Starting phenix.real_space_refine on Thu Feb 15 21:42:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aip_11801/02_2024/7aip_11801_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aip_11801/02_2024/7aip_11801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aip_11801/02_2024/7aip_11801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aip_11801/02_2024/7aip_11801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aip_11801/02_2024/7aip_11801_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aip_11801/02_2024/7aip_11801_updated.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 96 5.16 5 C 8769 2.51 5 N 2216 2.21 5 O 2442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 754": "OE1" <-> "OE2" Residue "A GLU 909": "OE1" <-> "OE2" Residue "A GLU 924": "OE1" <-> "OE2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B GLU 909": "OE1" <-> "OE2" Residue "B GLU 924": "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: 13535 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6670 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 867, 6663 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 37, 'TRANS': 829} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 66 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 Conformer: "B" Number of residues, atoms: 867, 6663 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 37, 'TRANS': 829} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 66 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 bond proxies already assigned to first conformer: 6811 Chain: "B" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6663 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 37, 'TRANS': 829} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 66 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 11.48, per 1000 atoms: 0.85 Number of scatterers: 13535 At special positions: 0 Unit cell: (109.65, 109.65, 150.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 10 15.00 Mg 2 11.99 O 2442 8.00 N 2216 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 F 1 " - " NAG F 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG F 1 " - " ASN A 361 " " NAG J 1 " - " ASN B 312 " " NAG M 1 " - " ASN B 361 " Time building additional restraints: 5.58 Conformation dependent library (CDL) restraints added in 3.8 seconds 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 8 sheets defined 53.1% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 121 through 132 removed outlier: 5.812A 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: 6.671A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 226 Proline residue: A 195 - end of helix removed outlier: 3.544A 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: 5.487A pdb=" N SER A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 4.240A 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 375 through 378 No H-bonds generated for 'chain 'A' and resid 375 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 447 through 476 Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 505 through 535 removed outlier: 3.527A 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 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 558 through 571 removed outlier: 4.494A pdb=" N ILE A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) 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 710 through 719 Processing helix chain 'A' and resid 740 through 755 Processing helix chain 'A' and resid 770 through 779 Processing helix chain 'A' and resid 805 through 819 removed outlier: 3.529A pdb=" N TRP A 808 " --> pdb=" O PRO A 805 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 809 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR A 810 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 811 " --> pdb=" O TRP A 808 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 819 " --> pdb=" O ARG A 816 " (cutoff:3.500A) 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 888 through 902 removed outlier: 3.797A pdb=" N HIS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 925 Processing helix chain 'A' and resid 1015 through 1032 Processing helix chain 'A' and resid 1053 through 1063 Processing helix chain 'B' and resid 121 through 132 removed outlier: 5.812A 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: 6.671A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 226 Proline residue: B 195 - end of helix removed outlier: 3.545A 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: 5.486A pdb=" N SER B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 4.240A 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 375 through 378 No H-bonds generated for 'chain 'B' and resid 375 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 420 through 430 Proline residue: B 429 - end of helix Processing helix chain 'B' and resid 447 through 476 Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 505 through 535 removed outlier: 3.527A 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: 4.494A pdb=" N ILE