Starting phenix.real_space_refine on Thu Feb 15 10:32:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj7_14743/02_2024/7zj7_14743.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj7_14743/02_2024/7zj7_14743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj7_14743/02_2024/7zj7_14743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj7_14743/02_2024/7zj7_14743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj7_14743/02_2024/7zj7_14743.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj7_14743/02_2024/7zj7_14743.pdb" } resolution = 3.95 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= 0.002 sd= 0.028 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 7431 2.51 5 N 2055 2.21 5 O 2415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B GLU 398": "OE1" <-> "OE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C GLU 403": "OE1" <-> "OE2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 449": "OE1" <-> "OE2" Residue "C ARG 456": "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: 11958 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3828 Classifications: {'peptide': 486} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 466} Chain: "B" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3828 Classifications: {'peptide': 486} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 466} Chain: "C" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3828 Classifications: {'peptide': 486} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 466} 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: 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: "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: 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: "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: 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: "M" 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: "N" 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: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.09, per 1000 atoms: 0.51 Number of scatterers: 11958 At special positions: 0 Unit cell: (106.92, 111.24, 145.8, 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 2415 8.00 N 2055 7.00 C 7431 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=2.01 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.02 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.02 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.00 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=2.04 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " 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 K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " 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 L 1 " - " FUC L 4 " NAG-ASN " NAG A 601 " - " ASN A 22 " " NAG B 601 " - " ASN B 22 " " NAG C 601 " - " 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 81 " " NAG M 1 " - " ASN C 38 " " NAG N 1 " - " ASN C 165 " " NAG O 1 " - " ASN C 285 " Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.0 seconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2682 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 33 sheets defined 33.3% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 4.135A pdb=" N ALA A 19 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL A 20 " --> pdb=" O HIS A 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 16 through 20' Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.909A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.763A pdb=" N LEU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 338 through 351 removed outlier: 4.369A pdb=" N GLY A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 347 " --> pdb=" O TRP A 343 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP A 350 " --> pdb=" O MET A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 removed outlier: 3.701A pdb=" N ASN A 378 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 456 removed outlier: 3.608A pdb=" N ASN A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 483 removed outlier: 3.895A pdb=" N ILE A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'B' and resid 16 through 20 removed outlier: 4.135A