Starting phenix.real_space_refine on Thu Feb 15 12:58:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj6_14742/02_2024/7zj6_14742.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj6_14742/02_2024/7zj6_14742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj6_14742/02_2024/7zj6_14742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj6_14742/02_2024/7zj6_14742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj6_14742/02_2024/7zj6_14742.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj6_14742/02_2024/7zj6_14742.pdb" } resolution = 2.6 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= 0.006 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 57 5.16 5 C 7623 2.51 5 N 2088 2.21 5 O 2514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 329": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12282 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3889 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain: "B" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3889 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain: "C" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3889 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain: "D" 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: "E" 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: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "I" 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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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: "M" 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: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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: "B" 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: "C" 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 Time building chain proxies: 6.61, per 1000 atoms: 0.54 Number of scatterers: 12282 At special positions: 0 Unit cell: (95.04, 93.96, 149.04, 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 57 16.00 O 2514 8.00 N 2088 7.00 C 7623 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.05 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.05 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.05 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.05 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.04 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.05 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.05 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.05 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.05 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " BETA1-6 " NAG E 1 " - " FUC E 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 4 " " NAG M 1 " - " FUC M 4 " NAG-ASN " NAG A 601 " - " ASN A 483 " " NAG A 602 " - " ASN A 22 " " NAG B 601 " - " ASN B 483 " " NAG B 602 " - " ASN B 22 " " NAG C 601 " - " ASN C 483 " " NAG C 602 " - " ASN C 22 " " NAG D 1 " - " ASN A 38 " " NAG E 1 " - " ASN A 81 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 285 " " NAG H 1 " - " ASN B 38 " " NAG I 1 " - " ASN B 81 " " NAG J 1 " - " ASN B 165 " " NAG K 1 " - " ASN B 285 " " NAG L 1 " - " ASN C 38 " " NAG M 1 " - " ASN C 81 " " NAG N 1 " - " ASN C 165 " " NAG O 1 " - " ASN C 285 " Time building additional restraints: 5.21 Conformation dependent library (CDL) restraints added in 2.3 seconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 36 sheets defined 27.1% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.711A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.555A pdb=" N GLY A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.981A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 378 removed outlier: 3.599A pdb=" N THR A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 404 through 455 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 487 through 490 Processing helix chain 'A' and resid 491 through 501 removed outlier: 3.622A pdb=" N GLN A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.712A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL B 78 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 79 " --> pdb=" O CYS B 76 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.555A pdb=" N GLY B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 removed outlier: 3.982A pdb=" N GLN B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.599A pdb=" N THR B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 404 through 455 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 487 through 490 Processing helix chain 'B' and resid 491 through 501 removed outlier: 3.622A pdb=" N GLN B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.711A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 79 " --> pdb=" O CYS C 76 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.555A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.981A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 