Starting phenix.real_space_refine on Fri Sep 27 20:22:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp7_41469/09_2024/8tp7_41469.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp7_41469/09_2024/8tp7_41469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp7_41469/09_2024/8tp7_41469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp7_41469/09_2024/8tp7_41469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp7_41469/09_2024/8tp7_41469.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp7_41469/09_2024/8tp7_41469.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.077 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: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 10668 2.51 5 N 2859 2.21 5 O 3396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17010 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "B" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "C" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "D" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "E" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "F" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "G" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 10.83, per 1000 atoms: 0.64 Number of scatterers: 17010 At special positions: 0 Unit cell: (117.3, 111.55, 180.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 3396 8.00 N 2859 7.00 C 10668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.06 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.06 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.06 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 3 " " NAG K 1 " - " FUC K 3 " NAG-ASN " NAG A 601 " - " ASN A 21 " " NAG A 602 " - " ASN A 33 " " NAG A 603 " - " ASN A 289 " " NAG B 601 " - " ASN B 21 " " NAG B 602 " - " ASN B 33 " " NAG B 603 " - " ASN B 289 " " NAG C 601 " - " ASN C 21 " " NAG C 602 " - " ASN C 33 " " NAG C 603 " - " ASN C 289 " " NAG I 1 " - " ASN A 169 " " NAG J 1 " - " ASN B 169 " " NAG K 1 " - " ASN C 169 " Time building additional restraints: 4.88 Conformation dependent library (CDL) restraints added in 2.3 seconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 51 sheets defined 19.4% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.989A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 125 through 127 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 366 through 387 Processing helix chain 'A' and resid 403 through 456 removed outlier: 3.665A pdb=" N GLN A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.989A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG B 78 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 125 through 127 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 403 through 456 removed outlier: 3.665A pdb=" N GLN B 454 " --> pdb=" O LYS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.989A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 125 through 127 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 366 through 387 Processing helix chain 'C' and resid 403 through 456 removed outlier: 3.664A pdb=" N GLN C 454 " --> pdb=" O LYS C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 482 Processing helix chain 'D' and resid 61 through 65 removed outlier: 4.049A pdb=" N GLU D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY D 65 " --> pdb=" O SER D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 65' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.050A pdb=" N GLU E 64 " --> pdb=" O PRO E 61 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY E 65 " --> pdb=" O SER E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 65' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.049A pdb=" N GLU H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY H 65 " --> pdb=" O SER H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.197A pdb=" N GLU A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.884A pdb=" N LEU A 51 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.493A pdb=" N LEU A 59 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.520A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.520A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.354A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB3, first strand: chain 'B' and resid 360 through 365 Processing sheet with id=AB4, first strand: chain 'B' and resid 24 through 26 removed outlier: 4.197A pdb=" N GLU B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.884A pdb=" N LEU B 51 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.493A pdb=" N LEU B 59 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.520A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.520A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.355A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'B' and