pdb=" N ALA B 19 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL B 20 " --> pdb=" O HIS B 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 16 through 20' Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.910A pdb=" N GLN B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.762A pdb=" N LEU B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 338 through 351 removed outlier: 4.372A pdb=" N GLY B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 347 " --> pdb=" O TRP B 343 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP B 350 " --> pdb=" O MET B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 378 removed outlier: 3.701A pdb=" N ASN B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 456 removed outlier: 3.607A pdb=" N ASN B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.894A pdb=" N ILE B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 491 through 499 Processing helix chain 'C' and resid 16 through 20 removed outlier: 4.135A pdb=" N ALA C 19 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL C 20 " --> pdb=" O HIS C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 20' Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.910A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.763A pdb=" N LEU C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 338 through 351 removed outlier: 4.369A pdb=" N GLY C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE C 347 " --> pdb=" O TRP C 343 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP C 350 " --> pdb=" O MET C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 378 removed outlier: 3.700A pdb=" N ASN C 378 " --> pdb=" O ILE C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 456 removed outlier: 3.607A pdb=" N ASN C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 483 removed outlier: 3.895A pdb=" N ILE C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 490 No H-bonds generated for 'chain 'C' and resid 488 through 490' Processing helix chain 'C' and resid 491 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.738A pdb=" N ILE A 34 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.397A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 177 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 8.085A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 286 through 287 removed outlier: 3.614A pdb=" N ILE A 282 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 461 Processing sheet with id=AB3, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.739A pdb=" N ILE B 34 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB6, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.395A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP B 101 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TRP B 234 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 177 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP B 101 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TRP B 234 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AC1, first strand: chain 'B' and resid 136 through 141 removed outlier: 8.084A pdb=" N ALA B 138 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 11.131A pdb=" N GLY B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC3, first strand: chain 'B' and resid 286 through 287 removed outlier: 3.613A pdb=" N ILE B 282 " --> pdb=" O TYR B 302 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AC5, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.738A pdb=" N ILE C 34 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC8, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.398A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 177 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD3, first strand: chain 'C' and resid 136 through 141 removed outlier: 8.084A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'C' and resid 286 through 287 removed outlier: 3.614A pdb=" N ILE C 282 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 459 through 461 504 hydrogen bonds defined for protein. 