Starting phenix.real_space_refine on Tue Aug 6 17:43:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp6_41468/08_2024/8tp6_41468.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp6_41468/08_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_41468/08_2024/8tp6_41468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp6_41468/08_2024/8tp6_41468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp6_41468/08_2024/8tp6_41468.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp6_41468/08_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-5409/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: 9.47, per 1000 atoms: 0.56 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: 6.03 Conformation dependent library (CDL) restraints added in 2.8 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: 3.01 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: 6.89 Time building geometry restraints manager: 6.67 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 3.120 nonbonded pdb=" OD2 ASP B 41 " pdb=" NZ LYS B 45 " model vdw 2.393 3.120 nonbonded pdb=" OD2 ASP E 41 " pdb=" NZ LYS E 45 " model vdw 2.393 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 3.310 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: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 47.510 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.620 ------------------------------------------------------------------------------- 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 : 1.974 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: 0.3165 time to fit residues: 210.7076 Evaluate side-chains 211 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.138 ------------------------------------------------------------------------------- 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: 0.6980 chunk 158 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 244 ASN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17371 Z= 0.234 Angle : 0.682 8.320 23534 Z= 0.364 Chirality : 0.046 0.208 2642 Planarity : 0.005 0.065 3008 Dihedral : 8.348 69.078 2846 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.56 % Allowed : 6.79 % Favored : 91.65 % 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: 0.89 (0.18), residues: 2102 helix: 1.60 (0.26), residues: 344 sheet: 1.12 (0.22), residues: 558 loop : 0.10 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 84 HIS 0.014 0.002 HIS B 354 PHE 0.017 0.002 PHE B 118 TYR 0.024 0.002 TYR A 168 ARG 0.006 0.001 ARG B 262a *********************** 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 294 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 265 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.5270 (mp0) cc_final: 0.4849 (mp0) REVERT: B 460 LYS cc_start: 0.8461 (pttt) cc_final: 0.8248 (ptmm) outliers start: 29 outliers final: 20 residues processed: 286 average time/residue: 0.2796 time to fit residues: 123.4406 Evaluate side-chains 225 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 1.940 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.0020 chunk 157 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 188 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- 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 A 244 ASN A 354 HIS A 355 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 HIS ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS C 58 ASN E 117 HIS E 344 GLN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17371 Z= 0.234 Angle : 0.616 10.231 23534 Z= 0.331 Chirality : 0.045 0.216 2642 Planarity : 0.004 0.050 3008 Dihedral : 6.585 42.484 2846 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.58 % Allowed : 8.56 % Favored : 88.85 % 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: 0.75 (0.18), residues: 2102 helix: 1.85 (0.27), residues: 345 sheet: 0.99 (0.21), residues: 564 loop : -0.11 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 84 HIS 0.016 0.002 HIS A 354 PHE 0.020 0.002 PHE A 439 TYR 0.026 0.002 TYR E 486 ARG 0.006 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 277 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 229 time to evaluate : 1.744 Fit side-chains outliers start: 48 outliers final: 31 residues processed: 261 average time/residue: 0.2663 time to fit residues: 106.8723 Evaluate side-chains 225 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 194 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 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 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 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 310 LYS 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 F residue 107 THR Chi-restraints excluded: chain G residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 187 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 180 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 HIS H 39 GLN H 58 ASN L 38 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN G 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17371 Z= 0.252 Angle : 0.602 9.919 23534 Z= 0.320 Chirality : 0.045 0.226 2642 Planarity : 0.004 0.052 3008 Dihedral : 5.788 40.055 2846 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.58 % Allowed : 9.42 % Favored : 87.99 % 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: 0.60 (0.18), residues: 2102 helix: 1.82 (0.27), residues: 345 sheet: 0.81 (0.21), residues: 580 loop : -0.21 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 84 HIS 0.014 0.002 HIS B 354 PHE 0.017 0.002 PHE B 467 TYR 0.023 0.002 TYR B 486 ARG 0.007 0.001 ARG G 24 *********************** 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 257 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 209 time to evaluate : 1.914 Fit side-chains REVERT: A 239 MET cc_start: 0.8274 (mtm) cc_final: 0.8045 (mtm) REVERT: B 413 MET cc_start: 0.8625 (mtp) cc_final: 0.8359 (ttm) REVERT: C 53 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7670 (p) REVERT: E 216 ASP cc_start: 0.8037 (t0) cc_final: 0.7720 (t0) REVERT: E 413 MET cc_start: 0.8670 (mtp) cc_final: 0.8375 (ttm) outliers start: 48 outliers final: 33 residues processed: 244 average time/residue: 0.2892 time to fit residues: 109.1740 Evaluate side-chains 232 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 198 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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 136 SER 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 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 