resid 286 through 287 Processing sheet with id=AC5, first strand: chain 'C' and resid 360 through 365 Processing sheet with id=AC6, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.197A pdb=" N GLU C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.883A pdb=" N LEU C 51 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.493A pdb=" N LEU C 59 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.519A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.519A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.355A pdb=" N ALA C 138 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N ASN C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AD7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.175A pdb=" N TRP D 35A" --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN D 50 " --> pdb=" O TRP D 35A" (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.977A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR D 98 " --> pdb=" O THR D 100E" (cutoff:3.500A) removed outlier: 5.708A pdb=" N THR D 100E" --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.175A pdb=" N TRP E 35A" --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN E 50 " --> pdb=" O TRP E 35A" (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.976A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR E 98 " --> pdb=" O THR E 100E" (cutoff:3.500A) removed outlier: 5.708A pdb=" N THR E 100E" --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.488A pdb=" N TRP F 35 " --> pdb=" O ILE F 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 9 through 13 Processing sheet with id=AE6, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.488A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AE9, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.175A pdb=" N TRP H 35A" --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.976A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR H 98 " --> pdb=" O THR H 100E" (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR H 100E" --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.488A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AF6, first strand: chain 'L' and resid 19 through 24 765 hydrogen bonds defined for protein. 1944 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: 7.04 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.25: 2835 1.25 - 1.41: 4628 1.41 - 1.57: 9682 1.57 - 1.72: 138 1.72 - 1.88: 120 Bond restraints: 17403 Sorted by residual: bond pdb=" C TYR G 30C" pdb=" O TYR G 30C" ideal model delta sigma weight residual 1.234 1.093 0.141 1.26e-02 6.30e+03 1.25e+02 bond pdb=" C TYR F 30C" pdb=" O TYR F 30C" ideal model delta sigma weight residual 1.234 1.093 0.141 1.26e-02 6.30e+03 1.25e+02 bond pdb=" C TYR L 30C" pdb=" O TYR L 30C" ideal model delta sigma weight residual 1.234 1.093 0.140 1.26e-02 6.30e+03 1.24e+02 bond pdb=" C ASN L 31 " pdb=" O ASN L 31 " ideal model delta sigma weight residual 1.235 1.107 0.129 1.26e-02 6.30e+03 1.04e+02 bond pdb=" C ASN G 31 " pdb=" O ASN G 31 " ideal model delta sigma weight residual 1.235 1.107 0.128 1.26e-02 6.30e+03 1.04e+02 ... (remaining 17398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.41: 23539 7.41 - 14.83: 61 14.83 - 22.24: 1 22.24 - 29.66: 0 29.66 - 37.07: 3 Bond angle restraints: 23604 Sorted by residual: angle pdb=" N GLY B 342 " pdb=" CA GLY B 342 " pdb=" C GLY B 342 " ideal model delta sigma weight residual 115.32 135.20 -19.88 1.48e+00 4.57e-01 1.80e+02 angle pdb=" C2 NAG C 603 " pdb=" N2 NAG C 603 " pdb=" C7 NAG C 603 " ideal model delta sigma weight residual 124.56 161.63 -37.07 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C2 NAG B 603 " pdb=" N2 NAG B 603 " pdb=" C7 NAG B 603 " ideal model delta sigma weight residual 124.56 161.60 -37.04 3.00e+00 1.11e-01 1.52e+02 angle pdb=" C2 NAG A 603 " pdb=" N2 NAG A 603 " pdb=" C7 NAG A 603 " ideal model delta sigma weight residual 124.56 161.57 -37.01 3.00e+00 1.11e-01 1.52e+02 angle pdb=" N THR B 318 " pdb=" CA THR B 318 " pdb=" C THR B 318 " ideal model delta sigma weight residual 114.04 103.44 10.60 1.24e+00 6.50e-01 7.31e+01 ... (remaining 23599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 10164 17.90 - 35.80: 251 35.80 - 53.69: 73 53.69 - 71.59: 30 71.59 - 89.49: 18 Dihedral angle restraints: 10536 sinusoidal: 4407 harmonic: 6129 Sorted by residual: dihedral pdb=" CB CYS B 64 " pdb=" SG CYS B 64 " pdb=" SG CYS B 76 " pdb=" CB CYS B 76 " ideal model delta sinusoidal sigma weight residual -86.00 -123.20 37.20 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 76 " pdb=" CB CYS A 76 " ideal model delta