Starting phenix.real_space_refine on Tue Aug 6 21:01:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjb_43279/08_2024/8vjb_43279_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjb_43279/08_2024/8vjb_43279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjb_43279/08_2024/8vjb_43279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjb_43279/08_2024/8vjb_43279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjb_43279/08_2024/8vjb_43279_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjb_43279/08_2024/8vjb_43279_neut.cif" } resolution = 3.6 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3510 atoms to isotropic. 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 120 5.16 5 C 9312 2.51 5 N 2528 2.21 5 O 2728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 533": "OD1" <-> "OD2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "F ASP 15": "OD1" <-> "OD2" Residue "F ASP 52": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14688 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6601 Classifications: {'peptide': 816} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 772} Chain breaks: 6 Chain: "B" Number of atoms: 6601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6601 Classifications: {'peptide': 816} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 772} Chain breaks: 6 Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "D" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Chain: "E" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "F" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Time building chain proxies: 8.35, per 1000 atoms: 0.57 Number of scatterers: 14688 At special positions: 0 Unit cell: (135, 119.88, 169.56, 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 120 16.00 O 2728 8.00 N 2528 7.00 C 9312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 860 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.02 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 860 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 47 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 51 " distance=2.04 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 47 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 51 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 47 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 60 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 51 " distance=2.03 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 Time building additional restraints: 5.39 Conformation dependent library (CDL) restraints added in 2.5 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3428 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 30 sheets defined 17.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 4.080A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.178A pdb=" N ASN A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.505A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.761A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.792A pdb=" N PHE A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 638 through 643' Processing helix chain 'A' and resid 692 through 714 removed outlier: 3.597A pdb=" N GLU A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'B' and resid 16 through 24 removed outlier: 4.074A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.185A pdb=" N ASN B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.502A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.768A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.783A pdb=" N PHE B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 643' Processing helix chain 'B' and resid 692 through 714 Processing helix chain 'B' and resid 862 through 869 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.869A pdb=" N LEU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 4.069A pdb=" N THR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 17 removed outlier: 4.037A pdb=" N ASP D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 52 through 58 removed outlier: 3.802A pdb=" N LEU D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.811A pdb=" N LEU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 60 removed outlier: 4.081A pdb=" N THR E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 17 removed outlier: 4.042A pdb=" N ASP F 15 " --> pdb=" O GLY F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 52 through 58 removed outlier: 3.756A pdb=" N LEU F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 