Starting phenix.real_space_refine on Mon Jul 22 05:50:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp6_41468/07_2024/8tp6_41468.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp6_41468/07_2024/8tp6_41468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp6_41468/07_2024/8tp6_41468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp6_41468/07_2024/8tp6_41468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp6_41468/07_2024/8tp6_41468.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp6_41468/07_2024/8tp6_41468.cif" } resolution = 3.1 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= 0.045 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 96 5.16 5 C 10626 2.51 5 N 2864 2.21 5 O 3422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17008 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3806 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 19, 'TRANS': 460} Chain breaks: 1 Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "B" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3806 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 19, 'TRANS': 460} Chain breaks: 1 Chain: "C" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "D" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "E" Number of atoms: 3801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3801 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 19, 'TRANS': 459} Chain breaks: 1 Chain: "F" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.54, per 1000 atoms: 0.62 Number of scatterers: 17008 At special positions: 0 Unit cell: (121.9, 124.2, 166.75, 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 96 16.00 O 3422 8.00 N 2864 7.00 C 10626 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=2.05 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E 466 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.05 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.02 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 477 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 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 K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG P 1 " - " NAG P 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG Y 1 " - " NAG Y 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG h 1 " - " NAG h 2 " BETA1-6 " NAG K 1 " - " FUC K 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 4 " " NAG d 1 " - " FUC d 4 " NAG-ASN " NAG A 501 " - " ASN A 21 " " NAG A 502 " - " ASN A 33 " " NAG A 503 " - " ASN A 483 " " NAG B 501 " - " ASN B 21 " " NAG B 502 " - " ASN B 33 " " NAG B 503 " - " ASN B 483 " " NAG E 501 " - " ASN E 21 " " NAG E 502 " - " ASN E 33 " " NAG E 503 " - " ASN E 483 " " NAG K 1 " - " ASN A 169 " " NAG P 1 " - " ASN A 289 " " NAG U 1 " - " ASN B 169 " " NAG Y 1 " - " ASN B 289 " " NAG d 1 " - " ASN E 169 " " NAG h 1 " - " ASN E 289 " Time building additional restraints: 10.98 Conformation dependent library (CDL) restraints added in 4.1 seconds 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3874 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 51 sheets defined 19.6% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.598A pdb=" N SER A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A 114 " --> pdb=" O HIS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 127 removed outlier: 3.803A pdb=" N TRP A 127 " --> pdb=" O LYS A 125a" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 366 through 387 Processing helix chain 'A' and resid 403 through 456 removed outlier: 4.025A pdb=" N LEU A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.112A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.598A pdb=" N SER B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER B 114 " --> pdb=" O HIS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 removed outlier: 3.804A pdb=" N TRP B 127 " --> pdb=" O LYS B 125a" (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 403 through 456 removed outlier: 4.025A pdb=" N LEU B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.112A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 104 through 114 removed outlier: 3.598A pdb=" N SER E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER E 114 " --> pdb=" O HIS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 127 removed outlier: 3.803A pdb=" N TRP E 127 " --> pdb=" O LYS E 125a" (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'E' and resid 366 through 387 Processing helix chain 'E' and resid 403 through 456 removed outlier: 4.025A pdb=" N LEU E 409 " --> pdb=" O ARG E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 Processing helix chain 'E' and resid 487 through 491 Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.112A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.468A 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: 6.315A pdb=" N LEU A 51 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 5.590A 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: 5.949A pdb=" N LEU A 59 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.336A 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 Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 102 removed