B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 601 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 740 through 755 Processing helix chain 'B' and resid 770 through 779 Processing helix chain 'B' and resid 805 through 819 removed outlier: 3.529A pdb=" N TRP B 808 " --> pdb=" O PRO B 805 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 809 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR B 810 " --> pdb=" O ALA B 807 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 811 " --> pdb=" O TRP B 808 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B 819 " --> pdb=" O ARG B 816 " (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 888 through 902 removed outlier: 3.797A pdb=" N HIS B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 925 Processing helix chain 'B' and resid 1015 through 1032 Processing helix chain 'B' and resid 1053 through 1063 Processing sheet with id= A, first strand: chain 'A' and resid 306 through 309 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: 4.112A pdb=" N VAL A1070 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A1072 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 697 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE A 761 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N SER A 729 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN A 763 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE A 731 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 6.663A 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: 5.982A pdb=" N ARG A 875 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 848 " --> pdb=" O ARG A 875 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG A 877 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU A 907 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N THR A 880 " --> pdb=" O GLU A 907 " (cutoff:3.500A) removed outlier: 6.982A 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 309 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: 4.112A pdb=" N VAL B1070 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B1072 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 697 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE B 761 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N SER B 729 " --> pdb=" O PHE B 761 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLN B 763 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE B 731 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 6.662A 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: 5.983A pdb=" N ARG B 875 " --> pdb=" O ILE B 846 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL B 848 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG B 877 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU B 907 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N THR B 880 " --> pdb=" O GLU B 907 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 909 " --> pdb=" O THR B 880 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 658 hydrogen bonds defined for protein. 1919 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: 4.35 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4213 1.34 - 1.47: 3483 1.47 - 1.59: 5975 1.59 - 1.72: 26 1.72 - 1.84: 152 Bond restraints: 13849 Sorted by residual: bond pdb=" C4 ATP B1201 " pdb=" C5 ATP B1201 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C4 ATP A1201 " pdb=" C5 ATP A1201 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.81e+01 bond pdb=" C5 ATP A1201 " pdb=" C6 ATP A1201 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.89e+01 bond pdb=" C5 ATP B1201 " pdb=" C6 ATP B1201 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.75e+01 bond pdb=" C8 ATP A1201 " pdb=" N7 ATP A1201 " ideal model delta sigma weight residual 1.310 1.355 -0.045 1.00e-02 1.00e+04 1.99e+01 ... (remaining 13844 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.85: 465 106.85 - 114.12: 8136 114.12 - 121.38: 7210 121.38 - 128.65: 2934 128.65 - 135.91: 133 Bond angle restraints: 18878 Sorted by residual: angle pdb=" PB ATP A1201 " pdb=" O3B ATP A1201 " pdb=" PG ATP A1201 " ideal model delta sigma weight residual 139.87 125.01 14.86 1.00e+00 1.00e+00 2.21e+02 angle pdb=" PB ATP B1201 " pdb=" O3B ATP B1201 " pdb=" PG ATP B1201 " ideal model delta sigma weight residual 139.87 125.02 14.85 1.00e+00 1.00e+00 2.21e+02 angle pdb=" PA ATP B1201 " pdb=" O3A ATP B1201 " pdb=" PB ATP B1201 " ideal model delta sigma weight residual 136.83 123.66 13.17 1.00e+00 1.00e+00 1.73e+02 angle pdb=" PA ATP A1201 " pdb=" O3A ATP A1201 " pdb=" PB ATP A1201 " ideal model delta sigma weight residual 136.83 123.69 13.14 1.00e+00 1.00e+00 1.73e+02 angle pdb=" C5 ATP B1201 " pdb=" C4 ATP B1201 " pdb=" N3 ATP B1201 " ideal model delta sigma weight residual 126.80 118.62 8.18 1.00e+00 1.00e+00 6.69e+01 ... (remaining 18873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 7388 21.43 - 42.85: 725 42.85 - 64.28: 131 64.28 - 85.71: 28 85.71 - 107.13: 12 Dihedral angle restraints: 8284 sinusoidal: 3302 harmonic: 4982 Sorted by residual: 