sinusoidal sigma weight residual -86.00 -123.19 37.19 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS C 76 " pdb=" CB CYS C 76 " ideal model delta sinusoidal sigma weight residual -86.00 -123.15 37.15 1 1.00e+01 1.00e-02 1.95e+01 ... (remaining 10533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1737 0.090 - 0.181: 683 0.181 - 0.271: 115 0.271 - 0.361: 48 0.361 - 0.452: 12 Chirality restraints: 2595 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.27e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.26e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 ... (remaining 2592 not shown) Planarity restraints: 3045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 195 " 0.068 2.00e-02 2.50e+03 3.57e-02 2.55e+01 pdb=" CG TYR A 195 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 195 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 195 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 195 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR A 195 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 195 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 195 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 195 " -0.068 2.00e-02 2.50e+03 3.57e-02 2.55e+01 pdb=" CG TYR B 195 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 195 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 195 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 195 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B 195 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 195 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 195 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 195 " 0.068 2.00e-02 2.50e+03 3.55e-02 2.52e+01 pdb=" CG TYR C 195 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR C 195 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR C 195 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR C 195 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR C 195 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR C 195 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 195 " 0.050 2.00e-02 2.50e+03 ... (remaining 3042 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 71 2.57 - 3.15: 13561 3.15 - 3.73: 25559 3.73 - 4.32: 39936 4.32 - 4.90: 63625 Nonbonded interactions: 142752 Sorted by model distance: nonbonded pdb=" CD2 LEU F 4 " pdb=" OD2 ASP F 29 " model vdw 1.987 3.460 nonbonded pdb=" CD2 LEU G 4 " pdb=" OD2 ASP G 29 " model vdw 1.987 3.460 nonbonded pdb=" CD2 LEU L 4 " pdb=" OD2 ASP L 29 " model vdw 1.987 3.460 nonbonded pdb=" OG SER B 136 " pdb=" NE2 GLN B 226 " model vdw 2.058 3.120 nonbonded pdb=" OG SER C 136 " pdb=" NE2 GLN C 226 " model vdw 2.059 3.120 ... (remaining 142747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 43.100 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.100 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.021 0.141 17403 Z= 1.391 Angle : 1.795 37.074 23604 Z= 1.192 Chirality : 0.102 0.452 2595 Planarity : 0.009 0.046 3033 Dihedral : 10.248 89.486 6576 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 0.83 (0.17), residues: 2121 helix: 0.89 (0.26), residues: 336 sheet: 0.92 (0.21), residues: 537 loop : 0.40 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.009 TRP L 35 HIS 0.006 0.002 HIS A 183 PHE 0.051 0.006 PHE C 118 TYR 0.068 0.010 TYR A 195 ARG 0.007 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8373 (mtp) cc_final: 0.7919 (mtp) REVERT: A 211 LYS cc_start: 0.8671 (tttp) cc_final: 0.8406 (tttm) REVERT: A 402 LEU cc_start: 0.8862 (mt) cc_final: 0.8515 (mm) REVERT: B 88 MET cc_start: 0.8276 (mtp) cc_final: 0.7774 (mtp) REVERT: C 88 MET cc_start: 0.8412 (mtp) cc_final: 0.7887 (mtp) REVERT: C 211 LYS cc_start: 0.8625 (tttp) cc_final: 0.8372 (tttm) REVERT: C 340 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7386 (pp20) REVERT: C 434 GLU cc_start: 0.7964 (tt0) cc_final: 0.7718 (tt0) REVERT: C 438 ASP cc_start: 0.7918 (m-30) cc_final: 0.7533 (m-30) REVERT: G 9 SER cc_start: 0.8356 (t) cc_final: 0.8150 (t) REVERT: L 26 THR cc_start: 0.8301 (p) cc_final: 0.7932 (t) outliers start: 0 outliers final: 2 residues processed: 388 average time/residue: 1.2750 time to fit residues: 552.8598 Evaluate side-chains 224 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 191 GLN A 224 ASN A 458 ASN B 130 HIS B 191 GLN B 210 ASN B 458 ASN C 130 HIS C 391 GLN C 458 ASN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN E 60 ASN G 53 HIS G 69 ASN H 5 GLN H 60 ASN L 69 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17403 Z= 0.223 Angle : 0.609 5.727 23604 Z= 0.341 Chirality : 0.044 0.187 2595 Planarity : 0.004 0.038 3033 Dihedral : 6.925 86.311 2686 