outlier: 7.873A 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: 7.225A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 9.700A 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 168 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288 removed outlier: 3.842A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.943A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG H 38 " --> pdb=" O CYS H 47 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N CYS H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.823A pdb=" N MET H 96 " --> pdb=" O PHE H 100D" (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE H 100D" --> pdb=" O MET H 96 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE H 98 " --> pdb=" O ASP H 100B" (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP H 100B" --> pdb=" O PHE H 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.603A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.603A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR L 97 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AC1, first strand: chain 'B' and resid 24 through 26 removed outlier: 4.467A pdb=" N GLU B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.314A pdb=" N LEU B 51 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 59 through 60 removed outlier: 5.950A pdb=" N LEU B 59 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AC7, first strand: chain 'B' and resid 100 through 102 removed outlier: 7.874A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.225A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 164 through 168 Processing sheet with id=AD1, first strand: chain 'B' and resid 286 through 288 removed outlier: 3.842A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.943A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG C 38 " --> pdb=" O CYS C 47 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N CYS C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.823A pdb=" N MET C 96 " --> pdb=" O PHE C 100D" (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE C 100D" --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE C 98 " --> pdb=" O ASP C 100B" (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP C 100B" --> pdb=" O PHE C 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.604A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.604A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR D 97 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 364 through 365 Processing sheet with id=AD9, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.467A pdb=" N GLU E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AE2, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.314A pdb=" N LEU E 51 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 59 through 60 removed outlier: 5.949A pdb=" N LEU E 59 " --> pdb=" O MET E 88 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE E 87 " --> pdb=" O MET E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AE6, first strand: chain 'E' and resid 100 through 102 removed outlier: 7.874A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.226A pdb=" N ALA E 138 " --> pdb=" O ASN E 144 " (cutoff:3.500A) removed outlier: 9.700A pdb=" N ASN E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 164 through 168 Processing sheet with id=AE9, first strand: chain 'E' and resid 286 through 288 removed outlier: 3.842A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.944A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG F 38 " --> pdb=" O CYS F 47 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N CYS F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.824A pdb=" N MET F 96 " --> pdb=" O PHE F 100D" (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE F 100D" --> pdb=" O MET F 96 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE F 98 " --> pdb=" O ASP F 100B" (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP F 100B" --> pdb=" O PHE F 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.604A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.604A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR G 97 " --> pdb=" O GLU G 90 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 1899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 11.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4469 1.33 - 1.46: 5295 1.46 - 1.60: 7442 1.60 - 1.73: 33 1.73 - 1.87: 132 Bond restraints: 17371 Sorted by residual: bond pdb=" CA VAL A 115 " pdb=" C VAL A 115 " ideal model delta sigma weight residual 1.526 1.436 0.090 9.00e-03 1.23e+04 9.94e+01 bond pdb=" CA VAL E 115 " pdb=" C VAL E 115 " ideal model delta sigma weight residual 1.526 1.437 0.089 9.00e-03 1.23e+04 9.87e+01 bond pdb=" CA VAL B 115 " pdb=" C VAL B 115 " ideal model delta sigma weight residual 1.526 1.437 0.089 9.00e-03 1.23e+04 9.87e+01 bond pdb=" CB HIS A 354 " pdb=" CG HIS A 354 " ideal model delta sigma weight residual 1.497 1.387 0.110 1.40e-02 5.10e+03 6.16e+01 bond pdb=" CB HIS E 354 " pdb=" CG HIS E 354 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.09e+01 ... (remaining 17366 not shown) Histogram of bond angle deviations from ideal: 97.24 - 104.65: 321 104.65 - 112.05: 7902 112.05 - 119.46: 6929 119.46 - 126.87: 8149 126.87 - 134.28: 233 Bond angle restraints: 23534 Sorted by residual: angle pdb=" CA PHE B 118 " pdb=" CB PHE B 118 " pdb=" CG PHE B 118 " ideal model delta sigma weight residual 113.80 124.92 -11.12 1.00e+00 1.00e+00 1.24e+02 angle pdb=" CA PHE A 118 " pdb=" CB PHE A 118 " pdb=" CG PHE A 118 " ideal model delta sigma weight residual 113.80 124.92 -11.12 1.00e+00 1.00e+00 1.24e+02 angle pdb=" CA PHE E 118 " pdb=" CB PHE E 118 " pdb=" CG PHE E 118 " ideal model delta sigma weight residual 113.80 124.91 -11.11 1.00e+00 1.00e+00 1.24e+02 angle pdb=" C GLY C 8 " pdb=" N PRO C 9 " pdb=" CA PRO C 9 " ideal model delta sigma weight residual 120.03 129.23 -9.20 9.90e-01 1.02e+00 8.64e+01 angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 120.03 129.19 -9.16 9.90e-01 1.02e+00 8.55e+01 ... (remaining 23529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 10379 21.06 - 42.11: 229 42.11 - 63.17: 60 63.17 - 84.22: 30 84.22 - 105.28: 21 Dihedral angle restraints: 10719 sinusoidal: 4638 harmonic: 6081 Sorted by residual: dihedral pdb=" C PHE B 118 " pdb=" N PHE B 118 " pdb=" CA PHE B 118 " pdb=" CB PHE B 118 " ideal model delta harmonic sigma weight residual -122.60 -111.56 -11.04 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" C PHE A 118 " pdb=" N PHE A 118 " pdb=" CA PHE A 118 " pdb=" CB PHE A 118 " ideal model delta harmonic sigma weight residual -122.60 -111.60 -11.00 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" C PHE E 118 " pdb=" N PHE E 118 " pdb=" CA PHE E 118 " pdb=" CB PHE E 118 " ideal model delta harmonic sigma weight residual -122.60 -111.61 -10.99 0 2.50e+00 1.60e-01 1.93e+01 ... (remaining 10716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1848 0.103 - 0.205: 622 0.205 - 0.308: 121 0.308 - 0.410: 24 0.410 - 0.513: 27 Chirality restraints: 2642 Sorted by residual: chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.66e+01 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 -2.59 0.19 2.00e-02 2.50e+03 9.50e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.39e+01 ... (remaining 2639 not shown) Planarity restraints: 3023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 33 " -0.057 2.00e-02 2.50e+03 5.91e-02 4.37e+01 pdb=" CG ASN E 33 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN E 33 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN E 33 " 0.091 2.00e-02 2.50e+03 pdb=" C1 NAG E 502 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 33 " 0.057 2.00e-02 2.50e+03 5.91e-02 4.37e+01 pdb=" CG ASN B 33 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 33 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 33 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 33 " -0.057 2.00e-02 2.50e+03 5.91e-02 4.36e+01 pdb=" CG ASN A 33 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 33 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 33 " 0.091 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.071 2.00e-02 2.50e+03 ... (remaining 3020 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5291 2.84 - 3.36: 15098 3.36 - 3.87: 29050 3.87 - 4.39: 34667 4.39 - 4.90: 57201 Nonbonded interactions: 141307 Sorted by model distance: nonbonded pdb=" N ILE B 335 " pdb=" N ALA B 336 " model vdw 2.326 2.560 nonbonded pdb=" C ALA B 334 " pdb=" N ALA B 336 " model vdw 2.385 3.350 nonbonded pdb=" OD2 ASP A 41 " pdb=" NZ LYS A 45 " model vdw 2.393 2.520 nonbonded pdb=" OD2 ASP B 41 " pdb=" NZ LYS B 45 " model vdw 2.393 2.520 nonbonded pdb=" OD2 ASP E 41 " pdb=" NZ LYS E 45 " model vdw 2.393 2.520 ... (remaining 141302 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 324 or resid 335 through 493 or resid 501 throu \ gh 503)) selection = (chain 'B' and (resid 11 through 324 or resid 335 through 493 or resid 501 throu \ gh 503)) selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'U' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'Y' selection = chain 'h' } 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: 4.310 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 57.900 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 0.115 17371 Z= 1.374 Angle : 1.775 12.143 23534 Z= 1.186 Chirality : 0.114 0.513 2642 Planarity : 0.009 0.043 3008 Dihedral : 11.866 105.278 6773 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2102 helix: 0.52 (0.24), residues: 341 sheet: 1.20 (0.20), residues: 561 loop : 0.61 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.008 TRP L 35 HIS 0.011 0.003 HIS B 354 PHE 0.052 0.008 PHE E 118 TYR 0.068 0.010 TYR E 448 ARG 0.006 0.001 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 LYS cc_start: 0.8461 (pttt) cc_final: 0.8220 (ptmm) REVERT: B 460 LYS cc_start: 0.8515 (pttt) cc_final: 0.8255 (ptmm) REVERT: E 474 ASP cc_start: 0.6531 (p0) cc_final: 0.6233 (t0) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.3191 time to fit residues: 210.8284 Evaluate side-chains 211 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 176 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 189 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17371 Z= 0.232 Angle : 0.667 7.899 23534 Z= 0.359 Chirality : 0.046 0.196 2642 