7.062A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 294 removed outlier: 3.617A pdb=" N THR A 302 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 321 removed outlier: 7.423A pdb=" N LEU A 368 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N LEU A 403 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE A 370 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AA9, first strand: chain 'A' and resid 479 through 480 removed outlier: 4.073A pdb=" N ARG A 479 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 486 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 530 through 533 removed outlier: 3.573A pdb=" N THR A 530 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 599 through 605 removed outlier: 5.397A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 759 through 762 removed outlier: 3.683A pdb=" N GLU A 760 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 630 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 627 " --> pdb=" O CYS A 786 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG A 794 " --> pdb=" O ASN A 787 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 759 through 762 removed outlier: 3.683A pdb=" N GLU A 760 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 630 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 627 " --> pdb=" O CYS A 786 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 815 through 822 removed outlier: 5.118A pdb=" N GLN A 833 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS A 872 " --> pdb=" O LEU A 830 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 842 through 851 removed outlier: 3.731A pdb=" N GLY A 880 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 905 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.695A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 65 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC1, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC2, first strand: chain 'B' and resid 292 through 294 removed outlier: 3.629A pdb=" N THR B 302 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AC4, first strand: chain 'B' and resid 320 through 321 removed outlier: 7.424A pdb=" N LEU B 368 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N LEU B 403 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE B 370 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC6, first strand: chain 'B' and resid 479 through 480 removed outlier: 4.012A pdb=" N ARG B 479 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 486 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 530 through 533 removed outlier: 3.576A pdb=" N THR B 530 " --> pdb=" O TYR B 507 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 599 through 605 removed outlier: 5.405A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.687A pdb=" N GLU B 760 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 627 " --> pdb=" O CYS B 786 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG B 794 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.687A pdb=" N GLU B 760 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 627 " --> pdb=" O CYS B 786 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 815 through 822 removed outlier: 5.119A pdb=" N GLN B 833 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 842 through 851 removed outlier: 3.732A pdb=" N GLY B 880 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 905 " --> pdb=" O GLY B 880 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 927 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: 4.98 Time building geometry restraints manager: 5.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4826 1.35 - 1.47: 3622 1.47 - 1.59: 6440 1.59 - 1.71: 0 1.71 - 1.83: 142 Bond restraints: 15030 Sorted by residual: bond pdb=" N ASP A 591 " pdb=" CA ASP A 591 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.34e-02 5.57e+03 8.57e+00 bond pdb=" N ASP B 591 " pdb=" CA ASP B 591 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.34e-02 5.57e+03 8.31e+00 bond pdb=" N ALA B 592 " pdb=" CA ALA B 592 " ideal model delta sigma weight residual 1.454 1.486 -0.031 1.16e-02 7.43e+03 7.36e+00 bond pdb=" N ALA A 592 " pdb=" CA ALA A 592 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.16e-02 7.43e+03 7.17e+00 bond pdb=" N THR B 593 " pdb=" CA THR B 593 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.53e-02 4.27e+03 5.03e+00 ... (remaining 15025 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.59: 446 106.59 - 113.54: 7970 113.54 - 120.48: 5660 120.48 - 127.42: 6109 127.42 - 134.36: 167 