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 93.00 141.07 -48.07 1 1.00e+01 1.00e-02 3.18e+01 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 93.00 141.04 -48.04 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" O4 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C5 BMA J 3 " pdb=" O5 BMA J 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.42 107.13 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 8281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1910 0.068 - 0.136: 296 0.136 - 0.203: 15 0.203 - 0.271: 8 0.271 - 0.339: 2 Chirality restraints: 2231 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 361 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 361 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C4 NAG M 1 " pdb=" C3 NAG M 1 " pdb=" C5 NAG M 1 " pdb=" O4 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2228 not shown) Planarity restraints: 2324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP B 808 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.59e+00 pdb=" C TRP B 808 " 0.048 2.00e-02 2.50e+03 pdb=" O TRP B 808 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS B 809 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 808 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C TRP A 808 " 0.048 2.00e-02 2.50e+03 pdb=" O TRP A 808 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS A 809 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 137 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C LEU A 137 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU A 137 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE A 138 " 0.014 2.00e-02 2.50e+03 ... (remaining 2321 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2071 2.75 - 3.29: 13027 3.29 - 3.83: 21388 3.83 - 4.36: 23860 4.36 - 4.90: 43638 Nonbonded interactions: 103984 Sorted by model distance: nonbonded pdb=" NZ LYS B 809 " pdb=" OD2 ASP B 813 " model vdw 2.215 2.520 nonbonded pdb=" NZ LYS A 809 " pdb=" OD2 ASP A 813 " model vdw 2.215 2.520 nonbonded pdb=" OG1 THR B 713 " pdb=" OE1 GLU B 756 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR A 713 " pdb=" OE1 GLU A 756 " model vdw 2.254 2.440 nonbonded pdb=" O ARG B 806 " pdb="MG MG B1202 " model vdw 2.256 2.170 ... (remaining 103979 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 775 or resid 777 through 1081 or resid 1201 th \ rough 1202)) selection = (chain 'B' and (resid 116 through 775 or resid 777 through 1081 or resid 1201 th \ rough 1202)) } ncs_group { reference = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'M' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 6.490 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 44.420 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 13849 Z= 0.453 Angle : 0.834 14.857 18878 Z= 0.483 Chirality : 0.050 0.339 2231 Planarity : 0.005 0.046 2320 Dihedral : 17.389 107.133 5076 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.71 % Allowed : 21.40 % Favored : 77.89 % 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: -1.49 (0.19), residues: 1707 helix: 0.28 (0.16), residues: 943 sheet: -2.10 (0.40), residues: 136 loop : -2.72 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 143 HIS 0.008 0.001 HIS A 853 PHE 0.020 0.002 PHE B 541 TYR 0.011 0.001 TYR A 739 ARG 0.003 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 200 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7243 (m-30) cc_final: 0.6872 (t0) REVERT: A 583 MET cc_start: 0.8014 (mmp) cc_final: 0.7740 (mmp) REVERT: A 903 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.5280 (pmt170) REVERT: B 443 ASP cc_start: 0.7219 (m-30) cc_final: 0.6844 (t0) REVERT: B 903 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.5205 (pmt170) outliers start: 10 outliers final: 6 residues processed: 210 average time/residue: 0.3140 time to fit residues: 90.5729 Evaluate side-chains 167 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 903 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 394 HIS A 593 ASN A 599 GLN A 655 GLN A 717 GLN A 747 GLN A 751 ASN A 776 HIS B A 853 HIS B 152 GLN B 344 HIS B 593 ASN B 599 GLN B 655 GLN B 717 GLN B 747 GLN B 751 ASN B 853 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13849 Z= 0.187 Angle : 0.595 9.678 18878 Z= 0.288 Chirality : 0.042 0.249 2231 Planarity : 0.004 0.039 2320 Dihedral : 10.051 86.076 2170 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.06 % Allowed : 23.32 % Favored : 74.63 % 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: -0.06 (0.20), residues: 1707 helix: 1.52 (0.17), residues: 927 sheet: -1.22 (0.41), residues: 136 loop : -2.21 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 143 HIS 0.012 0.001 HIS A 853 PHE 0.013 0.001 PHE B 541 TYR 0.010 0.001 TYR A1056 ARG 0.008 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7156 (m-30) cc_final: 0.6808 (t0) REVERT: A 543 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7338 (ttp80) REVERT: A 879 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.5532 (m-80) REVERT: B 