378 removed outlier: 3.600A pdb=" N THR C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 404 through 455 Processing helix chain 'C' and resid 474 through 484 Processing helix chain 'C' and resid 487 through 490 Processing helix chain 'C' and resid 491 through 501 removed outlier: 3.621A pdb=" N GLN C 501 " --> pdb=" O ASN C 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 363 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.565A pdb=" N THR 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: 5.869A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.320A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.174A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 8.115A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 166 through 169 removed outlier: 5.989A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.388A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.678A pdb=" N LYS A 391 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 361 through 363 Processing sheet with id=AB5, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.565A pdb=" N THR B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'B' and resid 51 through 54 removed outlier: 5.870A pdb=" N ILE B 51 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS B 277 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 53 " --> pdb=" O CYS B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.320A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 101 removed outlier: 5.175A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 removed outlier: 8.115A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'B' and resid 166 through 169 removed outlier: 5.991A pdb=" N ARG B 201 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 281 through 283 removed outlier: 4.387A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.680A pdb=" N LYS B 391 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 363 Processing sheet with id=AC8, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.565A pdb=" N THR C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.869A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.321A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.175A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 100 through 101 removed outlier: 8.116A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD7, first strand: chain 'C' and resid 166 through 169 removed outlier: 5.990A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.389A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 303 through 304 removed outlier: 3.678A pdb=" N LYS C 391 " --> pdb=" O GLY C 303 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1323 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: 5.22 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2417 1.33 - 1.45: 3130 1.45 - 1.57: 6900 1.57 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 12525 Sorted by residual: bond pdb=" N VAL B 384 " pdb=" CA VAL B 384 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.39e+01 bond pdb=" N VAL A 384 " pdb=" CA VAL A 384 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.38e+01 bond pdb=" N VAL C 384 " pdb=" CA VAL C 384 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.36e+01 bond pdb=" N GLY B 135 " pdb=" CA GLY B 135 " ideal model delta sigma weight residual 1.446 1.481 -0.035 9.50e-03 1.11e+04 1.34e+01 bond pdb=" N GLY A 135 " pdb=" CA GLY A 135 " ideal model delta sigma weight residual 1.446 1.481 -0.035 9.50e-03 1.11e+04 1.34e+01 ... (remaining 12520 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.79: 404 106.79 - 113.68: 6857 113.68 - 120.58: 5335 120.58 - 127.47: 4282 127.47 - 134.37: 108 Bond angle restraints: 16986 Sorted by residual: angle pdb=" CA ARG C 383 " pdb=" C ARG C 383 " pdb=" O ARG C 383 " ideal model delta sigma weight residual 120.55 114.69 5.86 1.06e+00 8.90e-01 3.05e+01 angle pdb=" CA ARG B 383 " pdb=" C ARG B 383 " pdb=" O ARG B 383 " ideal model delta sigma weight residual 120.55 114.72 5.83 1.06e+00 8.90e-01 3.03e+01 angle pdb=" CA ARG A 383 " pdb=" C ARG A 383 " pdb=" O ARG A 383 " ideal model delta sigma weight residual 120.55 114.76 5.79 1.06e+00 8.90e-01 2.98e+01 angle pdb=" CA GLY C 61 " pdb=" C GLY C 61 " pdb=" O GLY C 61 " ideal model delta sigma weight residual 121.58 116.74 4.84 9.00e-01 1.23e+00 2.89e+01 angle pdb=" CA GLY A 61 " pdb=" C GLY A 61 " pdb=" O GLY A 61 " ideal model delta sigma weight residual 121.58 116.80 4.78 9.00e-01 1.23e+00 2.82e+01 ... (remaining 16981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 7494 23.07 - 46.15: 468 46.15 - 69.22: 75 69.22 - 92.29: 60 92.29 - 115.36: 36 Dihedral angle restraints: 8133 sinusoidal: 3876 harmonic: 4257 Sorted by residual: dihedral pdb=" CA ASP B 60 " pdb=" C