1404 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: 3.65 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2001 1.31 - 1.43: 3302 1.43 - 1.56: 6817 1.56 - 1.69: 0 1.69 - 1.82: 78 Bond restraints: 12198 Sorted by residual: bond pdb=" N ILE C 335 " pdb=" CA ILE C 335 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.11e-02 8.12e+03 1.56e+01 bond pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta sigma weight residual 1.456 1.499 -0.044 1.11e-02 8.12e+03 1.56e+01 bond pdb=" N ARG B 220 " pdb=" CA ARG B 220 " ideal model delta sigma weight residual 1.453 1.489 -0.035 9.20e-03 1.18e+04 1.47e+01 bond pdb=" N ILE B 335 " pdb=" CA ILE B 335 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.14e-02 7.69e+03 1.43e+01 bond pdb=" N ARG A 220 " pdb=" CA ARG A 220 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.42e+01 ... (remaining 12193 not shown) Histogram of bond angle deviations from ideal: 100.00 - 107.01: 478 107.01 - 114.01: 6574 114.01 - 121.01: 5519 121.01 - 128.02: 3860 128.02 - 135.02: 108 Bond angle restraints: 16539 Sorted by residual: angle pdb=" CA GLU A 340 " pdb=" C GLU A 340 " pdb=" N ASN A 341 " ideal model delta sigma weight residual 116.97 123.63 -6.66 1.20e+00 6.94e-01 3.08e+01 angle pdb=" CA GLU C 340 " pdb=" C GLU C 340 " pdb=" N ASN C 341 " ideal model delta sigma weight residual 116.97 123.62 -6.65 1.20e+00 6.94e-01 3.07e+01 angle pdb=" CA GLU B 340 " pdb=" C GLU B 340 " pdb=" N ASN B 341 " ideal model delta sigma weight residual 116.97 123.58 -6.61 1.20e+00 6.94e-01 3.03e+01 angle pdb=" C THR A 361 " pdb=" N GLY A 362 " pdb=" CA GLY A 362 " ideal model delta sigma weight residual 119.94 125.50 -5.56 1.09e+00 8.42e-01 2.60e+01 angle pdb=" C THR C 361 " pdb=" N GLY C 362 " pdb=" CA GLY C 362 " ideal model delta sigma weight residual 119.94 125.50 -5.56 1.09e+00 8.42e-01 2.60e+01 ... (remaining 16534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.00: 7073 21.00 - 42.00: 547 42.00 - 62.99: 87 62.99 - 83.99: 54 83.99 - 104.99: 30 Dihedral angle restraints: 7791 sinusoidal: 3606 harmonic: 4185 Sorted by residual: dihedral pdb=" CA VAL B 323 " pdb=" C VAL B 323 " pdb=" N PRO B 324 " pdb=" CA PRO B 324 " ideal model delta harmonic sigma weight residual -180.00 -151.41 -28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL A 323 " pdb=" C VAL A 323 " pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta harmonic sigma weight residual -180.00 -151.41 -28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL C 323 " pdb=" C VAL C 323 " pdb=" N PRO C 324 " pdb=" CA PRO C 324 " ideal model delta harmonic sigma weight residual -180.00 -151.41 -28.59 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1202 0.087 - 0.173: 625 0.173 - 0.259: 76 0.259 - 0.346: 7 0.346 - 0.432: 7 Chirality restraints: 1917 Sorted by residual: chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.55e+01 chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.50e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.25e+01 ... (remaining 1914 not shown) Planarity restraints: 2133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.319 2.00e-02 2.50e+03 2.76e-01 9.55e+02 pdb=" C7 NAG I 2 " -0.136 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.001 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.442 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " 0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.319 2.00e-02 2.50e+03 2.76e-01 9.55e+02 pdb=" C7 NAG L 2 " 0.136 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.001 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.442 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.319 2.00e-02 2.50e+03 2.76e-01 9.55e+02 pdb=" C7 NAG E 2 " 0.136 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.001 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.442 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.258 2.00e-02 2.50e+03 ... (remaining 2130 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2403 2.84 - 3.36: 11621 3.36 - 3.87: 18611 3.87 - 4.39: 20879 4.39 - 4.90: 34171 Nonbonded interactions: 87685 Sorted by model distance: nonbonded pdb=" O HIS A 184 " pdb=" OG SER A 228 " model vdw 2.329 2.440 nonbonded pdb=" O HIS B 184 " pdb=" OG SER B 228 " model vdw 2.329 2.440 nonbonded pdb=" O HIS C 184 " pdb=" OG SER C 228 " model vdw 