380 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8958 (tt) REVERT: B 443 ASP cc_start: 0.7146 (m-30) cc_final: 0.6788 (t0) REVERT: B 543 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7301 (ttp80) REVERT: B 591 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: B 737 GLU cc_start: 0.7532 (pp20) cc_final: 0.7211 (pp20) REVERT: B 817 CYS cc_start: 0.7768 (t) cc_final: 0.7330 (m) outliers start: 29 outliers final: 16 residues processed: 187 average time/residue: 0.2574 time to fit residues: 70.2850 Evaluate side-chains 176 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 1073 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 HIS A 868 HIS A1026 ASN B 853 HIS B 868 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13849 Z= 0.200 Angle : 0.571 9.648 18878 Z= 0.273 Chirality : 0.041 0.267 2231 Planarity : 0.004 0.034 2320 Dihedral : 8.972 87.694 2160 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.91 % Allowed : 23.74 % Favored : 73.35 % 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: 0.43 (0.21), residues: 1707 helix: 1.86 (0.18), residues: 925 sheet: -0.73 (0.42), residues: 136 loop : -1.94 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 143 HIS 0.009 0.001 HIS A 853 PHE 0.023 0.001 PHE A 863 TYR 0.007 0.001 TYR A1056 ARG 0.006 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 167 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8929 (tt) REVERT: A 443 ASP cc_start: 0.7190 (m-30) cc_final: 0.6832 (t0) REVERT: A 543 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7401 (ttp80) REVERT: A 817 CYS cc_start: 0.7705 (t) cc_final: 0.7337 (m) REVERT: A 879 PHE cc_start: 0.5923 (OUTLIER) cc_final: 0.5515 (m-80) REVERT: B 152 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7498 (mt0) REVERT: B 380 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8933 (tt) REVERT: B 443 ASP cc_start: 0.7215 (m-30) cc_final: 0.6843 (t0) REVERT: B 543 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7362 (ttp80) REVERT: B 591 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7471 (m-10) REVERT: B 817 CYS cc_start: 0.7695 (t) cc_final: 0.7351 (m) REVERT: B 879 PHE cc_start: 0.5957 (OUTLIER) cc_final: 0.5578 (m-80) outliers start: 41 outliers final: 25 residues processed: 191 average time/residue: 0.2552 time to fit residues: 72.6469 Evaluate side-chains 194 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 HIS A 853 HIS B 394 HIS B 853 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13849 Z= 0.437 Angle : 0.675 9.911 18878 Z= 0.331 Chirality : 0.047 0.283 2231 Planarity : 0.004 0.037 2320 Dihedral : 8.883 88.725 2160 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.76 % Allowed : 23.25 % Favored : 73.00 % 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: 0.12 (0.20), residues: 1707 helix: 1.48 (0.17), residues: 929 sheet: -0.79 (0.41), residues: 136 loop : -1.88 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 143 HIS 0.006 0.001 HIS A 853 PHE 0.028 0.002 PHE A 863 TYR 0.015 0.002 TYR A 654 ARG 0.004 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 164 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8969 (tt) REVERT: A 443 ASP cc_start: 0.7357 (m-30) cc_final: 0.6944 (t0) REVERT: A 543 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7443 (ttp80) REVERT: A 591 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7720 (m-10) REVERT: A 623 MET cc_start: 0.7843 (ttp) cc_final: 0.7617 (ttt) REVERT: A 879 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.5788 (m-80) REVERT: B 380 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8990 (tt) REVERT: B 443 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7000 (t0) REVERT: B 543 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7413 (ttp80) REVERT: B 591 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7653 (m-10) outliers start: 53 outliers final: 34 residues processed: 203 average time/residue: 0.2517 time to fit residues: 75.4303 Evaluate side-chains 201 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 HIS B 853 HIS B1026 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13849 Z= 0.177 Angle : 0.544 9.603 18878 Z= 0.262 Chirality : 0.041 0.255 2231 Planarity : 0.003 0.037 2320 Dihedral : 8.130 89.964 2158 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.69 % Allowed : 24.88 % Favored : 72.43 % 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: 0.79 (0.21), residues: 1707 helix: 1.95 (0.18), residues: 945 sheet: -0.28 (0.43), residues: 136 loop : -1.59 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 635 HIS 0.007 0.001 HIS A 853 PHE 0.018 0.001 PHE B1059 TYR 0.009 0.001 TYR B 636 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8953 (tt) REVERT: A 443 ASP cc_start: 0.7268 (m-30) cc_final: 0.6879 (t0) REVERT: A 543 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7425 (ttp80) REVERT: A 591 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7634 (m-10) REVERT: A 817 CYS cc_start: 0.7805 (t) cc_final: 0.7487 (m) REVERT: A 879 PHE cc_start: 0.5916 (OUTLIER) cc_final: 