ASP B 60 " pdb=" N GLY B 61 " pdb=" CA GLY B 61 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASP C 60 " pdb=" C ASP C 60 " pdb=" N GLY C 61 " pdb=" CA GLY C 61 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASP A 60 " pdb=" C ASP A 60 " pdb=" N GLY A 61 " pdb=" CA GLY A 61 " ideal model delta harmonic sigma weight residual 180.00 158.05 21.95 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 8130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1397 0.093 - 0.186: 544 0.186 - 0.278: 63 0.278 - 0.371: 3 0.371 - 0.464: 3 Chirality restraints: 2010 Sorted by residual: chirality pdb=" C1 MAN F 5 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 5 " pdb=" O5 MAN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 2.93e+01 chirality pdb=" C1 FUC I 4 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 4 " pdb=" O5 FUC I 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 2.76e+01 chirality pdb=" C1 MAN N 5 " pdb=" O6 BMA N 3 " pdb=" C2 MAN N 5 " pdb=" O5 MAN N 5 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.70e+01 ... (remaining 2007 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.209 2.00e-02 2.50e+03 1.83e-01 4.18e+02 pdb=" C7 NAG H 2 " 0.106 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.291 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.207 2.00e-02 2.50e+03 1.81e-01 4.11e+02 pdb=" C7 NAG D 2 " -0.106 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.288 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " 0.207 2.00e-02 2.50e+03 1.81e-01 4.11e+02 pdb=" C7 NAG L 2 " -0.106 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " -0.288 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " 0.023 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 5878 3.00 - 3.47: 10440 3.47 - 3.95: 19940 3.95 - 4.42: 21669 4.42 - 4.90: 35462 Nonbonded interactions: 93389 Sorted by model distance: nonbonded pdb=" N ILE C 34 " pdb=" O ILE C 34 " model vdw 2.524 2.496 nonbonded pdb=" N ILE A 34 " pdb=" O ILE A 34 " model vdw 2.524 2.496 nonbonded pdb=" N ILE B 34 " pdb=" O ILE B 34 " model vdw 2.525 2.496 nonbonded pdb=" N LYS A 391 " pdb=" O LYS A 391 " model vdw 2.574 2.496 nonbonded pdb=" N LYS B 391 " pdb=" O LYS B 391 " model vdw 2.574 2.496 ... (remaining 93384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.470 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 36.810 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.013 0.047 12525 Z= 0.870 Angle : 1.771 8.223 16986 Z= 1.261 Chirality : 0.091 0.464 2010 Planarity : 0.011 0.183 2154 Dihedral : 18.227 115.364 5349 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.46 % Allowed : 11.14 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.99 (0.17), residues: 1476 helix: -0.33 (0.25), residues: 330 sheet: -0.07 (0.34), residues: 210 loop : -2.12 (0.15), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP B 234 HIS 0.012 0.004 HIS C 488 PHE 0.036 0.004 PHE C 125 TYR 0.026 0.004 TYR A 161 ARG 0.006 0.001 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 211 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ASP cc_start: 0.8417 (p0) cc_final: 0.8216 (p0) REVERT: A 119 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7940 (tt0) REVERT: A 137 ASN cc_start: 0.8019 (m-40) cc_final: 0.7810 (m-40) REVERT: A 187 THR cc_start: 0.7691 (p) cc_final: 0.7279 (t) REVERT: A 188 ASN cc_start: 0.7552 (t0) cc_final: 0.7207 (m-40) REVERT: A 189 GLN cc_start: 0.7517 (tm-30) cc_final: 0.7103 (tp40) REVERT: A 275 ASP cc_start: 0.7315 (t0) cc_final: 0.7013 (p0) REVERT: A 341 ASN cc_start: 0.6868 (p0) cc_final: 0.6657 (p0) REVERT: A 382 ASN cc_start: 0.7294 (m-40) cc_final: 0.7021 (m110) REVERT: A 401 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7440 (mp0) REVERT: A 444 MET cc_start: 0.8094 (tpt) cc_final: 0.7787 (tpt) REVERT: A 449 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6956 (mm-30) REVERT: A 452 ARG cc_start: 0.6256 (ttp80) cc_final: 0.5877 (tmt170) REVERT: A 468 LYS cc_start: 0.6776 (tttt) cc_final: 0.6511 (ttmm) REVERT: A 482 ARG cc_start: 0.6853 (mtm-85) cc_final: 0.6562 (mtm-85) REVERT: B 14 CYS cc_start: 0.6513 (m) cc_final: 0.6310 (m) REVERT: B 137 ASN cc_start: 0.7884 (m-40) cc_final: 0.7593 (m-40) REVERT: B 188 ASN cc_start: 0.7529 (t0) cc_final: 0.7253 (m-40) REVERT: B 189 GLN cc_start: 0.7472 (tm-30) cc_final: 0.6928 (tp40) REVERT: B 208 ARG cc_start: 0.7030 (ptt180) cc_final: 0.6664 (ptm160) REVERT: B 275 ASP cc_start: 0.6808 (t0) cc_final: 0.6549 (p0) REVERT: B 341 ASN cc_start: 0.6879 (p0) cc_final: 0.6640 (p0) REVERT: B 376 GLN cc_start: 0.7011 (mt0) cc_final: 0.6740 (mt0) REVERT: B 382 ASN cc_start: 0.7449 (m-40) cc_final: 0.7110 (m110) REVERT: B 401 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7540 (mm-30) REVERT: B 449 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7052 (mm-30) REVERT: B 