346 MET Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 409 LEU 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 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 136 SER Chi-restraints excluded: chain E residue 310 LYS 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 G residue 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 168 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 172 optimal weight: 0.0770 chunk 139 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN D 38 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17371 Z= 0.353 Angle : 0.636 8.777 23534 Z= 0.337 Chirality : 0.046 0.232 2642 Planarity : 0.005 0.056 3008 Dihedral : 5.762 38.812 2846 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.58 % Allowed : 9.53 % Favored : 87.88 % 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: 0.34 (0.18), residues: 2102 helix: 1.66 (0.26), residues: 345 sheet: 0.74 (0.22), residues: 568 loop : -0.44 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 84 HIS 0.013 0.002 HIS E 355 PHE 0.026 0.002 PHE A 118 TYR 0.022 0.002 TYR B 486 ARG 0.011 0.001 ARG E 262a *********************** 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 260 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 2.025 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.8302 (mtm) cc_final: 0.8067 (mtm) REVERT: H 58 ASN cc_start: 0.8774 (m-40) cc_final: 0.8451 (m110) REVERT: L 24 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7410 (ttp80) REVERT: B 413 MET cc_start: 0.8679 (mtp) cc_final: 0.8383 (ttm) REVERT: B 485 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7481 (m) REVERT: C 53 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7766 (p) REVERT: E 413 MET cc_start: 0.8612 (mtp) cc_final: 0.8300 (ttm) REVERT: F 52 TYR cc_start: 0.8415 (m-80) cc_final: 0.8163 (m-80) outliers start: 48 outliers final: 37 residues processed: 249 average time/residue: 0.2927 time to fit residues: 111.5306 Evaluate side-chains 239 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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 136 SER 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 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 34 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 485 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 78 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 5 THR 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 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 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: 6.9990 chunk 181 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 167 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN D 3 GLN E 355 HIS E 471 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17371 Z= 0.289 Angle : 0.602 9.133 23534 Z= 0.319 Chirality : 0.045 0.223 2642 Planarity : 0.004 0.058 3008 Dihedral : 5.653 38.262 2846 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.53 % Allowed : 10.12 % Favored : 87.35 % 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: 1.72 (0.26), residues: 345 sheet: 0.71 (0.22), residues: 566 loop : -0.49 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 84 HIS 0.012 0.002 HIS B 355 PHE 0.034 0.002 PHE A 118 TYR 0.022 0.002 TYR B 486 ARG 0.007 0.001 ARG H 81 *********************** 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 263 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 216 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8309 (mtm) cc_final: 0.8106 (mtm) REVERT: L 24 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7461 (ttp80) REVERT: B 485 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7529 (m) REVERT: E 413 MET cc_start: 0.8535 (mtp) cc_final: 0.8218 (ttm) outliers start: 47 outliers final: 35 residues processed: 250 average time/residue: 0.2760 time to fit residues: 106.2009 Evaluate side-chains 235 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 199 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 118 PHE 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 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 176 MET Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE 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 118 PHE 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 107 THR Chi-restraints excluded: chain G residue 20 THR 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: 3.9990 chunk 22 optimal weight: 0.9980 chunk 115 optimal weight: 0.0010 chunk 147 optimal weight: 0.8980 chunk 114 optimal weight: 0.3980 chunk 170 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 ASN E 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17371 Z= 0.169 Angle : 0.561 12.054 23534 Z= 0.295 Chirality : 0.043 0.223 2642 Planarity : 0.004 0.057 3008 Dihedral : 5.320 36.883 2846 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.05 % Allowed : 11.15 % Favored : 86.81 % 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: 0.42 (0.18), residues: 2102 helix: 1.91 (0.26), residues: 344 sheet: 0.81 (0.22), residues: 571 loop : -0.47 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 84 HIS 0.014 0.001 HIS B 355 PHE 0.029 0.002 PHE A 118 TYR 0.022 0.001 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 257 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 219 time to evaluate : 2.017 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.8308 (mtm) cc_final: 0.8094 (mtm) REVERT: A 279 THR cc_start: 0.6419 (t) cc_final: 0.6120 (t) REVERT: H 58 ASN cc_start: 0.8768 (m-40) cc_final: 0.8436 (m110) REVERT: L 24 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.7432 (ttp80) REVERT: L 83 PHE cc_start: 0.7714 (m-80) cc_final: 0.7513 (m-80) REVERT: C 73 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8183 (m) REVERT: E 413 MET cc_start: 0.8491 (mtp) cc_final: 0.8256 (ttm) outliers start: 38 outliers final: 28 residues processed: 244 average time/residue: 0.2761 time to fit residues: 103.8620 Evaluate side-chains 227 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 277 CYS Chi-restraints excluded: chain A residue 413 MET 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 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 277 CYS Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 92 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 124 optimal weight: 9.9990 chunk 80 optimal weight: 0.0060 chunk 120 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN E 355 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17371 