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.94 % Allowed : 8.72 % Favored : 89.34 % 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: 0.76 (0.17), residues: 2121 helix: 2.37 (0.28), residues: 333 sheet: 0.95 (0.22), residues: 543 loop : -0.19 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 35A HIS 0.002 0.001 HIS C 354 PHE 0.026 0.002 PHE B 118 TYR 0.019 0.002 TYR E 35 ARG 0.004 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 278 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8204 (mtp) cc_final: 0.7717 (mtp) REVERT: A 211 LYS cc_start: 0.8612 (tttp) cc_final: 0.8085 (tttm) REVERT: A 340 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7292 (pp20) REVERT: A 438 ASP cc_start: 0.8174 (m-30) cc_final: 0.7841 (m-30) REVERT: B 88 MET cc_start: 0.8177 (mtp) cc_final: 0.7847 (mtp) REVERT: B 438 ASP cc_start: 0.7931 (m-30) cc_final: 0.7592 (m-30) REVERT: C 211 LYS cc_start: 0.8591 (tttp) cc_final: 0.8303 (tttm) REVERT: C 340 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7124 (pp20) REVERT: C 344 GLN cc_start: 0.8511 (mt0) cc_final: 0.8168 (mt0) REVERT: C 438 ASP cc_start: 0.7918 (m-30) cc_final: 0.7536 (m-30) REVERT: D 6 GLU cc_start: 0.8378 (mp0) cc_final: 0.8149 (mp0) REVERT: H 6 GLU cc_start: 0.8366 (mp0) cc_final: 0.8066 (mp0) outliers start: 36 outliers final: 19 residues processed: 295 average time/residue: 1.1022 time to fit residues: 368.0103 Evaluate side-chains 242 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 223 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain H residue 25 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 0.0980 chunk 129 optimal weight: 5.9990 chunk 52 optimal weight: 0.0970 chunk 191 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 189 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 186 ASN B 196 GLN B 389 ASN C 322 ASN C 379 ASN C 479 ASN E 60 ASN E 77 GLN H 60 ASN H 77 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17403 Z= 0.199 Angle : 0.536 9.129 23604 Z= 0.296 Chirality : 0.042 0.144 2595 Planarity : 0.004 0.031 3033 Dihedral : 6.344 85.963 2684 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.64 % Allowed : 11.04 % Favored : 86.32 % 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: 0.77 (0.18), residues: 2121 helix: 2.66 (0.28), residues: 333 sheet: 0.76 (0.21), residues: 579 loop : -0.19 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 35A HIS 0.023 0.001 HIS C 471 PHE 0.023 0.002 PHE B 118 TYR 0.015 0.002 TYR H 102 ARG 0.003 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 256 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8106 (mtp) cc_final: 0.7770 (mtp) REVERT: A 211 LYS cc_start: 0.8806 (tttp) cc_final: 0.8087 (tttm) REVERT: A 340 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7220 (pp20) REVERT: A 438 ASP cc_start: 0.8175 (m-30) cc_final: 0.7874 (m-30) REVERT: A 445 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7657 (mtmt) REVERT: A 490 LYS cc_start: 0.7713 (ttpt) cc_final: 0.7478 (ttmm) REVERT: B 210 ASN cc_start: 0.8290 (t0) cc_final: 0.8074 (t0) REVERT: C 211 LYS cc_start: 0.8625 (tttp) cc_final: 0.8281 (tttm) REVERT: C 322 ASN cc_start: 0.8539 (t0) cc_final: 0.8324 (t0) REVERT: C 340 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7042 (pp20) REVERT: C 438 ASP cc_start: 0.7949 (m-30) cc_final: 0.7602 (m-30) REVERT: C 445 LYS cc_start: 0.7825 (mtpp) cc_final: 0.7508 (mtmt) REVERT: D 6 GLU cc_start: 0.8218 (mp0) cc_final: 0.7978 (mp0) REVERT: E 67 VAL cc_start: 0.8458 (p) cc_final: 0.8216 (t) REVERT: H 6 GLU cc_start: 0.8326 (mp0) cc_final: 0.7990 (mp0) outliers start: 49 outliers final: 25 residues processed: 286 average time/residue: 1.1611 time to fit residues: 374.1146 Evaluate side-chains 242 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.9990 chunk 143 optimal weight: 0.0980 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 91 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 355 HIS C 389 ASN C 391 GLN E 77 GLN H 77 GLN L 69 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17403 Z= 0.234 Angle : 0.526 4.744 23604 Z= 0.287 Chirality : 0.042 0.141 2595 Planarity : 0.004 0.032 3033 Dihedral : 6.220 85.094 2684 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.12 % Allowed : 12.01 % Favored : 84.87 % 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: 0.74 (0.18), residues: 2121 helix: 2.78 (0.28), residues: 333 sheet: 0.64 (0.21), residues: 582 loop : -0.21 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 35A HIS 0.008 0.001 HIS C 471 PHE 0.026 0.002 PHE B 118 TYR 0.016 0.002 TYR D 102 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 235 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 CYS cc_start: 