Bond angle restraints: 20352 Sorted by residual: angle pdb=" N ILE A 692 " pdb=" CA ILE A 692 " pdb=" C ILE A 692 " ideal model delta sigma weight residual 113.53 108.26 5.27 9.80e-01 1.04e+00 2.89e+01 angle pdb=" N ILE B 692 " pdb=" CA ILE B 692 " pdb=" C ILE B 692 " ideal model delta sigma weight residual 113.53 108.27 5.26 9.80e-01 1.04e+00 2.88e+01 angle pdb=" CB MET A 831 " pdb=" CG MET A 831 " pdb=" SD MET A 831 " ideal model delta sigma weight residual 112.70 124.27 -11.57 3.00e+00 1.11e-01 1.49e+01 angle pdb=" N ASN A 15 " pdb=" CA ASN A 15 " pdb=" CB ASN A 15 " ideal model delta sigma weight residual 114.17 109.85 4.32 1.14e+00 7.69e-01 1.44e+01 angle pdb=" CA LEU C 13 " pdb=" CB LEU C 13 " pdb=" CG LEU C 13 " ideal model delta sigma weight residual 116.30 128.55 -12.25 3.50e+00 8.16e-02 1.22e+01 ... (remaining 20347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 7744 18.02 - 36.04: 1081 36.04 - 54.06: 221 54.06 - 72.09: 49 72.09 - 90.11: 31 Dihedral angle restraints: 9126 sinusoidal: 3818 harmonic: 5308 Sorted by residual: dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -172.54 86.54 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -171.04 85.04 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS A 241 " pdb=" SG CYS A 241 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual -86.00 -163.61 77.61 1 1.00e+01 1.00e-02 7.54e+01 ... (remaining 9123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1380 0.031 - 0.061: 527 0.061 - 0.092: 156 0.092 - 0.122: 130 0.122 - 0.153: 21 Chirality restraints: 2214 Sorted by residual: chirality pdb=" CA THR A 790 " pdb=" N THR A 790 " pdb=" C THR A 790 " pdb=" CB THR A 790 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA THR B 790 " pdb=" N THR B 790 " pdb=" C THR B 790 " pdb=" CB THR B 790 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CB ILE A 174 " pdb=" CA ILE A 174 " pdb=" CG1 ILE A 174 " pdb=" CG2 ILE A 174 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 2211 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 590 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C THR A 590 " -0.032 2.00e-02 2.50e+03 pdb=" O THR A 590 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP A 591 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 899 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO B 900 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 900 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 900 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 899 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 900 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 900 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 900 " -0.025 5.00e-02 4.00e+02 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 900 2.73 - 3.27: 14950 3.27 - 3.82: 24209 3.82 - 4.36: 27942 4.36 - 4.90: 47401 Nonbonded interactions: 115402 Sorted by model distance: nonbonded pdb=" OG SER A 878 " pdb=" OH TYR A 882 " model vdw 2.190 3.040 nonbonded pdb=" OG SER B 878 " pdb=" OH TYR B 882 " model vdw 2.191 3.040 nonbonded pdb=" O PRO A 716 " pdb=" OH TYR F 27 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.222 3.040 ... (remaining 115397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.520 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.002 0.039 15030 Z= 0.160 Angle : 0.604 12.248 20352 Z= 0.317 Chirality : 0.043 0.153 2214 Planarity : 0.003 0.045 2632 Dihedral : 17.036 90.106 5560 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.13 % Favored : 92.64 % Rotamer: Outliers : 0.24 % Allowed : 28.00 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.46 (0.20), residues: 1780 helix: -0.03 (0.38), residues: 196 sheet: -0.37 (0.28), residues: 358 loop : -1.39 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 559 HIS 0.003 0.000 HIS B 100 PHE 0.030 0.001 PHE A 572 TYR 0.009 0.001 TYR B 512 ARG 0.004 0.000 ARG A 870 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 MET cc_start: 0.8681 (tpp) cc_final: 0.7805 (mmm) REVERT: B 831 MET cc_start: 0.8350 (tpt) cc_final: 0.7303 (mmm) outliers start: 4 outliers final: 3 residues processed: 70 average time/residue: 0.2514 time to fit residues: 28.3253 Evaluate side-chains 69 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 51 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 50.0000 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN A 513 GLN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 HIS ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN B 513 