0.5466 (m-80) REVERT: B 171 MET cc_start: 0.7028 (tpt) cc_final: 0.6826 (tpt) REVERT: B 380 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8951 (tt) REVERT: B 443 ASP cc_start: 0.7295 (m-30) cc_final: 0.6948 (t0) REVERT: B 543 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7372 (ttp80) REVERT: B 591 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: B 817 CYS cc_start: 0.7807 (t) cc_final: 0.7500 (m) outliers start: 38 outliers final: 25 residues processed: 192 average time/residue: 0.2567 time to fit residues: 72.2916 Evaluate side-chains 195 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 739 TYR Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 HIS B 853 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13849 Z= 0.171 Angle : 0.543 9.657 18878 Z= 0.260 Chirality : 0.040 0.264 2231 Planarity : 0.003 0.039 2320 Dihedral : 7.812 89.966 2158 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.05 % Allowed : 25.09 % Favored : 71.86 % 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: 1.08 (0.21), residues: 1707 helix: 2.17 (0.18), residues: 941 sheet: -0.07 (0.42), residues: 136 loop : -1.44 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 850 HIS 0.006 0.001 HIS A 853 PHE 0.017 0.001 PHE A1059 TYR 0.008 0.001 TYR A1056 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 166 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8948 (tt) REVERT: A 443 ASP cc_start: 0.7285 (m-30) cc_final: 0.6898 (t0) REVERT: A 543 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7450 (ttp80) REVERT: A 817 CYS cc_start: 0.7710 (t) cc_final: 0.7446 (m) REVERT: A 879 PHE cc_start: 0.6043 (OUTLIER) cc_final: 0.5530 (m-80) REVERT: B 380 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8939 (tt) REVERT: B 443 ASP cc_start: 0.7308 (m-30) cc_final: 0.6969 (t0) REVERT: B 543 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7364 (ttp80) REVERT: B 817 CYS cc_start: 0.7727 (t) cc_final: 0.7452 (m) outliers start: 43 outliers final: 33 residues processed: 196 average time/residue: 0.2425 time to fit residues: 70.2749 Evaluate side-chains 196 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 158 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 739 TYR Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 121 optimal weight: 0.0770 chunk 140 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13849 Z= 0.184 Angle : 0.545 9.671 18878 Z= 0.261 Chirality : 0.041 0.264 2231 Planarity : 0.003 0.039 2320 Dihedral : 7.639 89.857 2158 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.91 % Allowed : 25.73 % Favored : 71.37 % 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: 1.18 (0.21), residues: 1707 helix: 2.24 (0.18), residues: 939 sheet: 0.01 (0.43), residues: 134 loop : -1.36 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 850 HIS 0.004 0.001 HIS B 853 PHE 0.022 0.001 PHE A1059 TYR 0.007 0.001 TYR A1056 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 1.418 Fit side-chains REVERT: A 380 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8941 (tt) REVERT: A 443 ASP cc_start: 0.7272 (m-30) cc_final: 0.6905 (t0) REVERT: A 543 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7498 (ttp80) REVERT: A 817 CYS cc_start: 0.7708 (t) cc_final: 0.7467 (m) REVERT: B 152 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: B 171 MET cc_start: 0.6995 (tpt) cc_final: 0.6780 (tpt) REVERT: B 380 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8931 (tt) REVERT: B 443 ASP cc_start: 0.7331 (m-30) cc_final: 0.6982 (t0) REVERT: B 543 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7379 (ttp80) REVERT: B 591 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 817 CYS cc_start: 0.7706 (t) cc_final: 0.7446 (m) outliers start: 41 outliers final: 32 residues processed: 192 average time/residue: 0.2401 time to fit residues: 68.7896 Evaluate side-chains 194 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 739 TYR Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 822 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13849 Z= 0.304 Angle : 0.605 9.798 18878 Z= 0.293 Chirality : 0.043 0.271 2231 Planarity : 0.004 0.040 2320 Dihedral : 7.693 89.475 2156 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.91 % Allowed : 25.94 % Favored : 71.16 % 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: 0.99 (0.21), residues: 1707 helix: 2.04 (0.18), residues: 941 sheet: -0.12 (0.42), residues: 138 loop : -1.39 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 850 HIS 0.002 0.001 HIS A 838 PHE 0.022 0.001 PHE B1059 TYR 0.011 0.001 TYR A 654 ARG 0.003 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 1.364 Fit side-chains REVERT: A 380 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8972 (tt) REVERT: A 443 ASP cc_start: 0.7324 (m-30) cc_final: 0.6958 (t0) REVERT: A 543 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7509 (ttp80) REVERT: A 817 CYS cc_start: 0.7944 (t) cc_final: 0.7562 (m) REVERT: B 380 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8948 (tt) REVERT: B 543 