2.330 2.440 nonbonded pdb=" OG1 THR B 28 " pdb=" O ASP B 31 " model vdw 2.369 2.440 nonbonded pdb=" OG1 THR A 28 " pdb=" O ASP A 31 " model vdw 2.369 2.440 ... (remaining 87680 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 'F' selection = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'L' } 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 group one per residue 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: 1.460 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: 6.280 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 31.480 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 0.046 12198 Z= 0.886 Angle : 1.895 14.465 16539 Z= 1.336 Chirality : 0.093 0.432 1917 Planarity : 0.017 0.276 2118 Dihedral : 17.474 104.989 5055 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.55 % Allowed : 10.46 % Favored : 88.99 % 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: -3.03 (0.16), residues: 1452 helix: -0.97 (0.21), residues: 408 sheet: -0.99 (0.31), residues: 192 loop : -2.95 (0.15), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP A 350 HIS 0.013 0.003 HIS C 56 PHE 0.023 0.004 PHE C 294 TYR 0.044 0.004 TYR C 423 ARG 0.006 0.001 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 220 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8714 (t0) cc_final: 0.8417 (t0) REVERT: A 204 VAL cc_start: 0.9609 (t) cc_final: 0.9257 (m) REVERT: A 244 VAL cc_start: 0.9158 (t) cc_final: 0.8952 (t) REVERT: A 344 GLU cc_start: 0.8753 (tt0) cc_final: 0.8163 (tt0) REVERT: A 383 ARG cc_start: 0.8866 (mtt180) cc_final: 0.8653 (mmt90) REVERT: A 399 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8620 (t80) REVERT: B 104 ASP cc_start: 0.8527 (t0) cc_final: 0.8289 (t0) REVERT: B 204 VAL cc_start: 0.9651 (t) cc_final: 0.9292 (m) REVERT: B 236 ILE cc_start: 0.9127 (mt) cc_final: 0.8783 (tt) REVERT: B 244 VAL cc_start: 0.9178 (t) cc_final: 0.8779 (t) REVERT: B 264 LYS cc_start: 0.8551 (mmtt) cc_final: 0.7973 (pptt) REVERT: B 399 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8531 (t80) REVERT: C 85 ASP cc_start: 0.8851 (m-30) cc_final: 0.7986 (t70) REVERT: C 104 ASP cc_start: 0.8523 (t0) cc_final: 0.8241 (t0) REVERT: C 222 TRP cc_start: 0.8968 (m100) cc_final: 0.8546 (m100) REVERT: C 244 VAL cc_start: 0.9195 (t) cc_final: 0.8841 (t) REVERT: C 252 ILE cc_start: 0.8529 (mm) cc_final: 0.8246 (mm) REVERT: C 344 GLU cc_start: 0.8733 (tt0) cc_final: 0.8410 (tt0) REVERT: C 383 ARG cc_start: 0.8700 (mtt180) cc_final: 0.8447 (mmt90) REVERT: C 399 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8667 (t80) REVERT: C 433 ASN cc_start: 0.8743 (m-40) cc_final: 0.8335 (m110) outliers start: 7 outliers final: 0 residues processed: 226 average time/residue: 0.2200 time to fit residues: 72.8383 Evaluate side-chains 118 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 130 optimal weight: 0.2980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS C 54 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12198 Z= 0.262 Angle : 0.742 10.129 16539 Z= 0.376 Chirality : 0.048 0.429 1917 Planarity : 0.004 0.039 2118 Dihedral : 11.899 69.705 2316 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.52 % Allowed : 15.33 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.36 (0.19), residues: 1452 helix: 1.91 (0.24), residues: 414 sheet: -0.52 (0.33), residues: 198 loop : -2.66 (0.15), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 343 HIS 0.004 0.001 HIS B 17 PHE 0.013 0.001 PHE B 294 TYR 0.019 0.002 TYR C 105 ARG 0.003 0.001 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8727 (t0) cc_final: 0.8462 (t0) REVERT: A 226 LEU cc_start: 0.6121 (mt) cc_final: 0.5709 (mp) REVERT: A 341 ASN cc_start: 0.7562 (m-40) cc_final: 0.6590 (p0) REVERT: A 344 GLU cc_start: 0.8730 (tt0) cc_final: 0.8209 (mt-10) REVERT: A 390 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9189 (pp20) REVERT: A 399 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8607 (t80) REVERT: A 451 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9085 (p) REVERT: B 104 ASP cc_start: 0.8610 (t0) cc_final: 0.8271 (t0) REVERT: B 177 LEU cc_start: 0.8470 (tp) cc_final: 0.7979 (tt) REVERT: B 222 TRP cc_start: 