Z= 0.205 Angle : 0.576 10.658 23534 Z= 0.301 Chirality : 0.044 0.232 2642 Planarity : 0.004 0.053 3008 Dihedral : 5.268 36.755 2846 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.62 % Allowed : 11.69 % Favored : 86.70 % 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 (0.18), residues: 2102 helix: 1.99 (0.26), residues: 344 sheet: 0.90 (0.22), residues: 561 loop : -0.49 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 84 HIS 0.007 0.001 HIS B 355 PHE 0.040 0.002 PHE A 118 TYR 0.022 0.001 TYR B 486 ARG 0.008 0.000 ARG H 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 238 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 1.875 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.8308 (mtm) cc_final: 0.8092 (mtm) REVERT: H 58 ASN cc_start: 0.8791 (m-40) cc_final: 0.8440 (m110) REVERT: L 24 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7452 (ttp80) REVERT: C 73 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8168 (m) REVERT: E 413 MET cc_start: 0.8517 (mtp) cc_final: 0.8273 (ttm) outliers start: 30 outliers final: 25 residues processed: 231 average time/residue: 0.2767 time to fit residues: 97.6021 Evaluate side-chains 220 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 413 MET 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 107 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR 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 107 THR Chi-restraints excluded: chain G residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 192 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN H 39 GLN L 79 GLN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 17371 Z= 0.451 Angle : 0.707 10.050 23534 Z= 0.372 Chirality : 0.049 0.259 2642 Planarity : 0.005 0.061 3008 Dihedral : 6.003 44.041 2846 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.99 % Allowed : 11.85 % 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: -0.08 (0.18), residues: 2102 helix: 1.63 (0.26), residues: 345 sheet: 0.31 (0.22), residues: 570 loop : -0.74 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 84 HIS 0.008 0.002 HIS A 18 PHE 0.043 0.003 PHE A 118 TYR 0.023 0.002 TYR L 49 ARG 0.007 0.001 ARG H 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 238 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 201 time to evaluate : 1.770 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.8341 (mtm) cc_final: 0.8120 (mtm) REVERT: L 24 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7512 (ttp80) REVERT: L 83 PHE cc_start: 0.7649 (m-80) cc_final: 0.7350 (m-80) REVERT: E 413 MET cc_start: 0.8571 (mtp) cc_final: 0.8335 (ttm) REVERT: F 52 TYR cc_start: 0.8555 (m-80) cc_final: 0.8278 (m-80) outliers start: 37 outliers final: 33 residues processed: 229 average time/residue: 0.2986 time to fit residues: 103.5166 Evaluate side-chains 229 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 196 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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 268 MET Chi-restraints excluded: chain A residue 413 MET 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 107 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 176 MET Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 33 LEU 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 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 107 THR Chi-restraints excluded: chain G residue 20 THR 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: 2.9990 chunk 94 optimal weight: 0.0370 chunk 137 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN B 276 ASN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** E 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 17371 Z= 0.195 Angle : 0.590 10.354 23534 Z= 0.312 Chirality : 0.045 0.237 2642 Planarity : 0.004 0.060 3008 Dihedral : 5.627 41.588 2846 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.51 % Allowed : 12.65 % Favored : 85.84 % 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: 0.18 (0.18), residues: 2102 helix: 1.75 (0.26), residues: 345 sheet: 0.78 (0.22), residues: 532 loop : -0.67 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 35 HIS 0.009 0.001 HIS E 471 PHE 0.036 0.002 PHE E 467 TYR 0.022 0.001 TYR B 486 ARG 0.008 0.000 ARG H 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 230 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8327 (mtm) cc_final: 0.8116 (mtm) REVERT: H 58 ASN cc_start: 0.8775 (m-40) cc_final: 0.8276 (t0) REVERT: L 24 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7432 (ttp80) REVERT: L 83 PHE cc_start: 0.7569 (m-80) cc_final: 0.7282 (m-80) REVERT: B 460 LYS cc_start: 0.8086 (ptmt) cc_final: 0.7875 (pttt) REVERT: C 73 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8101 (m) REVERT: E 413 MET cc_start: 0.8544 (mtp) cc_final: 0.8314 (ttm) REVERT: F 52 TYR cc_start: 0.8349 (m-80) cc_final: 0.8130 (m-80) outliers start: 28 outliers final: 25 residues processed: 222 average time/residue: 0.2903 time to fit residues: 99.1265 Evaluate side-chains 219 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 1.850 ------------------------------------------------------------------------------- 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 413 MET 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 B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 118 PHE 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 107 THR Chi-restraints excluded: chain G residue 20 THR 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 50 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 chunk 145 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109448 restraints weight = 25844.210| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.59 r_work: 0.3317 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.271 17371 Z= 0.321 Angle : 0.794 59.199 23534 Z= 0.461 Chirality : 0.047 0.519 2642 Planarity : 0.004 0.059 3008 Dihedral : 5.618 41.529 2846 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.96 % Rotamer: Outliers : 1.45 % Allowed : 12.65 % Favored : 85.89 % 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: 0.18 (0.18), residues: 2102 helix: 1.75 (0.26), residues: 345 sheet: 0.79 (0.22), residues: 532 loop : -0.67 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 84 HIS 0.006 0.001 HIS E 471 PHE 0.034 0.002 PHE E 467 TYR 0.021 0.001 TYR B 486 ARG 0.007 0.000 ARG H 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3839.88 seconds wall clock time: 69 minutes 38.41 seconds (4178.41 seconds total)