Planarity : 0.004 0.041 3008 Dihedral : 8.421 70.720 2846 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.78 % Allowed : 6.73 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.87 (0.17), residues: 2102 helix: 1.66 (0.26), residues: 340 sheet: 1.07 (0.21), residues: 558 loop : 0.09 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 84 HIS 0.012 0.002 HIS A 471 PHE 0.018 0.002 PHE B 118 TYR 0.023 0.002 TYR A 168 ARG 0.005 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 263 time to evaluate : 1.970 Fit side-chains revert: symmetry clash REVERT: A 491 TYR cc_start: 0.6893 (m-80) cc_final: 0.6651 (m-80) REVERT: H 6 GLU cc_start: 0.5341 (mp0) cc_final: 0.5037 (mp0) REVERT: H 108 MET cc_start: 0.6984 (tpt) cc_final: 0.6528 (tpt) REVERT: B 460 LYS cc_start: 0.8419 (pttt) cc_final: 0.8218 (ptmm) outliers start: 33 outliers final: 25 residues processed: 285 average time/residue: 0.2951 time to fit residues: 127.0226 Evaluate side-chains 230 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 205 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 64 optimal weight: 0.1980 chunk 152 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS A 471 HIS H 39 GLN L 38 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS C 39 GLN D 38 GLN E 244 ASN E 344 GLN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN G 38 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17371 Z= 0.356 Angle : 0.678 10.510 23534 Z= 0.362 Chirality : 0.048 0.226 2642 Planarity : 0.005 0.054 3008 Dihedral : 6.950 43.099 2846 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.07 % Allowed : 8.19 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.46 (0.17), residues: 2102 helix: 1.56 (0.26), residues: 345 sheet: 0.73 (0.21), residues: 576 loop : -0.25 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 84 HIS 0.017 0.003 HIS A 354 PHE 0.025 0.003 PHE E 467 TYR 0.031 0.002 TYR A 448 ARG 0.005 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 223 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 MET cc_start: 0.7043 (tpt) cc_final: 0.6697 (tpt) REVERT: L 24 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.7328 (ttp80) REVERT: B 460 LYS cc_start: 0.8418 (pttt) cc_final: 0.8201 (ptmt) REVERT: C 53 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7802 (m) REVERT: G 24 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.7413 (ttp80) outliers start: 57 outliers final: 37 residues processed: 260 average time/residue: 0.2803 time to fit residues: 110.5824 Evaluate side-chains 237 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 199 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 310 LYS Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 187 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS H 58 ASN L 79 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 17371 Z= 0.546 Angle : 0.751 10.754 23534 Z= 0.396 Chirality : 0.051 0.247 2642 Planarity : 0.006 0.067 3008 Dihedral : 6.744 47.065 2846 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.72 % Allowed : 8.89 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2102 helix: 1.15 (0.26), residues: 343 sheet: 0.23 (0.21), residues: 591 loop : -0.69 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 84 HIS 0.009 0.002 HIS E 471 PHE 0.030 0.003 PHE B 118 TYR 0.027 0.003 TYR L 49 ARG 0.006 0.001 ARG B 262a *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 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: 69 poor density : 217 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8341 (mtm) cc_final: 0.8077 (mtm) REVERT: H 108 MET cc_start: 0.6983 (tpt) cc_final: 0.6677 (tpt) REVERT: L 24 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7474 (ttp80) REVERT: B 460 LYS cc_start: 0.8496 (pttt) cc_final: 0.8270 (ptmt) REVERT: C 53 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7722 (p) REVERT: C 108 MET cc_start: 0.6713 (tpt) cc_final: 0.6445 (tpt) REVERT: D 24 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7574 (ttp80) REVERT: E 413 MET cc_start: 0.8736 (mtp) cc_final: 0.8509 (ttm) REVERT: G 24 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7513 (ttp80) outliers start: 69 outliers final: 52 residues processed: 267 average time/residue: 0.2854 time to fit residues: 115.9722 Evaluate side-chains 253 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 200 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 30 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 168 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.0000 chunk 172 optimal weight: 0.3980 chunk 139 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 181 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS H 58 ASN B 276 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 HIS ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17371 Z= 0.157 Angle : 0.559 8.643 23534 Z= 0.297 Chirality : 0.043 0.232 2642 Planarity : 0.004 0.060 3008 Dihedral : 5.965 43.697 2846 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.99 % Allowed : 10.99 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.25 (0.18), residues: 2102 helix: 1.56 (0.27), residues: 345 sheet: 0.71 (0.22), residues: 561 loop : -0.50 