GLN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 820 HIS ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN D 18 GLN F 18 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 15030 Z= 0.579 Angle : 0.787 11.024 20352 Z= 0.399 Chirality : 0.049 0.160 2214 Planarity : 0.005 0.042 2632 Dihedral : 4.974 43.011 1997 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.31 % Favored : 91.57 % Rotamer: Outliers : 3.82 % Allowed : 24.12 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.80 (0.20), residues: 1780 helix: -0.43 (0.35), residues: 214 sheet: -0.82 (0.27), residues: 368 loop : -1.54 (0.19), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 551 HIS 0.007 0.001 HIS A 440 PHE 0.026 0.002 PHE B 506 TYR 0.024 0.002 TYR A 374 ARG 0.005 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 72 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7960 (pp) REVERT: A 38 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7912 (mmm) REVERT: A 412 TRP cc_start: 0.8961 (OUTLIER) cc_final: 0.7503 (m-90) REVERT: A 442 MET cc_start: 0.9107 (tpp) cc_final: 0.8632 (tpp) REVERT: A 482 PHE cc_start: 0.8041 (t80) cc_final: 0.7720 (t80) REVERT: A 831 MET cc_start: 0.9007 (tpp) cc_final: 0.8079 (mmm) REVERT: B 2 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7992 (pp) REVERT: B 110 MET cc_start: 0.8454 (mmm) cc_final: 0.8200 (mmm) REVERT: B 412 TRP cc_start: 0.8951 (OUTLIER) cc_final: 0.7478 (m-90) REVERT: B 442 MET cc_start: 0.9109 (tpp) cc_final: 0.8614 (tpp) REVERT: B 482 PHE cc_start: 0.8056 (t80) cc_final: 0.7686 (t80) REVERT: B 504 MET cc_start: 0.8172 (mmp) cc_final: 0.7806 (mmm) REVERT: B 831 MET cc_start: 0.8597 (tpt) cc_final: 0.8393 (tpt) outliers start: 63 outliers final: 30 residues processed: 130 average time/residue: 0.2278 time to fit residues: 47.0915 Evaluate side-chains 97 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 62 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 53 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 788 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15030 Z= 0.211 Angle : 0.598 10.098 20352 Z= 0.308 Chirality : 0.044 0.157 2214 Planarity : 0.004 0.043 2632 Dihedral : 4.623 41.361 1995 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.85 % Favored : 93.03 % Rotamer: Outliers : 3.45 % Allowed : 25.15 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.63 (0.20), residues: 1780 helix: -0.10 (0.36), residues: 198 sheet: -0.80 (0.28), residues: 344 loop : -1.40 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 897 HIS 0.002 0.001 HIS A 429 PHE 0.018 0.001 PHE A 572 TYR 0.018 0.001 TYR B 374 ARG 0.006 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 62 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8122 (mmt) cc_final: 0.7899 (mmm) REVERT: A 412 TRP cc_start: 0.8865 (OUTLIER) cc_final: 0.7417 (m-90) REVERT: A 442 MET cc_start: 0.8959 (tpp) cc_final: 0.8378 (tpp) REVERT: A 465 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: A 797 VAL cc_start: 0.9221 (OUTLIER) cc_final: 0.8980 (p) REVERT: A 831 MET cc_start: 0.9071 (tpp) cc_final: 0.8212 (mmm) REVERT: B 233 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9001 (pt) REVERT: B 412 TRP cc_start: 0.8868 (OUTLIER) cc_final: 0.7374 (m-90) REVERT: B 442 MET cc_start: 0.8982 (tpp) cc_final: 0.8400 (tpp) REVERT: B 504 MET cc_start: 0.8082 (mmp) cc_final: 0.7834 (mmm) REVERT: B 797 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.9025 (p) REVERT: B 831 MET cc_start: 0.8560 (tpt) cc_final: 0.8337 (tpt) outliers start: 57 outliers final: 30 residues processed: 113 average time/residue: 0.2213 time to fit residues: 40.6487 Evaluate side-chains 97 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 61 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 819 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 53 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 40.0000 chunk 109 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 173 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 155 optimal weight: 40.0000 chunk 46 optimal weight: 0.1980 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 GLN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 15030 Z= 0.376 Angle : 0.642 9.694 20352 Z= 0.326 Chirality : 0.045 0.151 2214 Planarity : 0.004 0.043 2632 Dihedral : 4.724 43.748 1995 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.15 % Favored : 91.74 % Rotamer: Outliers : 3.70 % Allowed : 24.91 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.85 (0.20), residues: 1780 helix: -0.58 (0.35), residues: 218 sheet: -0.87 (0.27), residues: 358 loop : -1.54 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 551 HIS 0.003 0.001 HIS A 440 PHE 0.016 0.002 PHE B 506 TYR 0.019 0.001 TYR A 374 ARG 0.005 0.001 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 62 time to evaluate : 1.834 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8061 (pp) REVERT: A 38 MET cc_start: 0.8205 (mmt) cc_final: 0.7974 (mmm) REVERT: A 412 TRP cc_start: 0.8954 (OUTLIER) cc_final: 0.7419 (m-90) REVERT: A 442 MET cc_start: 0.9060 (tpp) cc_final: 0.8470 (tpp) REVERT: A 452 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8251 (mm-40) REVERT: A 465 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: A 797 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.9014 (p) REVERT: A 831 MET cc_start: 0.9124 (tpp) cc_final: 0.8269 (mmm) REVERT: B 2 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7988 (pp) REVERT: B 412 TRP cc_start: 0.8933 (OUTLIER) cc_final: 0.7463 (m-90) REVERT: B 442 MET cc_start: 0.9072 (tpp) cc_final: 0.8494 (tpp) REVERT: B 504 MET cc_start: 0.8144 (mmp) cc_final: 0.7883 (mmm) REVERT: B 797 VAL cc_start: 0.9289 (OUTLIER) cc_final: 0.9070 (p) REVERT: B 831 MET cc_start: 0.8530 (tpt) cc_final: 0.7973 (tpt) outliers start: 61 outliers final: 31 residues processed: 118 average time/residue: 0.2262 time to fit residues: 42.8196 Evaluate side-chains 97 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 58 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN E 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15030 Z= 0.278 Angle : 0.600 9.640 20352 Z= 0.305 Chirality : 0.044 0.149 2214 Planarity : 0.004 0.044 2632 Dihedral : 4.648 44.739 1995 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.30 % Favored : 92.58 % Rotamer: Outliers : 3.82 % Allowed : 25.15 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.80 (0.20), residues: 1780 helix: -0.63 (0.34), residues: 216 sheet: -0.80 (0.27), residues: 354 loop : -1.49 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 559 HIS 0.002 0.001 HIS B 429 PHE 0.014 0.001 PHE B 506 TYR 0.018 0.001 TYR A 374 ARG 0.008 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 59 time to evaluate : 1.783 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8191 (mmt) cc_final: 0.7986 (mmm) REVERT: A 412 TRP cc_start: 0.8955 (OUTLIER) cc_final: 0.7402 (m-90) REVERT: A 442 MET cc_start: 0.9111 (tpp) cc_final: 0.8744 (tpp) REVERT: A 465 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: A 797 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.9075 (p) REVERT: A 831 MET cc_start: 0.9160 (tpp) cc_final: 0.8279 (mmm) REVERT: B 2 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8051 (pp) REVERT: B 412 TRP cc_start: 0.8923 (OUTLIER) cc_final: 0.7368 (m-90) REVERT: B 442 MET cc_start: 0.9130 (tpp) cc_final: 0.8754 (tpp) REVERT: B 452 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8297 (mm-40) REVERT: B 504 MET cc_start: 0.8078 (mmp) cc_final: 0.7819 (mmm) REVERT: B 797 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.9056 (p) REVERT: B 831 MET cc_start: 0.8356 (tpt) cc_final: 0.8021 (tpt) REVERT: F 27 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7802 (p90) outliers start: 63 outliers final: 39 residues processed: 116 average time/residue: 0.2367 time to fit residues: 42.7582 Evaluate side-chains 104 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 57 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 56 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 80 optimal weight: 50.0000 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15030 Z= 0.219 Angle : 0.583 12.746 20352 Z= 0.296 Chirality : 0.044 0.148 2214 Planarity : 0.003 0.043 2632 Dihedral : 4.542 45.424 1995 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.58 % Favored : 92.30 % Rotamer: Outliers : 3.45 % Allowed : 25.52 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.75 (0.20), residues: 1780 helix: -0.61 (0.34), residues: 216 sheet: -0.63 (0.28), residues: 334 loop : -1.50 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 559 HIS 0.002 0.000 HIS A 429 PHE 0.024 0.001 PHE A 572 TYR 0.017 0.001 TYR B 374 ARG 0.011 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 55 time to evaluate : 1.679 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8143 (pp) REVERT: A 37 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8924 (mt) REVERT: A 56 MET cc_start: 0.7643 (ttt) cc_final: 0.7311 (ttt) REVERT: A 412 TRP cc_start: 0.8915 (OUTLIER) cc_final: 0.7500 (m-90) REVERT: A 442 MET cc_start: 0.9060 (tpp) cc_final: 0.8494 (tpp) REVERT: A 465 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: A 797 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.9086 (p) REVERT: A 831 MET cc_start: 0.9205 (tpp) cc_final: 0.8163 (mmm) REVERT: B 2 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8030 (pp) REVERT: B 412 TRP cc_start: 0.8883 (OUTLIER) cc_final: 0.7467 (m-90) REVERT: B 442 MET cc_start: 0.9072 (tpp) cc_final: 0.8490 (tpp) REVERT: B 797 VAL cc_start: 0.9298 (OUTLIER) cc_final: 0.9094 (p) REVERT: B 831 MET cc_start: 0.8321 (tpt) cc_final: 0.7952 (tpt) outliers start: 57 outliers final: 39 residues processed: 106 average time/residue: 0.1941 time to fit residues: 35.2330 Evaluate side-chains 100 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 53 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 56 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 80 optimal weight: 40.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN E 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15030 Z= 0.160 Angle : 0.565 11.933 20352 Z= 0.286 Chirality : 0.043 0.147 2214 Planarity : 0.003 0.043 2632 Dihedral : 4.429 46.052 1995 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.52 % Favored : 93.37 % Rotamer: Outliers : 3.27 % Allowed : 26.48 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.57 (0.20), residues: 1780 helix: -0.11 (0.36), residues: 200 sheet: -0.54 (0.28), residues: 330 loop : -1.42 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 559 HIS 0.002 0.000 HIS B 429 PHE 0.016 0.001 PHE A 705 TYR 0.015 0.001 TYR A 374 ARG 0.005 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 56 time to evaluate : 1.923 Fit side-chains REVERT: A 2 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8091 (pp) REVERT: A 37 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8940 (mt) REVERT: A 56 MET cc_start: 0.7604 (ttt) cc_final: 0.7326 (ttt) REVERT: A 412 TRP cc_start: 0.8905 (OUTLIER) cc_final: 0.7513 (m-90) REVERT: A 442 MET cc_start: 0.9041 (tpp) cc_final: 0.8493 (tpp) REVERT: A 465 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: A 831 MET cc_start: 0.9152 (tpp) cc_final: 0.8282 (mmm) REVERT: B 412 TRP cc_start: 0.8878 (OUTLIER) cc_final: 0.7480 (m-90) REVERT: B 442 MET cc_start: 0.9056 (tpp) cc_final: 0.8496 (tpp) REVERT: B 465 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: B 831 MET cc_start: 0.8238 (tpt) cc_final: 0.7846 (tpt) outliers start: 54 outliers final: 36 residues processed: 103 average time/residue: 0.2059 time to fit residues: 35.6874 Evaluate side-chains 97 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 55 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 52 optimal weight: 0.0370 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 136 optimal weight: 0.7980 overall best weight: 2.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15030 Z= 0.304 Angle : 0.609 14.621 20352 Z= 0.305 Chirality : 0.044 0.166 2214 Planarity : 0.003 0.043 2632 Dihedral : 4.504 46.821 1995 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.75 % Favored : 92.13 % Rotamer: Outliers : 3.39 % Allowed : 26.24 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.70 (0.20), residues: 1780 helix: -0.52 (0.34), residues: 218 sheet: -0.68 (0.27), residues: 350 loop : -1.45 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.003 0.001 HIS A 199 PHE 0.014 0.001 PHE B 482 TYR 0.018 0.001 TYR A 374 ARG 0.006 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 53 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8160 (pp) REVERT: A 412 TRP cc_start: 0.8966 (OUTLIER) cc_final: 0.7567 (m-90) REVERT: A 442 MET cc_start: 0.9069 (tpp) cc_final: 0.8469 (tpp) REVERT: A 465 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8325 (pm20) REVERT: A 831 MET cc_start: 0.9124 (tpp) cc_final: 0.8236 (mmm) REVERT: B 2 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8033 (pp) REVERT: B 412 TRP cc_start: 0.8951 (OUTLIER) cc_final: 0.7559 (m-90) REVERT: B 442 MET cc_start: 0.9085 (tpp) cc_final: 0.8473 (tpp) REVERT: B 452 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8287 (mm-40) REVERT: B 465 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: B 831 MET cc_start: 0.8288 (tpt) cc_final: 0.7902 (tpt) outliers start: 56 outliers final: 41 residues processed: 103 average time/residue: 0.2058 time to fit residues: 36.5013 Evaluate side-chains 100 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 52 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 10.0000 chunk 166 