0.8852 (m100) cc_final: 0.7990 (t-100) REVERT: B 236 ILE cc_start: 0.9051 (mt) cc_final: 0.8778 (tt) REVERT: B 341 ASN cc_start: 0.7766 (m-40) cc_final: 0.6838 (p0) REVERT: B 344 GLU cc_start: 0.8655 (tt0) cc_final: 0.8138 (mt-10) REVERT: B 399 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8530 (t80) REVERT: C 85 ASP cc_start: 0.8964 (m-30) cc_final: 0.8016 (t70) REVERT: C 104 ASP cc_start: 0.8626 (t0) cc_final: 0.8325 (t0) REVERT: C 177 LEU cc_start: 0.8186 (tp) cc_final: 0.7783 (tt) REVERT: C 341 ASN cc_start: 0.7644 (m-40) cc_final: 0.6722 (p0) REVERT: C 344 GLU cc_start: 0.8775 (tt0) cc_final: 0.8233 (mt-10) REVERT: C 383 ARG cc_start: 0.8725 (mtt180) cc_final: 0.8522 (mpt-90) REVERT: C 399 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8629 (t80) REVERT: C 433 ASN cc_start: 0.8870 (m-40) cc_final: 0.8238 (m110) REVERT: C 451 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.8907 (p) REVERT: C 452 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7551 (tpm170) outliers start: 32 outliers final: 9 residues processed: 164 average time/residue: 0.2752 time to fit residues: 65.4640 Evaluate side-chains 113 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 399 PHE Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 452 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 216 ASN C 216 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12198 Z= 0.304 Angle : 0.741 14.053 16539 Z= 0.369 Chirality : 0.048 0.343 1917 Planarity : 0.004 0.054 2118 Dihedral : 9.008 55.116 2316 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.75 % Allowed : 17.45 % Favored : 79.80 % 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: -0.88 (0.20), residues: 1452 helix: 2.56 (0.25), residues: 414 sheet: 0.09 (0.38), residues: 168 loop : -2.52 (0.16), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 343 HIS 0.005 0.001 HIS B 17 PHE 0.009 0.001 PHE A 87 TYR 0.016 0.002 TYR B 423 ARG 0.003 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8640 (t0) cc_final: 0.8254 (t0) REVERT: A 341 ASN cc_start: 0.7528 (m-40) cc_final: 0.7198 (p0) REVERT: A 390 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9153 (pp20) REVERT: B 104 ASP cc_start: 0.8493 (t0) cc_final: 0.8074 (t0) REVERT: B 341 ASN cc_start: 0.7819 (m-40) cc_final: 0.7332 (p0) REVERT: B 390 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9126 (pp20) REVERT: B 399 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8456 (t80) REVERT: C 85 ASP cc_start: 0.8987 (m-30) cc_final: 0.8016 (t70) REVERT: C 104 ASP cc_start: 0.8503 (t0) cc_final: 0.8093 (t0) REVERT: C 341 ASN cc_start: 0.7613 (m-40) cc_final: 0.6677 (p0) REVERT: C 344 GLU cc_start: 0.8805 (tt0) cc_final: 0.8296 (mt-10) REVERT: C 383 ARG cc_start: 0.8781 (mtt180) cc_final: 0.8518 (mpt-90) REVERT: C 390 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9145 (pp20) REVERT: C 399 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8633 (t80) REVERT: C 451 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8931 (p) outliers start: 35 outliers final: 15 residues processed: 141 average time/residue: 0.2496 time to fit residues: 51.0883 Evaluate side-chains 105 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 399 PHE Chi-restraints excluded: chain C residue 451 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 139 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN C 433 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12198 Z= 0.285 Angle : 0.711 11.652 16539 Z= 0.357 Chirality : 0.046 0.313 1917 Planarity : 0.004 0.060 2118 Dihedral : 7.660 54.453 2314 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.28 % Allowed : 19.26 % Favored : 78.46 % 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: -0.84 (0.20), residues: 1452 helix: 2.62 (0.25), residues: 414 sheet: -0.15 (0.32), residues: 213 loop : -2.55 (0.17), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 343 HIS 0.007 0.001 HIS A 75 PHE 0.017 0.002 PHE A 467 TYR 0.018 0.002 TYR B 195 ARG 0.006 0.000 ARG C 329 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8548 (m-30) cc_final: 0.7984 (t0) REVERT: A 85 ASP cc_start: 0.8978 (m-30) cc_final: 0.8130 (t70) REVERT: A 260 MET