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 84 HIS 0.010 0.001 HIS B 355 PHE 0.016 0.002 PHE L 54 TYR 0.022 0.001 TYR B 486 ARG 0.004 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 234 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 MET cc_start: 0.8667 (mtp) cc_final: 0.8465 (ttm) REVERT: H 25 SER cc_start: 0.8145 (p) cc_final: 0.7942 (m) REVERT: H 108 MET cc_start: 0.6920 (tpt) cc_final: 0.6543 (tpt) REVERT: L 24 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7384 (ttp80) REVERT: B 485 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7393 (m) REVERT: C 53 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7652 (p) REVERT: G 24 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7430 (ttp80) outliers start: 37 outliers final: 24 residues processed: 259 average time/residue: 0.2932 time to fit residues: 113.3768 Evaluate side-chains 238 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 212 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain G residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 67 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN B 382 ASN D 79 GLN ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17371 Z= 0.309 Angle : 0.615 8.404 23534 Z= 0.324 Chirality : 0.045 0.225 2642 Planarity : 0.004 0.059 3008 Dihedral : 5.970 44.689 2846 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.80 % Allowed : 10.93 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2102 helix: 1.62 (0.26), residues: 345 sheet: 0.55 (0.22), residues: 567 loop : -0.57 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 84 HIS 0.008 0.002 HIS B 354 PHE 0.023 0.002 PHE E 118 TYR 0.022 0.002 TYR B 486 ARG 0.006 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 214 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 MET cc_start: 0.8660 (mtp) cc_final: 0.8335 (ttm) REVERT: H 25 SER cc_start: 0.8213 (p) cc_final: 0.7991 (m) REVERT: H 108 MET cc_start: 0.6935 (tpt) cc_final: 0.6608 (tpt) REVERT: L 24 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7444 (ttp80) REVERT: B 478 MET cc_start: 0.6874 (mmm) cc_final: 0.6616 (mmm) REVERT: C 53 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7693 (p) REVERT: C 108 MET cc_start: 0.6724 (tpt) cc_final: 0.6481 (tpt) REVERT: D 24 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.7420 (ttm-80) REVERT: G 24 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7464 (ttp80) outliers start: 52 outliers final: 38 residues processed: 255 average time/residue: 0.2883 time to fit residues: 111.5641 Evaluate side-chains 243 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 204 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 194 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 ASN ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17371 Z= 0.274 Angle : 0.598 10.064 23534 Z= 0.315 Chirality : 0.045 0.240 2642 Planarity : 0.004 0.060 3008 Dihedral : 5.927 44.327 2846 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.85 % Allowed : 10.99 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.16 (0.18), residues: 2102 helix: 1.60 (0.26), residues: 344 sheet: 0.65 (0.22), residues: 559 loop : -0.61 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 84 HIS 0.006 0.001 HIS B 355 PHE 0.024 0.002 PHE E 118 TYR 0.023 0.002 TYR B 486 ARG 0.007 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 215 time to evaluate : 2.113 Fit side-chains revert: symmetry clash REVERT: A 478 MET cc_start: 0.6730 (mmm) cc_final: 0.6339 (mmm) REVERT: H 25 SER cc_start: 0.8233 (p) cc_final: 0.8004 (m) REVERT: H 58 ASN cc_start: 0.8823 (m-40) cc_final: 0.8472 (m110) REVERT: H 108 MET cc_start: 0.6924 (tpt) cc_final: 0.6565 (tpt) REVERT: L 24 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7427 (ttp80) REVERT: B 478 MET cc_start: 0.6891 (mmm) cc_final: 0.6615 (mmm) REVERT: C 53 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7673 (p) REVERT: C 108 MET cc_start: 0.6695 (tpt) cc_final: 0.6465 (tpt) REVERT: D 24 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7547 (ttm-80) REVERT: G 24 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7439 (ttp80) outliers start: 53 outliers final: 42 residues processed: 252 average time/residue: 0.2866 time to fit residues: 109.2409 Evaluate side-chains 250 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 207 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 124 optimal weight: 0.0050 chunk 80 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 128 optimal weight: 0.3980 chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17371 Z= 0.163 Angle : 0.557 11.014 23534 Z= 0.292 Chirality : 0.044 0.233 2642 Planarity : 0.004 0.058 3008 Dihedral : 5.549 42.579 2846 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.83 % Allowed : 11.95 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.31 (0.18), residues: 2102 helix: 1.76 (0.27), residues: 345 sheet: 0.89 (0.23), residues: 539 loop : -0.57 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 84 HIS 0.007 0.001 HIS B 355 PHE 0.019 0.002 PHE E 118 TYR 0.023 0.001 TYR B 486 ARG 0.008 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 227 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 