0.6730 (m) cc_final: 0.6301 (m) REVERT: A 88 MET cc_start: 0.8175 (mtp) cc_final: 0.7943 (mtp) REVERT: A 157 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8439 (tttt) REVERT: A 211 LYS cc_start: 0.8775 (tttp) cc_final: 0.8061 (tttm) REVERT: A 340 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7355 (pp20) REVERT: A 438 ASP cc_start: 0.8175 (m-30) cc_final: 0.7834 (m-30) REVERT: A 445 LYS cc_start: 0.7861 (mtpp) cc_final: 0.7508 (mtmt) REVERT: A 490 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7647 (ttmm) REVERT: B 210 ASN cc_start: 0.8287 (t0) cc_final: 0.8084 (t0) REVERT: C 340 GLU cc_start: 0.8090 (mm-30) cc_final: 0.6994 (pp20) REVERT: C 344 GLN cc_start: 0.8668 (mt0) cc_final: 0.8433 (mm-40) REVERT: C 438 ASP cc_start: 0.7983 (m-30) cc_final: 0.7682 (m-30) REVERT: C 445 LYS cc_start: 0.7724 (mtpp) cc_final: 0.7473 (mtpt) REVERT: E 67 VAL cc_start: 0.8483 (p) cc_final: 0.8233 (t) REVERT: H 6 GLU cc_start: 0.8334 (mp0) cc_final: 0.8010 (mp0) outliers start: 58 outliers final: 41 residues processed: 268 average time/residue: 1.2269 time to fit residues: 368.5356 Evaluate side-chains 254 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 211 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 182 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN C 355 HIS E 60 ASN F 38 ASN G 38 ASN H 77 GLN L 38 ASN L 53 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17403 Z= 0.350 Angle : 0.592 6.564 23604 Z= 0.319 Chirality : 0.045 0.143 2595 Planarity : 0.004 0.041 3033 Dihedral : 6.312 84.034 2684 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.66 % Allowed : 11.90 % Favored : 84.44 % 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: 0.48 (0.18), residues: 2121 helix: 2.65 (0.28), residues: 327 sheet: 0.39 (0.20), residues: 597 loop : -0.35 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 103 HIS 0.017 0.002 HIS B 471 PHE 0.031 0.003 PHE A 118 TYR 0.016 0.002 TYR D 100F ARG 0.002 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 227 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8286 (mtp) cc_final: 0.7604 (ttm) REVERT: A 157 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8532 (tttt) REVERT: A 211 LYS cc_start: 0.8816 (tttp) cc_final: 0.8059 (tttm) REVERT: A 340 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7291 (pp20) REVERT: A 413 MET cc_start: 0.8895 (ttp) cc_final: 0.8555 (ttp) REVERT: A 414 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8072 (mp0) REVERT: A 445 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7616 (mtmt) REVERT: A 472 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7326 (mptp) REVERT: B 64 CYS cc_start: 0.6490 (m) cc_final: 0.6001 (m) REVERT: B 137 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8209 (mmt90) REVERT: B 210 ASN cc_start: 0.8378 (t0) cc_final: 0.8169 (t0) REVERT: B 450 LYS cc_start: 0.9019 (tttm) cc_final: 0.8749 (tttp) REVERT: C 64 CYS cc_start: 0.6933 (m) cc_final: 0.6473 (m) REVERT: C 137 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7800 (mpt180) REVERT: C 230 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8396 (mtt) REVERT: C 340 GLU cc_start: 0.8115 (mm-30) cc_final: 0.6914 (pp20) REVERT: C 344 GLN cc_start: 0.8746 (mt0) cc_final: 0.8441 (mt0) REVERT: C 445 LYS cc_start: 0.7775 (mtpp) cc_final: 0.7500 (mtpt) REVERT: D 34 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: H 6 GLU cc_start: 0.8373 (mp0) cc_final: 0.8070 (mp0) outliers start: 68 outliers final: 47 residues processed: 267 average time/residue: 1.1743 time to fit residues: 353.6052 Evaluate side-chains 268 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 214 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17403 Z= 0.267 Angle : 0.538 5.926 23604 Z= 0.290 Chirality : 0.043 0.154 2595 Planarity : 0.004 0.033 3033 Dihedral : 6.161 84.915 2684 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.82 % Allowed : 12.28 % Favored : 83.90 % 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: 0.50 (0.18), residues: 2121 helix: 2.87 (0.28), residues: 327 sheet: 0.44 (0.21), residues: 579 loop : -0.41 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 35A HIS 0.010 0.001 HIS B 471 PHE 0.026 0.002 PHE A 118 TYR 0.013 0.002 TYR D 100F ARG 0.003 0.000 ARG A 435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 222 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8273 (mtp) cc_final: 0.7627 (ttm) REVERT: A 340 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7270 (pp20) REVERT: A 414 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8103 (mp0) REVERT: A 445 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7533 (mtmt) REVERT: A 472 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7333 (mptp) REVERT: A 490 LYS cc_start: 0.8002 (ttpp) cc_final: 0.7664 (ttmm) REVERT: B 195 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: C 137 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7805 (mpt180) REVERT: C 230 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8390 (mtt) REVERT: C 340 GLU cc_start: 0.8068 (mm-30) cc_final: 0.6925 (pp20) REVERT: C 344 GLN cc_start: 0.8716 (mt0) cc_final: 0.8446 (mt0) REVERT: C 445 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7487 (mtpt) REVERT: D 34 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: H 6 GLU cc_start: 0.8371 (mp0) cc_final: 0.8063 (mp0) outliers start: 71 outliers final: 46 residues processed: 264 average time/residue: 1.0965 time to fit residues: 327.6062 Evaluate side-chains 260 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 208 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 148 optimal weight: 0.0670 chunk 114 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 chunk 126 optimal weight: 0.4980 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN B 389 ASN L 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17403 Z= 0.148 Angle : 0.470 4.844 23604 Z= 0.256 Chirality : 0.040 0.168 2595 Planarity : 0.003 0.030 3033 Dihedral : 5.853 86.589 2684 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.48 % Allowed : 13.84 % Favored : 83.68 % 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: 0.68 (0.18), residues: 2121 helix: 3.01 (0.28), residues: 330 sheet: 0.61 (0.21), residues: 558 loop : -0.32 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35A HIS 0.006 0.001 HIS B 471 PHE 0.020 0.001 PHE A 118 TYR 0.010 0.001 TYR D 35 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7123 (pp20) REVERT: A 402 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8351 (mm) REVERT: A 413 MET cc_start: 0.8783 (ttp) cc_final: 0.8506 (ttp) REVERT: A 445 LYS cc_start: 0.7845 (mtpp) cc_final: 0.7489 (mtmt) REVERT: B 195 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: C 230 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8168 (mmt) REVERT: C 340 GLU cc_start: 0.7994 (mm-30) cc_final: 0.6845 (pp20) REVERT: C 344 GLN cc_start: 0.8704 (mt0) cc_final: 0.8484 (mt0) REVERT: C 445 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7398 (mtmt) REVERT: D 34 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: H 2 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7380 (p) REVERT: H 6 GLU cc_start: 0.8375 (mp0) cc_final: 0.8033 (mp0) REVERT: H 34 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: L 70 THR cc_start: 0.8722 (m) cc_final: 0.8476 (m) outliers start: 46 outliers final: 26 residues processed: 250 average time/residue: 1.1600 time to fit residues: 327.4057 Evaluate side-chains 243 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 210 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 overall best weight: 2.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 17403 Z= 0.461 Angle : 0.652 7.561 23604 Z= 0.345 Chirality : 0.047 0.169 2595 Planarity : 0.005 0.052 3033 Dihedral : 6.349 85.325 2684 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.98 % Allowed : 12.92 % Favored : 83.09 % 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: 0.32 (0.18), residues: 2121 helix: 2.68 (0.27), residues: 327 sheet: 0.33 (0.21), residues: 549 loop : -0.51 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 343 HIS 0.006 0.002 HIS B 295 PHE 0.039 0.003 PHE C 118 TYR 0.021 0.003 TYR E 102 ARG 0.004 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 221 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8562 (tttt) REVERT: A 340 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7312 (pp20) REVERT: A 445 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7667 (mtmt) REVERT: B 137 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8271 (mmt90) REVERT: B 195 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: B 450 LYS cc_start: 0.9038 (tttm) cc_final: 0.8781 (tttp) REVERT: C 230 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8437 (mtt) REVERT: C 340 GLU cc_start: 0.8138 (mm-30) cc_final: 0.6969 (pp20) REVERT: C 445 LYS cc_start: 0.7856 (mtpp) cc_final: 0.7553 (mtpt) REVERT: D 34 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: H 6 GLU cc_start: 0.8386 (mp0) cc_final: 0.8088 (mp0) REVERT: H 34 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: L 70 THR cc_start: 0.8771 (m) cc_final: 0.8539 (m) outliers start: 74 outliers final: 50 residues processed: 264 average time/residue: 1.1201 time to fit residues: 334.7222 Evaluate side-chains 276 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 219 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 