cc_start: 0.8072 (tpt) cc_final: 0.7465 (tmm) REVERT: A 341 ASN cc_start: 0.7482 (m-40) cc_final: 0.7152 (p0) REVERT: A 390 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9182 (pp20) REVERT: B 222 TRP cc_start: 0.8937 (m100) cc_final: 0.8492 (m100) REVERT: B 390 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9123 (pp20) REVERT: C 85 ASP cc_start: 0.9005 (m-30) cc_final: 0.8051 (t70) REVERT: C 341 ASN cc_start: 0.7551 (m-40) cc_final: 0.7165 (p0) REVERT: C 383 ARG cc_start: 0.8802 (mtt180) cc_final: 0.8550 (mpt-90) REVERT: C 390 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9158 (pp20) REVERT: C 399 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8633 (t80) outliers start: 29 outliers final: 16 residues processed: 124 average time/residue: 0.2187 time to fit residues: 40.7104 Evaluate side-chains 92 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 246 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 246 ASN C 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12198 Z= 0.232 Angle : 0.645 13.231 16539 Z= 0.324 Chirality : 0.045 0.298 1917 Planarity : 0.004 0.058 2118 Dihedral : 7.194 57.410 2312 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.12 % Allowed : 20.13 % Favored : 77.75 % 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: -0.69 (0.21), residues: 1452 helix: 2.64 (0.25), residues: 414 sheet: -0.11 (0.32), residues: 213 loop : -2.38 (0.17), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 343 HIS 0.008 0.001 HIS C 17 PHE 0.019 0.002 PHE C 467 TYR 0.013 0.002 TYR C 423 ARG 0.008 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8527 (m-30) cc_final: 0.7955 (t0) REVERT: A 85 ASP cc_start: 0.8962 (m-30) cc_final: 0.8149 (t70) REVERT: A 341 ASN cc_start: 0.7473 (m-40) cc_final: 0.6295 (p0) REVERT: A 344 GLU cc_start: 0.8732 (tt0) cc_final: 0.8255 (mt-10) REVERT: A 390 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9224 (pp20) REVERT: B 222 TRP cc_start: 0.8980 (m100) cc_final: 0.8542 (m100) REVERT: B 341 ASN cc_start: 0.7882 (m-40) cc_final: 0.7570 (p0) REVERT: B 390 GLU cc_start: 0.9435 (mm-30) cc_final: 0.9072 (pp20) REVERT: C 85 ASP cc_start: 0.8980 (m-30) cc_final: 0.8151 (t70) REVERT: C 341 ASN cc_start: 0.7652 (m-40) cc_final: 0.7265 (p0) REVERT: C 383 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8563 (mpt-90) REVERT: C 390 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9167 (pp20) REVERT: C 399 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8603 (t80) outliers start: 27 outliers final: 16 residues processed: 111 average time/residue: 0.1769 time to fit residues: 31.4205 Evaluate side-chains 93 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN C 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12198 Z= 0.172 Angle : 0.631 12.139 16539 Z= 0.311 Chirality : 0.043 0.293 1917 Planarity : 0.004 0.053 2118 Dihedral : 7.182 59.886 2312 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.57 % Allowed : 20.91 % Favored : 77.52 % 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: -0.58 (0.21), residues: 1452 helix: 2.77 (0.25), residues: 414 sheet: -0.20 (0.33), residues: 219 loop : -2.30 (0.17), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 343 HIS 0.005 0.001 HIS C 75 PHE 0.016 0.001 PHE C 467 TYR 0.013 0.001 TYR B 195 ARG 0.002 0.000 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8537 (m-30) cc_final: 0.7982 (t0) REVERT: A 85 ASP cc_start: 0.8924 (m-30) cc_final: 0.8093 (t70) REVERT: A 260 MET cc_start: 0.8055 (tpt) cc_final: 0.7841 (tpt) REVERT: A 341 ASN cc_start: 0.7488 (m-40) cc_final: 0.6256 (p0) REVERT: A 344 GLU cc_start: 0.8700 (tt0) cc_final: 0.8237 (mt-10) REVERT: A 390 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9212 (pp20) REVERT: B 222 TRP cc_start: 0.8955 (m100) cc_final: 0.8529 (m100) REVERT: B 341 ASN cc_start: 0.7817 (m-40) cc_final: 0.7529 (p0) REVERT: B 390 GLU cc_start: 0.9425 (mm-30) cc_final: 0.9043 (pp20) REVERT: C 85 ASP cc_start: 0.8923 (m-30) cc_final: 0.8190 (t70) REVERT: C 341 ASN cc_start: 0.7620 (m-40) cc_final: 0.7303 (p0) REVERT: C 344 GLU cc_start: 0.8724 (tt0) cc_final: 0.8512 (mt-10) REVERT: C 383 ARG cc_start: 0.8821 (mtt180) cc_final: 