MET cc_start: 0.6696 (mmm) cc_final: 0.6290 (mmm) REVERT: H 25 SER cc_start: 0.8212 (p) cc_final: 0.7993 (m) REVERT: H 58 ASN cc_start: 0.8830 (m-40) cc_final: 0.8515 (m110) REVERT: H 89 VAL cc_start: 0.8103 (t) cc_final: 0.7678 (t) REVERT: H 108 MET cc_start: 0.6926 (tpt) cc_final: 0.6577 (tpt) REVERT: L 24 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7401 (ttp80) REVERT: C 53 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7603 (p) REVERT: C 108 MET cc_start: 0.6663 (tpt) cc_final: 0.6419 (tpt) REVERT: G 24 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.7367 (ttp80) outliers start: 34 outliers final: 25 residues processed: 251 average time/residue: 0.2898 time to fit residues: 110.2761 Evaluate side-chains 243 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 217 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 192 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 0.0070 chunk 57 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 overall best weight: 2.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17371 Z= 0.385 Angle : 0.656 9.873 23534 Z= 0.342 Chirality : 0.047 0.250 2642 Planarity : 0.005 0.058 3008 Dihedral : 5.919 45.520 2846 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.15 % Allowed : 11.85 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2102 helix: 1.57 (0.26), residues: 344 sheet: 0.61 (0.23), residues: 516 loop : -0.74 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 84 HIS 0.007 0.002 HIS B 184 PHE 0.025 0.002 PHE E 118 TYR 0.023 0.002 TYR B 486 ARG 0.008 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 204 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 MET cc_start: 0.6744 (mmm) cc_final: 0.6325 (mmm) REVERT: H 25 SER cc_start: 0.8245 (p) cc_final: 0.8037 (m) REVERT: H 108 MET cc_start: 0.6933 (tpt) cc_final: 0.6653 (tpt) REVERT: L 24 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7465 (ttp80) REVERT: C 53 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7684 (p) REVERT: C 71 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8514 (tp) REVERT: C 108 MET cc_start: 0.6710 (tpt) cc_final: 0.6467 (tpt) REVERT: G 24 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7430 (ttp80) outliers start: 40 outliers final: 31 residues processed: 234 average time/residue: 0.2948 time to fit residues: 104.2657 Evaluate side-chains 234 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 121 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 ASN ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17371 Z= 0.226 Angle : 0.586 10.518 23534 Z= 0.306 Chirality : 0.045 0.239 2642 Planarity : 0.004 0.059 3008 Dihedral : 5.724 44.971 2846 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.78 % Allowed : 12.49 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.10 (0.18), residues: 2102 helix: 1.67 (0.26), residues: 344 sheet: 0.74 (0.23), residues: 512 loop : -0.70 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 84 HIS 0.017 0.001 HIS E 354 PHE 0.021 0.002 PHE E 118 TYR 0.023 0.002 TYR B 486 ARG 0.008 0.000 ARG F 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 207 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 MET cc_start: 0.6618 (mmm) cc_final: 0.6219 (mmm) REVERT: H 25 SER cc_start: 0.8197 (p) cc_final: 0.7996 (m) REVERT: H 58 ASN cc_start: 0.8800 (m-40) cc_final: 0.8448 (m110) REVERT: H 108 MET cc_start: 0.6905 (tpt) cc_final: 0.6591 (tpt) REVERT: L 24 ARG cc_start: 0.7688 (ttm-80) cc_final: 0.7416 (ttp80) REVERT: C 108 MET cc_start: 0.6675 (tpt) cc_final: 0.6414 (tpt) REVERT: D 3 GLN cc_start: 0.8777 (tp40) cc_final: 0.8529 (tp-100) REVERT: G 24 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7399 (ttp80) outliers start: 33 outliers final: 30 residues processed: 233 average time/residue: 0.3138 time to fit residues: 112.6859 Evaluate side-chains 235 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 30 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 50 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 24 optimal weight: 0.0270 chunk 46 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** 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 = 0.3858 r_free = 0.3858 target = 0.140998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.110136 restraints weight = 26002.734| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.61 r_work: 0.3315 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 17371 Z= 0.273 Angle : 0.777 59.190 23534 Z= 0.452 Chirality : 0.046 0.563 2642 Planarity : 0.004 0.059 3008 Dihedral : 5.722 44.975 2846 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.56 % Allowed : 12.92 % Favored : 85.51 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.57 % 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: 0.11 (0.18), residues: 2102 helix: 1.68 (0.26), residues: 344 sheet: 0.74 (0.23), residues: 512 loop : -0.70 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 84 HIS 0.018 0.001 HIS E 354 PHE 0.021 0.002 PHE E 118 TYR 0.022 0.002 TYR B 486 ARG 0.007 0.000 ARG F 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3964.09 seconds wall clock time: 71 minutes 50.56 seconds (4310.56 seconds total)