041 0.204 2229 Planarity : 0.003 0.036 2326 Dihedral : 9.241 97.539 2101 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.66 % Allowed : 25.90 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.21), residues: 1731 helix: 2.22 (0.17), residues: 949 sheet: -0.10 (0.46), residues: 122 loop : -1.50 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 501 HIS 0.004 0.001 HIS A 845 PHE 0.026 0.001 PHE B 863 TYR 0.011 0.001 TYR B 649 ARG 0.003 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 159 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8208 (mtp) cc_final: 0.7656 (tmm) REVERT: A 186 TYR cc_start: 0.8954 (t80) cc_final: 0.8649 (t80) REVERT: A 480 VAL cc_start: 0.8577 (p) cc_final: 0.8340 (t) REVERT: A 536 ASP cc_start: 0.8794 (t70) cc_final: 0.8333 (t0) REVERT: A 658 GLU cc_start: 0.8311 (tt0) cc_final: 0.7846 (tp30) REVERT: A 752 MET cc_start: 0.9309 (tpp) cc_final: 0.8830 (tpp) REVERT: A 757 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8811 (mmmm) REVERT: A 792 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8918 (m) REVERT: A 859 MET cc_start: 0.9335 (mtp) cc_final: 0.8802 (mmp) REVERT: A 1041 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7356 (pt) REVERT: A 1042 ASN cc_start: 0.7960 (p0) cc_final: 0.7486 (p0) REVERT: A 1043 MET cc_start: 0.9158 (ptt) cc_final: 0.8779 (pmm) REVERT: A 1078 ARG cc_start: 0.8800 (mtm110) cc_final: 0.8575 (ptm160) REVERT: B 118 MET cc_start: 0.7981 (ptm) cc_final: 0.7682 (ptm) REVERT: B 258 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8174 (t80) REVERT: B 416 ILE cc_start: 0.9402 (tt) cc_final: 0.9131 (mm) REVERT: B 542 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8334 (pp) REVERT: B 576 MET cc_start: 0.8205 (mtp) cc_final: 0.7854 (mtp) REVERT: B 587 MET cc_start: 0.8865 (tpt) cc_final: 0.8591 (tpt) REVERT: B 630 MET cc_start: 0.8879 (ttm) cc_final: 0.8585 (ttm) REVERT: B 659 LYS cc_start: 0.8966 (tttt) cc_final: 0.8620 (ttmm) REVERT: B 750 LYS cc_start: 0.9350 (mttt) cc_final: 0.9067 (mtmm) REVERT: B 781 CYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8432 (m) REVERT: B 813 ASP cc_start: 0.9040 (m-30) cc_final: 0.8818 (t0) REVERT: B 857 MET cc_start: 0.8774 (ptm) cc_final: 0.8492 (pmm) REVERT: B 874 CYS cc_start: 0.8781 (m) cc_final: 0.7209 (t) REVERT: B 876 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8136 (ptm) REVERT: B 1055 ASN cc_start: 0.9182 (m110) cc_final: 0.8729 (t0) REVERT: B 1057 MET cc_start: 0.9237 (tpp) cc_final: 0.8980 (tpp) outliers start: 80 outliers final: 56 residues processed: 224 average time/residue: 0.1985 time to fit residues: 70.2985 Evaluate side-chains 219 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 157 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 876 MET Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13831 Z= 0.195 Angle : 0.569 8.105 18844 Z= 0.273 Chirality : 0.040 0.193 2229 Planarity : 0.003 0.041 2326 Dihedral : 8.964 92.711 2101 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.02 % Allowed : 27.03 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.21), residues: 1731 helix: 2.25 (0.17), residues: 945 sheet: -0.14 (0.49), residues: 108 loop : -1.49 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.005 0.001 HIS B 853 PHE 0.019 0.001 PHE B 261 TYR 0.013 0.001 TYR B1056 ARG 0.002 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 161 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8206 (mtp) cc_final: 0.7627 (tmm) REVERT: A 186 TYR cc_start: 0.9012 (t80) cc_final: 0.8662 (t80) REVERT: A 380 LEU cc_start: 0.9063 (tt) cc_final: 0.8848 (pp) REVERT: A 480 VAL cc_start: 0.8535 (p) cc_final: 0.8274 (t) REVERT: A 536 ASP cc_start: 0.8757 (t70) cc_final: 0.8304 (t0) REVERT: A 658 GLU cc_start: 0.8302 (tt0) cc_final: 0.7844 (tp30) REVERT: A 752 MET cc_start: 0.9321 (tpp) cc_final: 0.8825 (tpp) REVERT: A 757 LYS cc_start: 0.9119 (mmmm) cc_final: 0.8804 (mmmm) REVERT: A 792 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8914 (m) REVERT: A 859 MET cc_start: 0.9347 (mtp) cc_final: 0.8806 (mmp) REVERT: A 1041 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7347 (pt) REVERT: A 1042 ASN cc_start: 0.7926 (p0) cc_final: 0.7444 (p0) REVERT: A 1043 MET cc_start: 0.9166 (ptt) cc_final: 0.8809 (pmm) REVERT: A 1078 ARG cc_start: 0.8802 (mtm110) cc_final: 0.8563 (ptm160) REVERT: B 118 MET cc_start: 0.7892 (ptm) cc_final: 0.7561 (ptm) REVERT: B 258 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8175 (t80) REVERT: B 542 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8330 (pp) REVERT: B 576 MET cc_start: 0.8163 (mtp) cc_final: 0.7810 (mtp) REVERT: B 587 MET cc_start: 0.8892 (tpt) cc_final: 0.8558 (tpt) REVERT: B 630 MET cc_start: 0.8862 (ttm) cc_final: 0.8633 (ttm) REVERT: B 659 LYS cc_start: 0.8963 (tttt) cc_final: 0.8609 (ttmm) REVERT: B 781 CYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8408 (m) REVERT: B 813 ASP cc_start: 0.9040 (m-30) cc_final: 0.8835 (t0) REVERT: B 857 MET cc_start: 0.8776 (ptm) cc_final: 0.8505 (pmm) REVERT: B 874 CYS cc_start: 0.8786 (m) cc_final: 0.7205 (t) REVERT: B 876 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8129 (ptm) REVERT: B 1055 ASN cc_start: 0.9185 (m110) cc_final: 0.8737 (t0) outliers start: 71 outliers final: 58 residues processed: 216 average time/residue: 0.2008 time to fit residues: 68.3586 Evaluate side-chains 218 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 154 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 876 MET Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1043 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.0470 chunk 50 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13831 Z= 0.153 Angle : 0.570 8.690 18844 Z= 0.271 Chirality : 0.040 0.229 2229 Planarity : 0.003 0.041 2326 Dihedral : 8.468 85.766 2101 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.33 % Allowed : 28.52 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.21), residues: 1731 helix: 2.33 (0.17), residues: 947 sheet: 0.03 (0.50), residues: 102 loop : -1.41 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.002 0.001 HIS A 394 PHE 0.023 0.001 PHE B1059 TYR 0.011 0.001 TYR B 649 ARG 0.003 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 175 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8215 (mtp) cc_final: 0.7638 (tmm) REVERT: A 186 TYR cc_start: 0.8996 (t80) cc_final: 0.8652 (t80) REVERT: A 188 MET cc_start: 0.7037 (ttm) cc_final: 0.6798 (ttt) REVERT: A 380 LEU cc_start: 0.9038 (tt) cc_final: 0.8771 (pp) REVERT: A 480 VAL cc_start: 0.8546 (p) cc_final: 0.8246 (t) REVERT: A 536 ASP cc_start: 0.8742 (t70) cc_final: 0.8273 (t0) REVERT: A 658 GLU cc_start: 0.8271 (tt0) cc_final: 0.7827 (tp30) REVERT: A 752 MET cc_start: 0.9312 (tpp) cc_final: 0.8821 (tpp) REVERT: A 792 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8888 (m) REVERT: A 859 MET cc_start: 0.9337 (mtp) cc_final: 0.8781 (mmp) REVERT: A 1042 ASN cc_start: 0.7866 (p0) cc_final: 0.7321 (p0) REVERT: A 1043 MET cc_start: 0.9116 (ptt) cc_final: 0.8841 (pmm) REVERT: A 1073 VAL cc_start: 0.9484 (OUTLIER) cc_final: 0.9207 (m) REVERT: A 1078 ARG cc_start: 0.8790 (mtm110) cc_final: 0.8550 (ptm160) REVERT: B 258 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8214 (t80) REVERT: B 521 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8116 (tm-30) REVERT: B 542 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8322 (pp) REVERT: B 576 MET cc_start: 0.8189 (mtp) cc_final: 0.7847 (mtp) REVERT: B 587 MET cc_start: 0.8795 (tpt) cc_final: 0.8494 (tpt) REVERT: B 630 MET cc_start: 0.8856 (ttm) cc_final: 0.8616 (ttm) REVERT: B 659 LYS cc_start: 0.8938 (tttt) cc_final: 0.8541 (ttmm) REVERT: B 750 LYS cc_start: 0.9260 (mttt) cc_final: 0.8954 (mttp) REVERT: B 781 CYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8315 (m) REVERT: B 813 ASP cc_start: 0.9020 (m-30) cc_final: 0.8799 (t0) REVERT: B 857 MET cc_start: 0.8782 (ptm) cc_final: 0.8503 (pmm) REVERT: B 859 MET cc_start: 0.8754 (mmt) cc_final: 0.8541 (mmt) REVERT: B 874 CYS cc_start: 0.8763 (m) cc_final: 0.7207 (t) REVERT: B 876 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8091 (ptt) REVERT: B 1055 ASN cc_start: 0.9173 (m110) cc_final: 0.8726 (t0) outliers start: 47 outliers final: 34 residues processed: 212 average time/residue: 0.2012 time to fit residues: 67.5929 Evaluate side-chains 201 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 161 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 876 MET Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 6.9990 chunk 145 optimal weight: 0.0980 chunk 155 optimal weight: 0.4980 chunk 93 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 154 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13831 Z= 0.139 Angle : 0.581 11.796 18844 Z= 0.270 Chirality : 0.040 0.249 2229 Planarity : 0.003 0.041 2326 Dihedral : 8.021 77.896 2101 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.76 % Allowed : 29.44 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.21), residues: 1731 helix: 2.35 (0.17), residues: 946 sheet: 0.28 (0.51), residues: 102 loop : -1.39 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.005 0.001 HIS B 853 PHE 0.033 0.001 PHE B1059 TYR 0.010 0.001 TYR B 649 ARG 0.003 0.000 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 176 time to evaluate : 1.569 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8198 (mtp) cc_final: 0.7650 (tmm) REVERT: A 186 TYR cc_start: 0.9005 (t80) cc_final: 0.8694 (t80) REVERT: A 251 MET cc_start: 0.9142 (mmt) cc_final: 0.8803 (mmt) REVERT: A 358 MET cc_start: 0.9504 (mpp) cc_final: 0.9292 (pmm) REVERT: A 536 ASP cc_start: 0.8705 (t70) cc_final: 0.8229 (t0) REVERT: A 585 PHE cc_start: 0.7882 (m-80) cc_final: 0.7559 (m-10) REVERT: A 630 MET cc_start: 0.8452 (tpp) cc_final: 0.8086 (tpp) REVERT: A 658 GLU cc_start: 0.8214 (tt0) cc_final: 0.7776 (tp30) REVERT: A 752 MET cc_start: 0.9311 (tpp) cc_final: 0.8820 (tpp) REVERT: A 790 SER cc_start: 0.9632 (m) cc_final: 0.8843 (p) REVERT: A 792 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8893 (m) REVERT: A 859 MET cc_start: 0.9318 (mtp) cc_final: 0.8730 (mmp) REVERT: A 1042 ASN cc_start: 0.7793 (p0) cc_final: 0.7233 (p0) REVERT: A 1043 MET cc_start: 0.9107 (ptt) cc_final: 0.8848 (pmm) REVERT: A 1073 VAL cc_start: 0.9478 (OUTLIER) cc_final: 0.9209 (m) REVERT: A 1078 ARG cc_start: 0.8786 (mtm110) cc_final: 0.8549 (ptm160) REVERT: B 258 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8273 (t80) REVERT: B 521 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 542 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8280 (pp) REVERT: B 576 MET cc_start: 0.8224 (mtp) cc_final: 0.7904 (mtp) REVERT: B 587 MET cc_start: 0.8775 (tpt) cc_final: 0.8488 (tpt) REVERT: B 630 MET cc_start: 0.8828 (ttm) cc_final: 0.8606 (ttm) REVERT: B 659 LYS cc_start: 0.8940 (tttt) cc_final: 0.8530 (ttmm) REVERT: B 750 LYS cc_start: 0.9258 (mttt) cc_final: 0.8936 (mttp) REVERT: B 781 CYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8194 (m) REVERT: B 813 ASP cc_start: 0.9017 (m-30) cc_final: 0.8778 (t0) REVERT: B 874 CYS cc_start: 0.8772 (m) cc_final: 0.8192 (m) REVERT: B 1055 ASN cc_start: 0.9147 (m110) cc_final: 0.8699 (t0) outliers start: 39 outliers final: 30 residues processed: 205 average time/residue: 0.2076 time to fit residues: 66.8477 Evaluate side-chains 202 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 853 HIS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 0.1980 chunk 114 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 0.0970 chunk 109 optimal weight: 7.