Starting phenix.real_space_refine on Mon Jul 22 05:06:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp7_41469/07_2024/8tp7_41469.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp7_41469/07_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_41469/07_2024/8tp7_41469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp7_41469/07_2024/8tp7_41469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp7_41469/07_2024/8tp7_41469.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp7_41469/07_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 Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 174": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 9.36, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 7.65 Conformation dependent library (CDL) restraints added in 3.1 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: 2.81 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: 6.26 Time building geometry restraints manager: 8.27 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: 97.16 - 110.05: 4421 110.05 - 122.95: 17327 122.95 - 135.84: 1853 135.84 - 148.74: 0 148.74 - 161.63: 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 2.520 nonbonded pdb=" OG SER C 136 " pdb=" NE2 GLN C 226 " model vdw 2.059 2.520 ... (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 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: 2.260 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: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 48.120 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.320 ------------------------------------------------------------------------------- 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 : 1.774 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: 1.2803 time to fit residues: 553.1092 Evaluate side-chains 224 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 2.024 ------------------------------------------------------------------------------- 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: 0.9980 chunk 159 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.8223 moved from start: 0.2216 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= 0.230 Angle : 0.604 5.917 23604 Z= 0.336 Chirality : 0.044 0.150 2595 Planarity : 0.004 0.030 3033 Dihedral : 6.838 86.429 2686 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.37 % Allowed : 8.56 % Favored : 89.07 % 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: 0.74 (0.17), residues: 2121 helix: 2.42 (0.28), residues: 333 sheet: 0.95 (0.22), residues: 525 loop : -0.21 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 35A HIS 0.003 0.001 HIS C 298 PHE 0.027 0.002 PHE B 118 TYR 0.018 0.002 TYR E 35 ARG 0.003 0.001 ARG B 78 *********************** 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 322 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 278 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8253 (mtp) cc_final: 0.7722 (mtp) REVERT: A 211 LYS cc_start: 0.8647 (tttp) cc_final: 0.8080 (tttm) REVERT: A 340 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7296 (pp20) REVERT: A 438 ASP cc_start: 0.8179 (m-30) cc_final: 0.7839 (m-30) REVERT: B 88 MET cc_start: 0.8212 (mtp) cc_final: 0.7841 (mtp) REVERT: B 438 ASP cc_start: 0.7955 (m-30) cc_final: 0.7619 (m-30) REVERT: C 211 LYS cc_start: 0.8610 (tttp) cc_final: 0.8311 (tttm) REVERT: C 340 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7193 (pp20) REVERT: C 344 GLN cc_start: 0.8487 (mt0) cc_final: 0.8144 (mt0) REVERT: C 372 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8162 (ttpt) REVERT: C 438 ASP cc_start: 0.8019 (m-30) cc_final: 0.7659 (m-30) REVERT: H 6 GLU cc_start: 0.8357 (mp0) cc_final: 0.8137 (mp0) outliers start: 44 outliers final: 24 residues processed: 296 average time/residue: 1.0922 time to fit residues: 365.9406 Evaluate side-chains 255 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 230 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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 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 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 301 THR Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain F residue 26 THR 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 92 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 52 optimal weight: 0.0870 chunk 191 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 196 GLN B 389 ASN C 322 ASN C 379 ASN C 479 ASN E 77 GLN H 77 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17403 Z= 0.191 Angle : 0.516 5.219 23604 Z= 0.285 Chirality : 0.042 0.153 2595 Planarity : 0.004 0.031 3033 Dihedral : 6.551 87.912 2684 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.69 % Allowed : 10.93 % Favored : 86.38 % 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: 0.72 (0.17), residues: 2121 helix: 2.71 (0.28), residues: 333 sheet: 0.88 (0.22), residues: 531 loop : -0.31 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 35A HIS 0.023 0.001 HIS C 471 PHE 0.023 0.002 PHE B 118 TYR 0.016 0.002 TYR A 491 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 303 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 253 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8151 (mtp) cc_final: 0.7789 (mtp) REVERT: A 211 LYS cc_start: 0.8744 (tttp) cc_final: 0.8176 (tttm) REVERT: A 340 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7242 (pp20) REVERT: A 438 ASP cc_start: 0.8166 (m-30) cc_final: 0.7827 (m-30) REVERT: A 445 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7678 (mtmt) REVERT: A 490 LYS cc_start: 0.7755 (ttpt) cc_final: 0.7518 (ttmm) REVERT: B 89 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: B 344 GLN cc_start: 0.8812 (mt0) cc_final: 0.8552 (mm-40) REVERT: C 211 LYS cc_start: 0.8654 (tttp) cc_final: 0.8308 (tttm) REVERT: C 322 ASN cc_start: 0.8534 (t0) cc_final: 0.8263 (t0) REVERT: C 340 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7048 (pp20) REVERT: C 344 GLN cc_start: 0.8564 (mt0) cc_final: 0.8293 (mt0) REVERT: C 372 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8141 (ttpt) REVERT: C 438 ASP cc_start: 0.7950 (m-30) cc_final: 0.7578 (m-30) REVERT: C 445 LYS cc_start: 0.7831 (mtpp) cc_final: 0.7526 (mtmt) REVERT: H 6 GLU cc_start: 0.8351 (mp0) cc_final: 0.8124 (mp0) outliers start: 50 outliers final: 27 residues processed: 284 average time/residue: 1.1227 time to fit residues: 360.4640 Evaluate side-chains 250 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 220 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 340 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 301 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 301 THR Chi-restraints excluded: chain C residue 372 LYS 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 D residue 83 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 83 THR 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: 7.9990 chunk 143 optimal weight: 0.0040 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 overall best weight: 1.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 210 ASN C 389 ASN C 391 GLN E 77 GLN H 50 ASN H 77 GLN L 38 ASN L 69 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17403 Z= 0.296 Angle : 0.568 5.920 23604 Z= 0.306 Chirality : 0.044 0.148 2595 Planarity : 0.004 0.038 3033 Dihedral : 6.540 88.091 2684 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.82 % Allowed : 11.20 % Favored : 84.98 % 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: 0.60 (0.18), residues: 2121 helix: 2.62 (0.27), residues: 333 sheet: 0.56 (0.21), residues: 585 loop : -0.29 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 35A HIS 0.015 0.001 HIS B 471 PHE 0.031 0.003 PHE C 118 TYR 0.019 0.002 TYR D 102 ARG 0.004 0.000 ARG B 435 *********************** 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 301 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 230 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8259 (mtp) cc_final: 0.7829 (mtp) REVERT: A 211 LYS cc_start: 0.8785 (tttp) cc_final: 0.8176 (tttm) REVERT: A 340 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7337 (pp20) REVERT: A 438 ASP cc_start: 0.8152 (m-30) cc_final: 0.7792 (m-30) REVERT: A 445 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7620 (mtmt) REVERT: A 490 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7536 (ttmm) REVERT: B 89 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: C 137 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7697 (mpt180) REVERT: C 340 GLU cc_start: 0.8100 (mm-30) cc_final: 0.6981 (pp20) REVERT: C 344 GLN cc_start: 0.8592 (mt0) cc_final: 0.8223 (mt0) REVERT: C 372 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8168 (ttpt) REVERT: C 438 ASP cc_start: 0.8005 (m-30) cc_final: 0.7660 (m-30) REVERT: C 441 ASP cc_start: 0.7970 (m-30) cc_final: 0.7760 (m-30) REVERT: C 445 LYS cc_start: 0.7774 (mtpp) cc_final: 0.7509 (mtpt) REVERT: D 75 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8016 (mttt) REVERT: H 6 GLU cc_start: 0.8388 (mp0) cc_final: 0.8178 (mp0) outliers start: 71 outliers final: 47 residues processed: 266 average time/residue: 1.2348 time to fit residues: 369.7269 Evaluate side-chains 267 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 215 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 159 SER Chi-restraints excluded: chain A residue 197 ASN 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 462 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 197 ASN 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 279 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 301 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 291 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain D residue 75 LYS 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 26 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain H residue 25 SER 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: 4.9990 chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 483 ASN F 37 GLN L 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17403 Z= 0.195 Angle : 0.491 5.290 23604 Z= 0.266 Chirality : 0.041 0.145 2595 Planarity : 0.003 0.031 3033 Dihedral : 6.256 89.512 2684 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.12 % Allowed : 13.03 % Favored : 83.84 % 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: 0.69 (0.18), residues: 2121 helix: 2.84 (0.27), residues: 330 sheet: 0.67 (0.21), residues: 579 loop : -0.31 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 35A HIS 0.010 0.001 HIS B 471 PHE 0.023 0.002 PHE A 118 TYR 0.013 0.001 TYR D 102 ARG 0.004 0.000 ARG B 435 *********************** 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 282 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 224 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8221 (mtp) cc_final: 0.7926 (mtp) REVERT: A 137 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8036 (mpt180) REVERT: A 340 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7245 (pp20) REVERT: A 438 ASP cc_start: 0.8197 (m-30) cc_final: 0.7881 (m-30) REVERT: A 445 LYS cc_start: 0.7890 (mtpp) cc_final: 0.7529 (mtmt) REVERT: A 483 ASN cc_start: 0.7332 (m-40) cc_final: 0.7055 (m110) REVERT: A 490 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7637 (ttmm) REVERT: C 137 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7709 (mpt180) REVERT: C 340 GLU cc_start: 0.8052 (mm-30) cc_final: 0.6921 (pp20) REVERT: C 344 GLN cc_start: 0.8582 (mt0) cc_final: 0.8335 (mt0) REVERT: C 438 ASP cc_start: 0.7986 (m-30) cc_final: 0.7702 (m-30) REVERT: C 441 ASP cc_start: 0.7902 (m-30) cc_final: 0.7677 (m-30) REVERT: C 445 LYS cc_start: 0.7750 (mtpp) cc_final: 0.7460 (mtmt) outliers start: 58 outliers final: 41 residues processed: 256 average time/residue: 1.2242 time to fit residues: 351.2921 Evaluate side-chains 258 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 214 time to evaluate : 1.962 ------------------------------------------------------------------------------- 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 137 ARG 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 460 LYS 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 279 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 301 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 137 ARG Chi-restraints excluded: chain C residue 291 THR 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 78 VAL Chi-restraints excluded: chain D residue 83 THR 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 E residue 108 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 26 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 60 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN G 38 ASN L 53 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 17403 Z= 0.432 Angle : 0.627 6.939 23604 Z= 0.334 Chirality : 0.046 0.152 2595 Planarity : 0.004 0.049 3033 Dihedral : 6.529 88.552 2684 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.31 % Allowed : 11.95 % Favored : 83.74 % 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: 0.34 (0.18), residues: 2121 helix: 2.61 (0.28), residues: 324 sheet: 0.35 (0.21), residues: 597 loop : -0.50 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 343 HIS 0.007 0.002 HIS B 471 PHE 0.033 0.003 PHE C 118 TYR 0.018 0.003 TYR C 161 ARG 0.004 0.000 ARG B 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 305 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 225 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8330 (mtp) cc_final: 0.7673 (ttm) REVERT: A 137 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7955 (mpt180) REVERT: A 157 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8541 (tttt) REVERT: A 197 ASN cc_start: 0.9265 (OUTLIER) cc_final: 0.8959 (m-40) REVERT: A 340 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7326 (pp20) REVERT: A 445 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7657 (mtmt) REVERT: A 483 ASN cc_start: 0.7495 (m-40) cc_final: 0.7201 (m110) REVERT: B 89 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: B 195 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: B 479 ASN cc_start: 0.8188 (m110) cc_final: 0.7980 (m-40) REVERT: C 137 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7667 (mpt180) REVERT: C 340 GLU cc_start: 0.8128 (mm-30) cc_final: 0.6960 (pp20) REVERT: C 441 ASP cc_start: 0.7980 (m-30) cc_final: 0.7744 (m-30) REVERT: C 445 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7525 (mtpt) outliers start: 80 outliers final: 54 residues processed: 274 average time/residue: 1.0751 time to fit residues: 333.9079 Evaluate side-chains 275 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 214 time to evaluate : 1.902 ------------------------------------------------------------------------------- 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 137 ARG Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 197 ASN 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 460 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 GLU 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 197 ASN 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 279 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 301 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 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 26 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 60 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 171 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** C 298 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17403 Z= 0.167 Angle : 0.488 7.466 23604 Z= 0.264 Chirality : 0.041 0.157 2595 Planarity : 0.003 0.031 3033 Dihedral : 6.109 89.986 2684 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.32 % Allowed : 14.11 % Favored : 83.58 % 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: 2.92 (0.28), residues: 327 sheet: 0.45 (0.21), residues: 600 loop : -0.40 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 84 HIS 0.006 0.001 HIS A 471 PHE 0.022 0.002 PHE C 118 TYR 0.011 0.001 TYR E 102 ARG 0.004 0.000 ARG B 435 *********************** 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 273 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 230 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8196 (mtp) cc_final: 0.7965 (mtp) REVERT: A 137 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7952 (mpt180) REVERT: A 157 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8370 (tttt) REVERT: A 340 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7124 (pp20) REVERT: A 445 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7526 (mtmt) REVERT: A 483 ASN cc_start: 0.7483 (m-40) cc_final: 0.7158 (m110) REVERT: A 490 LYS cc_start: 0.8011 (ttpt) cc_final: 0.7706 (ttmm) REVERT: B 89 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: B 195 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: B 479 ASN cc_start: 0.8125 (m110) cc_final: 0.7923 (m-40) REVERT: C 340 GLU cc_start: 0.8068 (mm-30) cc_final: 0.6848 (pp20) REVERT: C 344 GLN cc_start: 0.8558 (mt0) cc_final: 0.8296 (mt0) REVERT: C 441 ASP cc_start: 0.7915 (m-30) cc_final: 0.7678 (m-30) REVERT: C 445 LYS cc_start: 0.7739 (mtpp) cc_final: 0.7449 (mtmt) REVERT: D 34 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7837 (m-80) outliers start: 43 outliers final: 22 residues processed: 258 average time/residue: 1.1642 time to fit residues: 338.7998 Evaluate side-chains 242 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 214 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 137 ARG 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 340 GLU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain B residue 89 GLU 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 195 TYR 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 89 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain G residue 60 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 120 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 298 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: 0.8348 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17403 Z= 0.301 Angle : 0.550 7.489 23604 Z= 0.293 Chirality : 0.043 0.148 2595 Planarity : 0.004 0.037 3033 Dihedral : 6.223 89.906 2684 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.61 % Allowed : 13.52 % Favored : 82.88 % 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: 2.85 (0.28), residues: 327 sheet: 0.40 (0.22), residues: 558 loop : -0.46 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 103 HIS 0.006 0.001 HIS B 471 PHE 0.031 0.002 PHE B 118 TYR 0.021 0.002 TYR E 102 ARG 0.006 0.000 ARG B 435 *********************** 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 286 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 219 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8277 (mtp) cc_final: 0.7556 (ttm) REVERT: A 137 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7946 (mpt180) REVERT: A 157 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8402 (tttt) REVERT: A 219 THR cc_start: 0.7986 (m) cc_final: 0.7679 (m) REVERT: A 340 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7248 (pp20) REVERT: A 445 LYS cc_start: 0.7948 (mtpp) cc_final: 0.7582 (mtpt) REVERT: A 483 ASN cc_start: 0.7523 (m-40) cc_final: 0.7206 (m110) REVERT: A 490 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7701 (ttmm) REVERT: B 89 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: B 195 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: B 479 ASN cc_start: 0.8148 (m110) cc_final: 0.7935 (m-40) REVERT: C 137 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7729 (mpt180) REVERT: C 230 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8310 (mmt) REVERT: C 340 GLU cc_start: 0.8098 (mm-30) cc_final: 0.6955 (pp20) REVERT: C 344 GLN cc_start: 0.8568 (mt0) cc_final: 0.8289 (mt0) REVERT: C 441 ASP cc_start: 0.7971 (m-30) cc_final: 0.7726 (m-30) REVERT: C 445 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7499 (mtmt) REVERT: D 34 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7863 (m-80) outliers start: 67 outliers final: 40 residues processed: 263 average time/residue: 1.1255 time to fit residues: 334.3739 Evaluate side-chains 263 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 215 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 137 ARG 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 340 GLU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 89 GLU 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 198 VAL Chi-restraints excluded: chain B residue 213 SER 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 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 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 26 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 26 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 89 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: 2.9990 chunk 176 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.8339 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17403 Z= 0.262 Angle : 0.534 8.292 23604 Z= 0.286 Chirality : 0.043 0.179 2595 Planarity : 0.004 0.033 3033 Dihedral : 6.189 89.863 2684 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.23 % Allowed : 13.52 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.46 (0.18), residues: 2121 helix: 2.87 (0.28), residues: 327 sheet: 0.35 (0.21), residues: 576 loop : -0.42 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 103 HIS 0.005 0.001 HIS B 471 PHE 0.027 0.002 PHE A 118 TYR 0.017 0.002 TYR E 102 ARG 0.004 0.000 ARG B 137 *********************** 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 282 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 222 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8265 (mtp) cc_final: 0.8051 (mtp) REVERT: A 137 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7941 (mpt180) REVERT: A 157 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8484 (tttt) REVERT: A 219 THR cc_start: 0.7976 (m) cc_final: 0.7649 (m) REVERT: A 340 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7149 (pp20) REVERT: A 414 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8128 (mp0) REVERT: A 445 LYS cc_start: 0.7936 (mtpp) cc_final: 0.7572 (mtpt) REVERT: A 483 ASN cc_start: 0.7513 (m-40) cc_final: 0.7188 (m110) REVERT: A 490 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7729 (ttmm) REVERT: B 89 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: B 195 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: B 479 ASN cc_start: 0.8135 (m110) cc_final: 0.7931 (m-40) REVERT: C 137 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7731 (mpt180) REVERT: C 230 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8321 (mmt) REVERT: C 340 GLU cc_start: 0.8059 (mm-30) cc_final: 0.6930 (pp20) REVERT: C 344 GLN cc_start: 0.8569 (mt0) cc_final: 0.8304 (mt0) REVERT: C 441 ASP cc_start: 0.7970 (m-30) cc_final: 0.7729 (m-30) REVERT: C 445 LYS cc_start: 0.7791 (mtpp) cc_final: 0.7479 (mtmt) REVERT: D 34 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: H 34 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7545 (m-80) outliers start: 60 outliers final: 44 residues processed: 261 average time/residue: 1.1448 time to fit residues: 336.4713 Evaluate side-chains 273 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 220 time to evaluate : 1.949 ------------------------------------------------------------------------------- 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 137 ARG 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 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 89 GLU 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 197 ASN 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 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 E residue 108 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 26 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 34 TYR Chi-restraints excluded: chain H residue 75 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 192 optimal weight: 0.0070 chunk 166 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 355 HIS ** C 298 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17403 Z= 0.186 Angle : 0.485 7.958 23604 Z= 0.262 Chirality : 0.041 0.145 2595 Planarity : 0.003 0.031 3033 Dihedral : 5.970 89.496 2684 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.64 % Allowed : 14.54 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2121 helix: 2.99 (0.28), residues: 327 sheet: 0.53 (0.21), residues: 567 loop : -0.38 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 35A HIS 0.004 0.001 HIS B 471 PHE 0.024 0.002 PHE B 118 TYR 0.014 0.001 TYR E 102 ARG 0.004 0.000 ARG B 435 ********************** 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 275 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 226 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8219 (mtp) cc_final: 0.8010 (mtp) REVERT: A 157 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8427 (tttt) REVERT: A 219 THR cc_start: 0.7970 (m) cc_final: 0.7626 (m) REVERT: A 340 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7150 (pp20) REVERT: A 402 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8300 (mm) REVERT: A 414 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8104 (mp0) REVERT: A 445 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7558 (mtpt) REVERT: A 490 LYS cc_start: 0.8039 (ttpt) cc_final: 0.7744 (ttmm) REVERT: B 89 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: B 195 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: B 479 ASN cc_start: 0.8123 (m110) cc_final: 0.7919 (m-40) REVERT: C 230 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8297 (mmt) REVERT: C 340 GLU cc_start: 0.8033 (mm-30) cc_final: 0.6902 (pp20) REVERT: C 344 GLN cc_start: 0.8510 (mt0) cc_final: 0.8261 (mt0) REVERT: C 441 ASP cc_start: 0.7931 (m-30) cc_final: 0.7705 (m-30) REVERT: C 445 LYS cc_start: 0.7716 (mtpp) cc_final: 0.7429 (mtmt) REVERT: D 34 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: H 2 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7195 (p) REVERT: H 34 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7384 (m-80) outliers start: 49 outliers final: 34 residues processed: 260 average time/residue: 1.2013 time to fit residues: 353.2736 Evaluate side-chains 259 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 216 time to evaluate : 1.853 ------------------------------------------------------------------------------- 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 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 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 89 GLU 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 197 ASN 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 23 THR Chi-restraints excluded: chain C residue 29 ILE 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 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 83 THR Chi-restraints excluded: chain E residue 108 LEU 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 L residue 20 THR 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: 0.9990 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 24 optimal weight: 0.0670 chunk 46 optimal weight: 0.4980 chunk 166 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 21 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 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** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.107147 restraints weight = 19267.630| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.71 r_work: 0.3074 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17403 Z= 0.146 Angle : 0.470 7.906 23604 Z= 0.254 Chirality : 0.041 0.143 2595 Planarity : 0.003 0.030 3033 Dihedral : 5.856 89.141 2684 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.15 % Allowed : 15.35 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.65 (0.18), residues: 2121 helix: 3.02 (0.28), residues: 327 sheet: 0.54 (0.21), residues: 570 loop : -0.32 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 35A HIS 0.007 0.001 HIS G 39 PHE 0.020 0.001 PHE B 118 TYR 0.012 0.001 TYR E 102 ARG 0.004 0.000 ARG C 435 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6347.24 seconds wall clock time: 112 minutes 7.58 seconds (6727.58 seconds total)