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7382 (ttp80) REVERT: B 591 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7693 (m-10) REVERT: B 817 CYS cc_start: 0.7957 (t) cc_final: 0.7582 (m) outliers start: 41 outliers final: 34 residues processed: 194 average time/residue: 0.2453 time to fit residues: 70.8857 Evaluate side-chains 201 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 162 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 739 TYR Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.7989 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13849 Z= 0.279 Angle : 0.590 9.696 18878 Z= 0.286 Chirality : 0.042 0.265 2231 Planarity : 0.004 0.061 2320 Dihedral : 7.638 88.531 2156 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.91 % Allowed : 26.01 % Favored : 71.08 % 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: 1.02 (0.21), residues: 1707 helix: 2.05 (0.17), residues: 941 sheet: -0.09 (0.42), residues: 138 loop : -1.36 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 635 HIS 0.002 0.001 HIS A1020 PHE 0.040 0.002 PHE A 591 TYR 0.009 0.001 TYR A 654 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 1.588 Fit side-chains REVERT: A 380 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8980 (tt) REVERT: A 443 ASP cc_start: 0.7310 (m-30) cc_final: 0.6955 (t0) REVERT: A 543 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7521 (ttp80) REVERT: A 817 CYS cc_start: 0.7943 (t) cc_final: 0.7567 (m) REVERT: B 171 MET cc_start: 0.7037 (tpt) cc_final: 0.6836 (tpt) REVERT: B 380 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8955 (tt) REVERT: B 543 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7400 (ttp80) REVERT: B 591 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7691 (m-10) REVERT: B 817 CYS cc_start: 0.7955 (t) cc_final: 0.7575 (m) outliers start: 41 outliers final: 35 residues processed: 191 average time/residue: 0.2394 time to fit residues: 68.0856 Evaluate side-chains 200 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 160 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 739 TYR Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 113 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.7937 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13849 Z= 0.175 Angle : 0.553 9.616 18878 Z= 0.266 Chirality : 0.041 0.259 2231 Planarity : 0.004 0.063 2320 Dihedral : 7.378 87.684 2156 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.48 % Allowed : 26.58 % Favored : 70.94 % 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: 1.33 (0.21), residues: 1707 helix: 2.33 (0.18), residues: 937 sheet: 0.07 (0.42), residues: 140 loop : -1.23 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 850 HIS 0.002 0.000 HIS A 853 PHE 0.033 0.001 PHE A 591 TYR 0.008 0.001 TYR B 636 ARG 0.004 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.445 Fit side-chains REVERT: A 320 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7887 (p90) REVERT: A 380 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8927 (tt) REVERT: A 443 ASP cc_start: 0.7254 (m-30) cc_final: 0.6917 (t0) REVERT: A 543 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7449 (ttp80) REVERT: A 817 CYS cc_start: 0.7744 (t) cc_final: 0.7476 (m) REVERT: A 859 MET cc_start: 0.7932 (mpp) cc_final: 0.7575 (mpp) REVERT: B 320 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7988 (p90) REVERT: B 380 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8935 (tt) REVERT: B 443 ASP cc_start: 0.7373 (m-30) cc_final: 0.6980 (t0) REVERT: B 543 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7405 (ttp80) REVERT: B 591 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: B 817 CYS cc_start: 0.7748 (t) cc_final: 0.7462 (m) REVERT: B 859 MET cc_start: 0.7860 (mpp) cc_final: 0.7469 (mpp) outliers start: 35 outliers final: 28 residues processed: 184 average time/residue: 0.2427 time to fit residues: 66.2959 Evaluate side-chains 188 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 739 TYR Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 37 optimal weight: 0.0370 chunk 136 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.170067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123761 restraints weight = 25109.968| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.36 r_work: 0.3277 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13849 Z= 0.184 Angle : 0.550 9.699 18878 Z= 0.265 Chirality : 0.041 0.264 2231 Planarity : 0.004 0.052 2320 Dihedral : 7.247 87.020 2156 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.76 % Allowed : 26.22 % Favored : 71.01 % 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: 1.46 (0.21), residues: 1707 helix: 2.41 (0.18), residues: 933 sheet: 0.33 (0.43), residues: 140 loop : -1.17 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 850 HIS 0.002 0.000 HIS A1020 PHE 0.033 0.001 PHE A 591 TYR 0.007 0.001 TYR B 636 ARG 0.004 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2867.63 seconds wall clock time: 52 minutes 44.30 seconds (3164.30 seconds total)