GLN L 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17403 Z= 0.242 Angle : 0.536 7.156 23604 Z= 0.287 Chirality : 0.042 0.147 2595 Planarity : 0.004 0.034 3033 Dihedral : 6.105 86.677 2684 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.64 % Allowed : 14.59 % Favored : 82.77 % 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: 0.44 (0.18), residues: 2121 helix: 2.90 (0.28), residues: 327 sheet: 0.32 (0.21), residues: 564 loop : -0.43 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35A HIS 0.005 0.001 HIS A 471 PHE 0.025 0.002 PHE C 118 TYR 0.016 0.002 TYR E 102 ARG 0.002 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 214 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7158 (pp20) REVERT: A 445 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7546 (mtmt) REVERT: B 137 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8244 (mmt90) REVERT: B 195 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: C 137 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7754 (mpt180) REVERT: C 230 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8201 (mtt) REVERT: C 340 GLU cc_start: 0.8062 (mm-30) cc_final: 0.6904 (pp20) REVERT: C 344 GLN cc_start: 0.8714 (mt0) cc_final: 0.8446 (mt0) REVERT: C 445 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7483 (mtpt) REVERT: D 34 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: H 6 GLU cc_start: 0.8413 (mp0) cc_final: 0.8099 (mp0) REVERT: H 34 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: L 70 THR cc_start: 0.8758 (m) cc_final: 0.8528 (m) outliers start: 49 outliers final: 37 residues processed: 247 average time/residue: 1.1273 time to fit residues: 314.7097 Evaluate side-chains 252 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 208 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 192 optimal weight: 0.0470 chunk 166 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17403 Z= 0.204 Angle : 0.510 6.052 23604 Z= 0.275 Chirality : 0.042 0.148 2595 Planarity : 0.003 0.032 3033 Dihedral : 5.975 88.041 2684 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.75 % Allowed : 14.59 % Favored : 82.66 % 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: 0.54 (0.18), residues: 2121 helix: 2.98 (0.27), residues: 327 sheet: 0.39 (0.21), residues: 564 loop : -0.37 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 35A HIS 0.004 0.001 HIS A 471 PHE 0.025 0.002 PHE C 118 TYR 0.013 0.001 TYR E 102 ARG 0.002 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 217 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7143 (pp20) REVERT: A 445 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7511 (mtmt) REVERT: B 137 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8226 (mmt90) REVERT: B 195 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: C 137 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7729 (mpt180) REVERT: C 230 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8130 (mtt) REVERT: C 340 GLU cc_start: 0.8053 (mm-30) cc_final: 0.6904 (pp20) REVERT: C 344 GLN cc_start: 0.8698 (mt0) cc_final: 0.8446 (mt0) REVERT: C 445 LYS cc_start: 0.7746 (mtpp) cc_final: 0.7470 (mtpt) REVERT: D 34 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: G 60 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7954 (m-40) REVERT: H 2 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7189 (p) REVERT: H 6 GLU cc_start: 0.8392 (mp0) cc_final: 0.8099 (mp0) REVERT: H 34 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7522 (m-80) REVERT: L 70 THR cc_start: 0.8723 (m) cc_final: 0.8481 (m) outliers start: 51 outliers final: 35 residues processed: 251 average time/residue: 1.1390 time to fit residues: 324.7705 Evaluate side-chains 251 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 207 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106550 restraints weight = 19862.906| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.80 r_work: 0.3105 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17403 Z= 0.236 Angle : 0.531 6.298 23604 Z= 0.285 Chirality : 0.042 0.165 2595 Planarity : 0.004 0.033 3033 Dihedral : 6.019 88.377 2684 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.69 % Allowed : 15.24 % Favored : 82.07 % 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: 0.51 (0.18), residues: 2121 helix: 2.94 (0.27), residues: 327 sheet: 0.38 (0.21), residues: 564 loop : -0.39 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 103 HIS 0.004 0.001 HIS A 471 PHE 0.026 0.002 PHE C 118 TYR 0.015 0.002 TYR E 102 ARG 0.002 0.000 ARG C 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6410.75 seconds wall clock time: 113 minutes 23.47 seconds (6803.47 seconds total)