0.8569 (mpt-90) REVERT: C 390 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9132 (pp20) REVERT: C 399 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8568 (t80) outliers start: 20 outliers final: 16 residues processed: 106 average time/residue: 0.2060 time to fit residues: 34.4027 Evaluate side-chains 101 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 10.0000 chunk 79 optimal weight: 0.0670 chunk 101 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 138 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12198 Z= 0.220 Angle : 0.612 9.649 16539 Z= 0.304 Chirality : 0.043 0.289 1917 Planarity : 0.004 0.058 2118 Dihedral : 7.150 56.974 2312 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.12 % Allowed : 20.83 % Favored : 77.04 % 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: -0.53 (0.21), residues: 1452 helix: 2.77 (0.25), residues: 414 sheet: -0.17 (0.33), residues: 219 loop : -2.24 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 180 HIS 0.006 0.001 HIS C 17 PHE 0.014 0.001 PHE C 467 TYR 0.012 0.002 TYR B 423 ARG 0.002 0.000 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8537 (m-30) cc_final: 0.8002 (t0) REVERT: A 85 ASP cc_start: 0.8950 (m-30) cc_final: 0.8185 (t70) REVERT: A 260 MET cc_start: 0.8012 (tpt) cc_final: 0.7792 (tpt) REVERT: A 341 ASN cc_start: 0.7441 (m-40) cc_final: 0.6224 (p0) REVERT: A 344 GLU cc_start: 0.8745 (tt0) cc_final: 0.8275 (mt-10) REVERT: A 390 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9231 (pp20) REVERT: B 341 ASN cc_start: 0.7829 (m-40) cc_final: 0.7544 (p0) REVERT: B 390 GLU cc_start: 0.9431 (mm-30) cc_final: 0.9055 (pp20) REVERT: C 85 ASP cc_start: 0.8950 (m-30) cc_final: 0.8253 (t70) REVERT: C 383 ARG cc_start: 0.8831 (mtt180) cc_final: 0.8572 (mpt-90) REVERT: C 390 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9133 (pp20) REVERT: C 399 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8561 (t80) outliers start: 27 outliers final: 18 residues processed: 111 average time/residue: 0.2005 time to fit residues: 34.7711 Evaluate side-chains 100 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12198 Z= 0.176 Angle : 0.601 12.808 16539 Z= 0.298 Chirality : 0.043 0.283 1917 Planarity : 0.004 0.058 2118 Dihedral : 7.191 59.354 2312 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.28 % Allowed : 20.99 % Favored : 76.73 % 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: -0.34 (0.21), residues: 1452 helix: 2.89 (0.25), residues: 414 sheet: 0.07 (0.34), residues: 213 loop : -2.13 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 180 HIS 0.004 0.001 HIS C 18 PHE 0.013 0.001 PHE C 467 TYR 0.012 0.001 TYR B 105 ARG 0.002 0.000 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8552 (m-30) cc_final: 0.8034 (t0) REVERT: A 85 ASP cc_start: 0.8936 (m-30) cc_final: 0.8192 (t70) REVERT: A 260 MET cc_start: 0.8006 (tpt) cc_final: 0.7801 (tpp) REVERT: A 341 ASN cc_start: 0.7451 (m-40) cc_final: 0.6233 (p0) REVERT: A 344 GLU cc_start: 0.8695 (tt0) cc_final: 0.8247 (mt-10) REVERT: A 390 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9211 (pp20) REVERT: B 52 CYS cc_start: 0.7767 (p) cc_final: 0.7538 (p) REVERT: B 341 ASN cc_start: 0.7790 (m-40) cc_final: 0.7522 (p0) REVERT: B 390 GLU cc_start: 0.9414 (mm-30) cc_final: 0.9059 (pp20) REVERT: C 85 ASP cc_start: 0.8931 (m-30) cc_final: 0.8297 (t70) REVERT: C 341 ASN cc_start: 0.7659 (m-40) cc_final: 0.7389 (p0) REVERT: C 344 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7791 (mt-10) REVERT: C 383 ARG cc_start: 0.8841 (mtt180) cc_final: 0.8590 (mpt-90) REVERT: C 390 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9109 (pp20) outliers start: 29 outliers final: 17 residues processed: 120 average time/residue: 0.2041 time to fit residues: 37.8610 Evaluate side-chains 102 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12198 Z= 0.263 Angle : 0.652 11.818 16539 Z= 0.324 Chirality : 0.044 0.282 1917 Planarity : 0.004 0.064 2118 Dihedral : 7.210 59.703 2312 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.73 % Allowed : 21.70 % Favored : 76.57 % 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: -0.35 (0.21), residues: 1452 helix: 