452 ARG cc_start: 0.6485 (ttp80) cc_final: 0.5955 (tmt170) REVERT: B 468 LYS cc_start: 0.6878 (tttt) cc_final: 0.6400 (tptp) REVERT: B 482 ARG cc_start: 0.6800 (mtm-85) cc_final: 0.6481 (mtm180) REVERT: C 78 VAL cc_start: 0.8289 (t) cc_final: 0.7999 (p) REVERT: C 159 SER cc_start: 0.7303 (m) cc_final: 0.7089 (p) REVERT: C 187 THR cc_start: 0.7818 (p) cc_final: 0.7322 (t) REVERT: C 188 ASN cc_start: 0.7418 (t0) cc_final: 0.7049 (m-40) REVERT: C 189 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7163 (tp40) REVERT: C 208 ARG cc_start: 0.7063 (ptt180) cc_final: 0.6816 (ptp-110) REVERT: C 264 LYS cc_start: 0.8612 (pttp) cc_final: 0.8402 (pttt) REVERT: C 275 ASP cc_start: 0.7152 (t0) cc_final: 0.6840 (p0) REVERT: C 371 GLN cc_start: 0.6839 (tp40) cc_final: 0.6300 (tp-100) REVERT: C 382 ASN cc_start: 0.7326 (m-40) cc_final: 0.6948 (m110) REVERT: C 401 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7483 (mm-30) REVERT: C 444 MET cc_start: 0.8039 (tpt) cc_final: 0.7440 (tpt) REVERT: C 446 LYS cc_start: 0.7708 (mtmt) cc_final: 0.7507 (mtmm) REVERT: C 449 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7083 (mm-30) REVERT: C 452 ARG cc_start: 0.6207 (ttp80) cc_final: 0.5922 (tmt170) REVERT: C 468 LYS cc_start: 0.6638 (tttt) cc_final: 0.6164 (tttp) REVERT: C 470 TYR cc_start: 0.7580 (m-80) cc_final: 0.7246 (m-80) outliers start: 6 outliers final: 3 residues processed: 214 average time/residue: 1.2229 time to fit residues: 285.2089 Evaluate side-chains 143 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 210 GLN A 376 GLN A 498 ASN B 54 ASN B 210 GLN B 248 ASN B 497 ASN C 54 ASN C 210 GLN C 295 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12525 Z= 0.185 Angle : 0.611 9.132 16986 Z= 0.316 Chirality : 0.045 0.186 2010 Planarity : 0.004 0.030 2154 Dihedral : 13.164 87.255 2574 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.47 % Allowed : 12.53 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.39 (0.19), residues: 1476 helix: 2.34 (0.26), residues: 333 sheet: -0.04 (0.29), residues: 303 loop : -1.51 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.007 0.002 HIS B 75 PHE 0.012 0.001 PHE C 258 TYR 0.010 0.001 TYR B 486 ARG 0.002 0.000 ARG C 329 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7570 (p) cc_final: 0.7236 (t) REVERT: A 188 ASN cc_start: 0.7639 (t0) cc_final: 0.7180 (m-40) REVERT: A 189 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7100 (tp40) REVERT: A 275 ASP cc_start: 0.7289 (t0) cc_final: 0.6656 (p0) REVERT: A 401 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6973 (mp0) REVERT: A 452 ARG cc_start: 0.6121 (ttp80) cc_final: 0.5828 (tmt170) REVERT: A 468 LYS cc_start: 0.6752 (tttt) cc_final: 0.6283 (ttmm) REVERT: A 482 ARG cc_start: 0.6795 (mtm-85) cc_final: 0.6189 (mtp180) REVERT: A 497 ASN cc_start: 0.7385 (m-40) cc_final: 0.7139 (m-40) REVERT: B 70 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8346 (tt) REVERT: B 188 ASN cc_start: 0.7665 (t0) cc_final: 0.7344 (m-40) REVERT: B 189 GLN cc_start: 0.7386 (tm-30) cc_final: 0.6947 (tp40) REVERT: B 208 ARG cc_start: 0.6781 (ptt180) cc_final: 0.6464 (ptm160) REVERT: B 341 ASN cc_start: 0.6750 (p0) cc_final: 0.6543 (p0) REVERT: B 401 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7155 (mp0) REVERT: B 449 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6555 (mm-30) REVERT: B 452 ARG cc_start: 0.6208 (ttp80) cc_final: 0.5627 (tmt170) REVERT: B 468 LYS cc_start: 0.6797 (tttt) cc_final: 0.6408 (tttp) REVERT: B 482 ARG cc_start: 0.6717 (mtm-85) cc_final: 0.6422 (mtm110) REVERT: B 487 ASP cc_start: 0.7343 (t0) cc_final: 0.7037 (t0) REVERT: C 78 VAL cc_start: 0.8159 (t) cc_final: 0.7844 (p) REVERT: C 159 SER cc_start: 0.7131 (m) cc_final: 0.6929 (p) REVERT: C 187 THR cc_start: 0.7740 (p) cc_final: 0.7297 (t) REVERT: C 188 ASN cc_start: 0.7460 (t0) cc_final: 0.7032 (m-40) REVERT: C 189 GLN cc_start: 0.7599 (tm-30) cc_final: 0.7098 (tp40) REVERT: C 264 LYS cc_start: 0.8440 (pttp) cc_final: 0.8210 (pttt) REVERT: C 321 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7376 (ptp-170) REVERT: C 371 GLN cc_start: 0.6819 (tp40) cc_final: 0.6152 (tp-100) REVERT: C 382 ASN cc_start: 0.7243 (m-40) cc_final: 0.7017 (m110) REVERT: C 401 GLU cc_start: 0.7554 (mt-10) cc_final: 0.6998 (mm-30) REVERT: C 444 MET cc_start: 0.8049 (tpt) cc_final: 0.7510 (tpt) REVERT: C 452 ARG cc_start: 0.6106 (ttp80) cc_final: 0.5752 (tmt170) REVERT: C 468 LYS cc_start: 0.6796 (tttt) cc_final: 0.6278 (tttp) REVERT: C 470 TYR cc_start: 0.7251 (m-80) cc_final: 0.6998 (m-80) outliers start: 32 outliers final: 11 residues processed: 176 average time/residue: 1.0604 time to fit residues: 205.9358 Evaluate side-chains 139 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain C residue 381 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 45 optimal weight: 