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15030 Z= 0.310 Angle : 0.621 14.617 20352 Z= 0.312 Chirality : 0.045 0.193 2214 Planarity : 0.004 0.043 2632 Dihedral : 4.627 48.736 1995 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.20 % Favored : 91.69 % Rotamer: Outliers : 3.39 % Allowed : 26.55 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.72 (0.20), residues: 1780 helix: -0.59 (0.35), residues: 218 sheet: -0.68 (0.27), residues: 360 loop : -1.46 (0.19), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 559 HIS 0.002 0.001 HIS B 440 PHE 0.014 0.001 PHE B 506 TYR 0.015 0.001 TYR B 374 ARG 0.008 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 53 time to evaluate : 1.732 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8906 (mt) REVERT: A 412 TRP cc_start: 0.8960 (OUTLIER) cc_final: 0.7525 (m-90) REVERT: A 442 MET cc_start: 0.9141 (tpp) cc_final: 0.8596 (tpp) REVERT: A 452 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8151 (mm-40) REVERT: A 465 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: A 831 MET cc_start: 0.9157 (tpp) cc_final: 0.8254 (mmm) REVERT: B 2 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8104 (pp) REVERT: B 412 TRP cc_start: 0.8950 (OUTLIER) cc_final: 0.7544 (m-90) REVERT: B 442 MET cc_start: 0.9176 (tpp) cc_final: 0.8617 (tpp) REVERT: B 452 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8281 (mm-40) REVERT: B 465 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: B 831 MET cc_start: 0.8305 (tpt) cc_final: 0.7909 (tpt) outliers start: 56 outliers final: 42 residues processed: 105 average time/residue: 0.1911 time to fit residues: 34.8642 Evaluate side-chains 103 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 53 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15030 Z= 0.195 Angle : 0.585 13.899 20352 Z= 0.296 Chirality : 0.044 0.196 2214 Planarity : 0.003 0.043 2632 Dihedral : 4.517 49.354 1995 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 2.97 % Allowed : 26.79 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.66 (0.20), residues: 1780 helix: -0.55 (0.35), residues: 218 sheet: -0.47 (0.28), residues: 340 loop : -1.47 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 559 HIS 0.002 0.000 HIS B 429 PHE 0.013 0.001 PHE A 705 TYR 0.016 0.001 TYR A 374 ARG 0.006 0.000 ARG A 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 54 time to evaluate : 1.819 Fit side-chains REVERT: A 37 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8979 (mt) REVERT: A 412 TRP cc_start: 0.8912 (OUTLIER) cc_final: 0.7556 (m-90) REVERT: A 442 MET cc_start: 0.9177 (tpp) cc_final: 0.8450 (tpp) REVERT: A 465 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: A 831 MET cc_start: 0.9193 (tpp) cc_final: 0.8314 (mmm) REVERT: B 2 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8129 (pp) REVERT: B 412 TRP cc_start: 0.8913 (OUTLIER) cc_final: 0.7532 (m-90) REVERT: B 442 MET cc_start: 0.9167 (tpp) cc_final: 0.8853 (tpp) REVERT: B 465 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: B 831 MET cc_start: 0.8271 (tpt) cc_final: 0.7886 (tpt) outliers start: 49 outliers final: 37 residues processed: 99 average time/residue: 0.1866 time to fit residues: 32.2245 Evaluate side-chains 96 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 53 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 21 optimal weight: 0.0770 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 40.0000 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.079634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.051310 restraints weight = 63790.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.053129 restraints weight = 31533.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.054259 restraints weight = 21283.828| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15030 Z= 0.176 Angle : 0.578 13.587 20352 Z= 0.291 Chirality : 0.044 0.189 2214 Planarity : 0.003 0.043 2632 Dihedral : 4.471 49.845 1995 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.63 % Favored : 93.26 % Rotamer: Outliers : 2.85 % Allowed : 26.97 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.53 (0.20), residues: 1780 helix: -0.11 (0.36), residues: 200 sheet: -0.45 (0.28), residues: 340 loop : -1.42 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 559 HIS 0.002 0.000 HIS A 429 PHE 0.015 0.001 PHE A 705 TYR 0.015 0.001 TYR A 374 ARG 0.005 0.000 ARG A 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2433.91 seconds wall clock time: 44 minutes 41.08 seconds (2681.08 seconds total)