2.88 (0.25), residues: 411 sheet: 0.25 (0.34), residues: 207 loop : -2.16 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 180 HIS 0.005 0.001 HIS C 17 PHE 0.011 0.001 PHE A 87 TYR 0.014 0.002 TYR B 423 ARG 0.005 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8565 (m-30) cc_final: 0.8077 (t0) REVERT: A 85 ASP cc_start: 0.8973 (m-30) cc_final: 0.8287 (t70) REVERT: A 260 MET cc_start: 0.7943 (tpt) cc_final: 0.7735 (tpp) REVERT: A 341 ASN cc_start: 0.7515 (m-40) cc_final: 0.6279 (p0) REVERT: A 344 GLU cc_start: 0.8752 (tt0) cc_final: 0.8312 (mt-10) REVERT: A 390 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9213 (pp20) REVERT: B 52 CYS cc_start: 0.7958 (p) cc_final: 0.7737 (p) REVERT: B 341 ASN cc_start: 0.7799 (m-40) cc_final: 0.7524 (p0) REVERT: B 390 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9067 (pp20) REVERT: C 52 CYS cc_start: 0.8085 (p) cc_final: 0.7870 (p) REVERT: C 85 ASP cc_start: 0.9001 (m-30) cc_final: 0.8366 (t0) REVERT: C 383 ARG cc_start: 0.8850 (mtt180) cc_final: 0.8595 (mpt-90) REVERT: C 390 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9115 (pp20) outliers start: 22 outliers final: 18 residues processed: 109 average time/residue: 0.1870 time to fit residues: 32.7160 Evaluate side-chains 101 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 143 optimal weight: 0.4980 chunk 132 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12198 Z= 0.287 Angle : 0.675 13.200 16539 Z= 0.335 Chirality : 0.045 0.281 1917 Planarity : 0.005 0.064 2118 Dihedral : 7.183 59.699 2312 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.42 % Allowed : 22.41 % Favored : 76.18 % 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: -0.46 (0.21), residues: 1452 helix: 2.79 (0.25), residues: 411 sheet: 0.00 (0.34), residues: 213 loop : -2.18 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 180 HIS 0.007 0.001 HIS C 17 PHE 0.011 0.001 PHE B 87 TYR 0.016 0.002 TYR B 423 ARG 0.006 0.000 ARG A 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8585 (m-30) cc_final: 0.8095 (t0) REVERT: A 85 ASP cc_start: 0.9001 (m-30) cc_final: 0.8347 (t70) REVERT: A 390 GLU cc_start: 0.9422 (mm-30) cc_final: 0.9217 (pp20) REVERT: B 52 CYS cc_start: 0.8032 (p) cc_final: 0.7768 (p) REVERT: B 341 ASN cc_start: 0.7822 (m-40) cc_final: 0.7553 (p0) REVERT: B 390 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9087 (pp20) REVERT: C 52 CYS cc_start: 0.8190 (p) cc_final: 0.7934 (p) REVERT: C 80 GLN cc_start: 0.8921 (mt0) cc_final: 0.8690 (mm-40) REVERT: C 85 ASP cc_start: 0.9048 (m-30) cc_final: 0.8386 (t0) REVERT: C 260 MET cc_start: 0.8567 (tmm) cc_final: 0.8330 (tmm) REVERT: C 383 ARG cc_start: 0.8830 (mtt180) cc_final: 0.8582 (mpt-90) REVERT: C 390 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9117 (pp20) outliers start: 18 outliers final: 18 residues processed: 107 average time/residue: 0.1818 time to fit residues: 31.7341 Evaluate side-chains 104 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 399 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 47 optimal weight: 0.0670 chunk 117 optimal weight: 9.9990 chunk 14 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.140481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.094346 restraints weight = 29441.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.097210 restraints weight = 17685.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098929 restraints weight = 13425.972| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12198 Z= 0.148 Angle : 0.606 12.035 16539 Z= 0.299 Chirality : 0.043 0.277 1917 Planarity : 0.004 0.049 2118 Dihedral : 6.721 55.983 2312 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.94 % Allowed : 22.96 % Favored : 76.10 % 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: -0.23 (0.21), residues: 1452 helix: 2.90 (0.26), residues: 423 sheet: 0.09 (0.34), residues: 213 loop : -2.05 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 180 HIS 0.004 0.001 HIS A 17 PHE 0.012 0.001 PHE C 467 TYR 0.013 0.001 TYR B 105 ARG 0.006 0.000 ARG A 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.18 seconds wall clock time: 39 minutes 59.16 seconds (2399.16 seconds total)