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13831 Z= 0.153 Angle : 0.597 11.536 18844 Z= 0.276 Chirality : 0.040 0.264 2229 Planarity : 0.003 0.046 2326 Dihedral : 7.680 72.704 2099 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.04 % Allowed : 29.16 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.31 (0.21), residues: 1731 helix: 2.36 (0.17), residues: 947 sheet: 0.28 (0.52), residues: 105 loop : -1.30 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 850 HIS 0.004 0.001 HIS B 853 PHE 0.016 0.001 PHE A 187 TYR 0.016 0.001 TYR A 466 ARG 0.002 0.000 ARG B 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 172 time to evaluate : 1.565 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8213 (mtp) cc_final: 0.7646 (tmm) REVERT: A 186 TYR cc_start: 0.9053 (t80) cc_final: 0.8733 (t80) REVERT: A 251 MET cc_start: 0.9192 (mmt) cc_final: 0.8962 (mmt) REVERT: A 536 ASP cc_start: 0.8707 (t70) cc_final: 0.8240 (t0) REVERT: A 576 MET cc_start: 0.7048 (tpt) cc_final: 0.6445 (tpp) REVERT: A 585 PHE cc_start: 0.7874 (m-80) cc_final: 0.7556 (m-10) REVERT: A 618 LEU cc_start: 0.8244 (mm) cc_final: 0.7978 (tp) REVERT: A 630 MET cc_start: 0.8457 (tpp) cc_final: 0.8005 (tpp) REVERT: A 636 TYR cc_start: 0.7881 (p90) cc_final: 0.7640 (p90) REVERT: A 658 GLU cc_start: 0.8192 (tt0) cc_final: 0.7786 (tp30) REVERT: A 752 MET cc_start: 0.9319 (tpp) cc_final: 0.8817 (tpp) REVERT: A 790 SER cc_start: 0.9644 (m) cc_final: 0.8858 (p) REVERT: A 792 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8919 (m) REVERT: A 859 MET cc_start: 0.9308 (mtp) cc_final: 0.8727 (mmp) REVERT: A 1042 ASN cc_start: 0.7786 (p0) cc_final: 0.7253 (p0) REVERT: A 1043 MET cc_start: 0.9119 (ptt) cc_final: 0.8871 (pmm) REVERT: A 1078 ARG cc_start: 0.8783 (mtm110) cc_final: 0.8542 (ptm160) REVERT: B 258 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8275 (t80) REVERT: B 521 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 542 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8305 (pp) REVERT: B 576 MET cc_start: 0.8226 (mtp) cc_final: 0.7893 (mtp) REVERT: B 587 MET cc_start: 0.8768 (tpt) cc_final: 0.8476 (tpt) REVERT: B 630 MET cc_start: 0.8856 (ttm) cc_final: 0.8616 (ttm) REVERT: B 659 LYS cc_start: 0.8933 (tttt) cc_final: 0.8528 (ttmm) REVERT: B 750 LYS cc_start: 0.9270 (mttt) cc_final: 0.8951 (mttp) REVERT: B 781 CYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8015 (m) REVERT: B 813 ASP cc_start: 0.8977 (m-30) cc_final: 0.8742 (t0) REVERT: B 874 CYS cc_start: 0.8803 (m) cc_final: 0.8232 (m) REVERT: B 1055 ASN cc_start: 0.9177 (m110) cc_final: 0.8739 (t0) outliers start: 43 outliers final: 34 residues processed: 206 average time/residue: 0.1999 time to fit residues: 65.7533 Evaluate side-chains 205 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 853 HIS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 1.9990 chunk 42 optimal weight: 0.0270 chunk 126 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.098073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.071943 restraints weight = 39096.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.075006 restraints weight = 18915.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.077153 restraints weight = 11756.892| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 13831 Z= 0.148 Angle : 0.604 10.236 18844 Z= 0.276 Chirality : 0.040 0.272 2229 Planarity : 0.003 0.042 2326 Dihedral : 7.349 69.494 2099 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.33 % Allowed : 29.30 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.36 (0.21), residues: 1731 helix: 2.40 (0.17), residues: 947 sheet: 0.44 (0.48), residues: 121 loop : -1.34 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.004 0.001 HIS B 853 PHE 0.023 0.001 PHE B1059 TYR 0.014 0.001 TYR A 216 ARG 0.003 0.000 ARG B 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2628.94 seconds wall clock time: 48 minutes 45.91 seconds (2925.91 seconds total)