0.0270 chunk 107 optimal weight: 0.8980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS B 376 GLN C 475 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12525 Z= 0.174 Angle : 0.582 8.139 16986 Z= 0.297 Chirality : 0.045 0.314 2010 Planarity : 0.004 0.031 2154 Dihedral : 10.937 80.502 2570 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.78 % Allowed : 13.15 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.14 (0.20), residues: 1476 helix: 2.80 (0.26), residues: 333 sheet: 0.29 (0.29), residues: 321 loop : -1.21 (0.18), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 421 HIS 0.012 0.001 HIS A 355 PHE 0.010 0.001 PHE C 258 TYR 0.009 0.001 TYR A 257 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7600 (p) cc_final: 0.7305 (t) REVERT: A 188 ASN cc_start: 0.7664 (t0) cc_final: 0.7161 (m-40) REVERT: A 361 THR cc_start: 0.6999 (m) cc_final: 0.6602 (p) REVERT: A 371 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6584 (tp40) REVERT: A 401 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6922 (mp0) REVERT: A 444 MET cc_start: 0.8082 (tpt) cc_final: 0.7863 (tpt) REVERT: A 449 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6466 (mm-30) REVERT: A 468 LYS cc_start: 0.6811 (tttt) cc_final: 0.6317 (ttmm) REVERT: A 482 ARG cc_start: 0.6759 (mtm-85) cc_final: 0.6294 (mtm-85) REVERT: A 497 ASN cc_start: 0.7501 (m-40) cc_final: 0.7288 (m-40) REVERT: B 188 ASN cc_start: 0.7618 (t0) cc_final: 0.7281 (m-40) REVERT: B 189 GLN cc_start: 0.7307 (tm-30) cc_final: 0.6867 (tp40) REVERT: B 208 ARG cc_start: 0.6841 (ptt180) cc_final: 0.6506 (ptm160) REVERT: B 242 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8443 (p) REVERT: B 275 ASP cc_start: 0.7135 (p0) cc_final: 0.6569 (p0) REVERT: B 401 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7130 (mp0) REVERT: B 452 ARG cc_start: 0.5981 (ttp80) cc_final: 0.5744 (tmt170) REVERT: B 468 LYS cc_start: 0.6795 (tttt) cc_final: 0.6343 (ttmm) REVERT: B 482 ARG cc_start: 0.6618 (mtm-85) cc_final: 0.6411 (mtm180) REVERT: C 78 VAL cc_start: 0.8187 (t) cc_final: 0.7893 (p) REVERT: C 187 THR cc_start: 0.7810 (p) cc_final: 0.7392 (t) REVERT: C 188 ASN cc_start: 0.7500 (t0) cc_final: 0.7039 (m-40) REVERT: C 189 GLN cc_start: 0.7321 (tm-30) cc_final: 0.6878 (tp40) REVERT: C 321 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7338 (ptp-170) REVERT: C 371 GLN cc_start: 0.6841 (tp40) cc_final: 0.6218 (tp-100) REVERT: C 401 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7079 (mm-30) REVERT: C 444 MET cc_start: 0.8073 (tpt) cc_final: 0.7538 (tpt) REVERT: C 468 LYS cc_start: 0.6771 (tttt) cc_final: 0.6309 (tttp) REVERT: C 487 ASP cc_start: 0.6937 (t0) cc_final: 0.6679 (t0) outliers start: 36 outliers final: 14 residues processed: 157 average time/residue: 0.9564 time to fit residues: 167.7882 Evaluate side-chains 130 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS C 295 GLN C 363 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 12525 Z= 0.276 Angle : 0.669 9.582 16986 Z= 0.345 Chirality : 0.047 0.234 2010 Planarity : 0.005 0.039 2154 Dihedral : 9.983 76.719 2568 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.09 % Allowed : 13.92 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.02 (0.20), residues: 1476 helix: 2.76 (0.26), residues: 333 sheet: 0.01 (0.27), residues: 354 loop : -1.26 (0.18), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 234 HIS 0.011 0.002 HIS A 355 PHE 0.015 0.002 PHE C 125 TYR 0.016 0.002 TYR B 308 ARG 0.004 0.001 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 115 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7638 (p) cc_final: 0.7300 (t) REVERT: A 188 ASN cc_start: 0.7697 (t0) cc_final: 0.7213 (m-40) REVERT: A 208 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7053 (ptm160) REVERT: A 275 ASP cc_start: 0.6898 (t0) cc_final: 0.6558 (p0) REVERT: A 361 THR cc_start: 0.6599 (m) cc_final: 0.6286 (p) REVERT: A 401 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7090 (mp0) REVERT: A 452 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6137 (tmt170) REVERT: A 468 LYS cc_start: 0.6957 (tttt) cc_final: 0.6455 (ttmm) REVERT: A 482 ARG cc_start: 0.6637 (mtm-85) cc_final: 0.6336 (mtm-85) REVERT: B 70 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8395 (tp) REVERT: B 208 ARG cc_start: 0.6926 (ptt180) cc_final: 0.6406 (ptm160) REVERT: B 371 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6168 (tp40) REVERT: B 401 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7373 (mp0) REVERT: B 462 MET cc_start: 0.7547 (mtp) cc_final: 0.7254 (mtm) REVERT: B 468 LYS cc_start: 0.6962 (tttt) cc_final: 0.6581 (tttp) REVERT: C 52 CYS cc_start: 0.6971 (m) cc_final: 0.6509 (m) REVERT: C 78 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7909 (p) REVERT: C 187 THR cc_start: 0.7855 (p) cc_final: 0.7432 (t) REVERT: C 188 ASN cc_start: 0.7564 (t0) cc_final: 0.7072 (m-40) REVERT: C 189 GLN cc_start: 0.7287 (tm-30) cc_final: 0.6828 (tp40) REVERT: C 321 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7425 (ptp-170) REVERT: C 371 GLN cc_start: 0.6732 (tp40) cc_final: 0.6035 (tp40) REVERT: C 401 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7228 (mm-30) REVERT: C 444 MET cc_start: 0.8005 (tpt) cc_final: 0.7594 (tpt) REVERT: C 468 LYS cc_start: 0.6870 (tttt) cc_final: 0.6385 (tttp) outliers start: 40 outliers final: 21 residues processed: 146 average time/residue: 0.9892 time to fit residues: 161.1871 Evaluate side-chains 132 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 458 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS C 363 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 12525 Z= 0.314 Angle : 0.669 10.075 16986 Z= 0.348 Chirality : 0.048 0.247 2010 Planarity : 0.005 0.039 2154 Dihedral : 9.730 73.044 2568 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.25 % Allowed : 14.93 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.13 (0.20), residues: 1476 helix: 2.63 (0.26), residues: 333 sheet: -0.10 (0.28), residues: 339 loop : -1.31 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 421 HIS 0.010 0.002 HIS A 355 PHE 0.016 0.002 PHE C 125 TYR 0.015 0.002 TYR B 308 ARG 0.005 0.001 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 110 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7780 (p) cc_final: 0.7364 (t) REVERT: A 208 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7042 (ptm160) REVERT: A 401 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7129 (mp0) REVERT: A 452 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6044 (tmt170) REVERT: A 468 LYS cc_start: 0.7018 (tttt) cc_final: 0.6604 (tttp) REVERT: A 482 ARG cc_start: 0.6599 (mtm-85) cc_final: 0.6209 (mtp180) REVERT: B 70 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8459 (tp) REVERT: B 208 ARG cc_start: 0.7113 (ptt180) cc_final: 0.6516 (ptm160) REVERT: B 371 GLN cc_start: 0.6901 (mm-40) cc_final: 0.6159 (tp40) REVERT: B 401 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7411 (mp0) REVERT: B 452 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6367 (tmt170) REVERT: B 468 LYS cc_start: 0.6862 (tttt) cc_final: 0.6505 (tttp) REVERT: C 78 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.7925 (p) REVERT: C 187 THR cc_start: 0.7855 (p) cc_final: 0.7472 (t) REVERT: C 188 ASN cc_start: 0.7761 (t0) cc_final: 0.7208 (m-40) REVERT: C 321 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7445 (ptp-170) REVERT: C 371 GLN cc_start: 0.6741 (tp40) cc_final: 0.6086 (tp40) REVERT: C 401 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7275 (mm-30) REVERT: C 444 MET cc_start: 0.7922 (tpt) cc_final: 0.7595 (tpt) REVERT: C 468 LYS cc_start: 0.6720 (tttt) cc_final: 0.6290 (tttp) outliers start: 42 outliers final: 24 residues processed: 141 average time/residue: 1.0300 time to fit residues: 161.1630 Evaluate side-chains 134 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 458 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 83 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 355 HIS C 216 ASN C 295 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 12525 Z= 0.237 Angle : 0.616 10.714 16986 Z= 0.321 Chirality : 0.045 0.290 2010 Planarity : 0.004 0.041 2154 Dihedral : 9.087 68.998 2568 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.78 % Allowed : 15.55 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1476 helix: 2.73 (0.26), residues: 333 sheet: -0.03 (0.28), residues: 354 loop : -1.26 (0.18), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 222 HIS 0.009 0.001 HIS A 355 PHE 0.011 0.001 PHE C 125 TYR 0.010 0.002 TYR A 257 ARG 0.003 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7830 (tt0) REVERT: A 187 THR cc_start: 0.7782 (p) cc_final: 0.7386 (t) REVERT: A 208 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7043 (ptm160) REVERT: A 401 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7087 (mp0) REVERT: A 452 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.5878 (tmt170) REVERT: A 468 LYS cc_start: 0.6971 (tttt) cc_final: 0.6557 (tttp) REVERT: B 70 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8446 (tp) REVERT: B 208 ARG cc_start: 0.7116 (ptt180) cc_final: 0.6525 (ptm160) REVERT: B 371 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6152 (tp40) REVERT: B 401 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7300 (mp0) REVERT: B 445 ASN cc_start: 0.7063 (t0) cc_final: 0.6445 (m-40) REVERT: B 468 LYS cc_start: 0.7038 (tttt) cc_final: 0.6654 (ttmm) REVERT: C 78 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7940 (p) REVERT: C 187 THR cc_start: 0.7839 (p) cc_final: 0.7461 (t) REVERT: C 188 ASN cc_start: 0.7737 (t0) cc_final: 0.7183 (m-40) REVERT: C 371 GLN cc_start: 0.6695 (tp40) cc_final: 0.6044 (tp40) REVERT: C 401 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7261 (mm-30) REVERT: C 444 MET cc_start: 0.7930 (tpt) cc_final: 0.7474 (tpt) REVERT: C 468 LYS cc_start: 0.6879 (tttt) cc_final: 0.6419 (tttp) outliers start: 36 outliers final: 24 residues processed: 140 average time/residue: 1.0081 time to fit residues: 156.5554 Evaluate side-chains 132 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 458 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 86 optimal weight: 0.0970 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12525 Z= 0.209 Angle : 0.598 11.696 16986 Z= 0.310 Chirality : 0.045 0.242 2010 Planarity : 0.004 0.042 2154 Dihedral : 8.714 66.238 2568 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.25 % Allowed : 15.55 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.09 (0.21), residues: 1476 helix: 2.86 (0.27), residues: 333 sheet: -0.01 (0.28), residues: 354 loop : -1.20 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 222 HIS 0.008 0.001 HIS A 75 PHE 0.010 0.001 PHE C 125 TYR 0.010 0.002 TYR A 257 ARG 0.007 0.000 ARG B 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 108 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.7659 (p) cc_final: 0.7295 (t) REVERT: A 208 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7097 (ptm160) REVERT: A 468 LYS cc_start: 0.7125 (tttt) cc_final: 0.6687 (tttp) REVERT: B 70 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8433 (tp) REVERT: B 208 ARG cc_start: 0.7108 (ptt180) cc_final: 0.6668 (ptm160) REVERT: B 371 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6155 (tp40) REVERT: B 401 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7276 (mp0) REVERT: B 445 ASN cc_start: 0.7032 (t0) cc_final: 0.6432 (m-40) REVERT: B 452 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6225 (tmt170) REVERT: C 78 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7896 (p) REVERT: C 187 THR cc_start: 0.7923 (p) cc_final: 0.7589 (t) REVERT: C 188 ASN cc_start: 0.7853 (t0) cc_final: 0.7134 (m-40) REVERT: C 371 GLN cc_start: 0.6697 (tp40) cc_final: 0.6066 (tp40) REVERT: C 401 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7251 (mm-30) REVERT: C 444 MET cc_start: 0.7936 (tpt) cc_final: 0.7519 (tpt) REVERT: C 468 LYS cc_start: 0.6707 (tttt) cc_final: 0.6212 (tttp) outliers start: 42 outliers final: 23 residues processed: 137 average time/residue: 0.9727 time to fit residues: 148.1182 Evaluate side-chains 129 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 458 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12525 Z= 0.227 Angle : 0.612 11.309 16986 Z= 0.318 Chirality : 0.045 0.242 2010 Planarity : 0.004 0.042 2154 Dihedral : 8.574 65.293 2568 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.55 % Allowed : 16.24 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.02 (0.21), residues: 1476 helix: 2.83 (0.26), residues: 333 sheet: -0.12 (0.28), residues: 339 loop : -1.26 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 222 HIS 0.005 0.001 HIS C 75 PHE 0.012 0.001 PHE C 125 TYR 0.011 0.002 TYR B 308 ARG 0.003 0.000 ARG B 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7121 (ptm160) REVERT: A 361 THR cc_start: 0.6735 (OUTLIER) cc_final: 0.6317 (p) REVERT: A 452 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.5853 (tmt170) REVERT: A 468 LYS cc_start: 0.7138 (tttt) cc_final: 0.6636 (ttmm) REVERT: B 70 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8463 (tp) REVERT: B 208 ARG cc_start: 0.7106 (ptt180) cc_final: 0.6663 (ptm160) REVERT: B 371 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6155 (tp40) REVERT: B 401 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7296 (mp0) REVERT: B 445 ASN cc_start: 0.7025 (t0) cc_final: 0.6424 (m-40) REVERT: B 452 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.6234 (tmt170) REVERT: C 78 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7872 (p) REVERT: C 187 THR cc_start: 0.7964 (p) cc_final: 0.7623 (t) REVERT: C 371 GLN cc_start: 0.6693 (tp40) cc_final: 0.6067 (tp40) REVERT: C 401 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7268 (mm-30) REVERT: C 444 MET cc_start: 0.7931 (tpt) cc_final: 0.7488 (tpt) REVERT: C 468 LYS cc_start: 0.6754 (tttt) cc_final: 0.6253 (tttp) outliers start: 33 outliers final: 24 residues processed: 124 average time/residue: 0.9909 time to fit residues: 137.5505 Evaluate side-chains 128 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 458 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 135 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 40 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN C 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12525 Z= 0.167 Angle : 0.549 10.459 16986 Z= 0.285 Chirality : 0.043 0.235 2010 Planarity : 0.004 0.043 2154 Dihedral : 8.178 62.235 2568 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.40 % Allowed : 16.71 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.28 (0.21), residues: 1476 helix: 3.09 (0.27), residues: 333 sheet: 0.14 (0.28), residues: 339 loop : -1.12 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 222 HIS 0.012 0.001 HIS B 17 PHE 0.007 0.001 PHE A 258 TYR 0.008 0.001 TYR C 257 ARG 0.003 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7064 (ptm160) REVERT: A 361 THR cc_start: 0.6786 (m) cc_final: 0.6385 (p) REVERT: A 445 ASN cc_start: 0.7000 (t0) cc_final: 0.6561 (m-40) REVERT: A 452 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5553 (tmt170) REVERT: A 468 LYS cc_start: 0.7109 (tttt) cc_final: 0.6593 (ttmm) REVERT: A 482 ARG cc_start: 0.6676 (mtm-85) cc_final: 0.6286 (mtm-85) REVERT: B 70 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8420 (tp) REVERT: B 208 ARG cc_start: 0.6986 (ptt180) cc_final: 0.6618 (ptm160) REVERT: B 371 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6128 (tp40) REVERT: B 401 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7233 (mp0) REVERT: B 445 ASN cc_start: 0.7010 (t0) cc_final: 0.6462 (m-40) REVERT: B 452 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.6149 (tmt170) REVERT: B 464 ASN cc_start: 0.7088 (m-40) cc_final: 0.6601 (t0) REVERT: C 78 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7814 (p) REVERT: C 187 THR cc_start: 0.7908 (p) cc_final: 0.7637 (t) REVERT: C 371 GLN cc_start: 0.6706 (tp40) cc_final: 0.6080 (tp40) REVERT: C 401 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7215 (mm-30) REVERT: C 444 MET cc_start: 0.7950 (tpt) cc_final: 0.7538 (tpt) REVERT: C 464 ASN cc_start: 0.7403 (t0) cc_final: 0.6910 (t160) REVERT: C 468 LYS cc_start: 0.6711 (tttt) cc_final: 0.6211 (tttp) outliers start: 31 outliers final: 20 residues processed: 133 average time/residue: 1.0035 time to fit residues: 148.9422 Evaluate side-chains 128 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 458 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12525 Z= 0.229 Angle : 0.608 11.888 16986 Z= 0.314 Chirality : 0.045 0.237 2010 Planarity : 0.004 0.040 2154 Dihedral : 8.325 62.396 2568 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.24 % Allowed : 17.32 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1476 helix: 2.98 (0.26), residues: 333 sheet: -0.01 (0.27), residues: 354 loop : -1.24 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 222 HIS 0.010 0.001 HIS C 75 PHE 0.012 0.001 PHE C 125 TYR 0.011 0.002 TYR A 257 ARG 0.003 0.000 ARG B 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7140 (ptm160) REVERT: A 361 THR cc_start: 0.6723 (m) cc_final: 0.6323 (p) REVERT: A 445 ASN cc_start: 0.7094 (t0) cc_final: 0.6600 (m-40) REVERT: A 452 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5796 (tmt170) REVERT: A 468 LYS cc_start: 0.7178 (tttt) cc_final: 0.6621 (ttmm) REVERT: B 70 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8454 (tp) REVERT: B 208 ARG cc_start: 0.6995 (ptt180) cc_final: 0.6603 (ptm160) REVERT: B 371 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6158 (tp40) REVERT: B 445 ASN cc_start: 0.7039 (t0) cc_final: 0.6479 (m-40) REVERT: B 452 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6261 (tmt170) REVERT: B 464 ASN cc_start: 0.7139 (m-40) cc_final: 0.6661 (t0) REVERT: C 187 THR cc_start: 0.7942 (p) cc_final: 0.7620 (t) REVERT: C 371 GLN cc_start: 0.6702 (tp40) cc_final: 0.6081 (tp40) REVERT: C 401 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7260 (mm-30) REVERT: C 444 MET cc_start: 0.7945 (tpt) cc_final: 0.7527 (tpt) REVERT: C 462 MET cc_start: 0.6832 (mtp) cc_final: 0.6627 (mtm) REVERT: C 464 ASN cc_start: 0.7391 (t0) cc_final: 0.6936 (t0) outliers start: 29 outliers final: 19 residues processed: 125 average time/residue: 0.9729 time to fit residues: 135.9319 Evaluate side-chains 122 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 458 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.152602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114134 restraints weight = 14787.118| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.08 r_work: 0.3172 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12525 Z= 0.169 Angle : 0.557 10.527 16986 Z= 0.287 Chirality : 0.044 0.237 2010 Planarity : 0.004 0.037 2154 Dihedral : 7.940 59.880 2568 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.93 % Allowed : 17.71 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1476 helix: 3.17 (0.26), residues: 333 sheet: 0.19 (0.28), residues: 339 loop : -1.12 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 222 HIS 0.005 0.001 HIS B 17 PHE 0.008 0.001 PHE A 258 TYR 0.008 0.001 TYR C 257 ARG 0.004 0.000 ARG A 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3761.21 seconds wall clock time: 68 minutes 7.26 seconds (4087.26 seconds total)