Starting phenix.real_space_refine on Wed Apr 10 02:05:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjb_43279/04_2024/8vjb_43279_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjb_43279/04_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_43279/04_2024/8vjb_43279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjb_43279/04_2024/8vjb_43279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjb_43279/04_2024/8vjb_43279_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjb_43279/04_2024/8vjb_43279_neut.pdb" } 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-5288/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: 7.84, per 1000 atoms: 0.53 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: 5.01 Conformation dependent library (CDL) restraints added in 2.9 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: 2.14 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: 5.33 Time building geometry restraints manager: 5.56 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 2.440 nonbonded pdb=" OG SER B 878 " pdb=" OH TYR B 882 " model vdw 2.191 2.440 nonbonded pdb=" O PRO A 716 " pdb=" OH TYR F 27 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.217 2.440 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.222 2.440 ... (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 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 4.830 Check model and map are aligned: 0.210 Set scattering table: 0.100 Process input model: 41.280 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.830 ------------------------------------------------------------------------------- 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 : 1.648 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: 0.2524 time to fit residues: 28.4799 Evaluate side-chains 69 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 2.370 ------------------------------------------------------------------------------- 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: 3.9990 chunk 136 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 15030 Z= 0.494 Angle : 0.719 11.551 20352 Z= 0.365 Chirality : 0.048 0.154 2214 Planarity : 0.005 0.040 2632 Dihedral : 4.916 43.240 1997 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.33 % Favored : 90.51 % Rotamer: Outliers : 3.45 % Allowed : 26.24 % Favored : 70.30 % 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: -0.35 (0.36), residues: 212 sheet: -0.80 (0.27), residues: 368 loop : -1.55 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 489 HIS 0.006 0.001 HIS B 829 PHE 0.024 0.002 PHE B 506 TYR 0.023 0.002 TYR A 374 ARG 0.004 0.001 ARG B 65 *********************** 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 126 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 69 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7950 (pp) REVERT: A 316 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8436 (pm20) REVERT: A 412 TRP cc_start: 0.8930 (OUTLIER) cc_final: 0.7455 (m-90) REVERT: A 442 MET cc_start: 0.9066 (tpp) cc_final: 0.8657 (tpp) REVERT: A 831 MET cc_start: 0.9018 (tpp) cc_final: 0.8069 (mmm) REVERT: B 110 MET cc_start: 0.8455 (mmm) cc_final: 0.8180 (mmm) REVERT: B 412 TRP cc_start: 0.8919 (OUTLIER) cc_final: 0.7557 (m-90) REVERT: B 442 MET cc_start: 0.9072 (tpp) cc_final: 0.8630 (tpp) REVERT: B 831 MET cc_start: 0.8572 (tpt) cc_final: 0.7413 (mmm) outliers start: 57 outliers final: 27 residues processed: 121 average time/residue: 0.2323 time to fit residues: 45.6272 Evaluate side-chains 96 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 65 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU 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 316 GLU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 593 THR 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 212 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 593 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 163 optimal weight: 0.0040 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** 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 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15030 Z= 0.148 Angle : 0.572 10.318 20352 Z= 0.291 Chirality : 0.043 0.157 2214 Planarity : 0.003 0.040 2632 Dihedral : 4.523 42.380 1997 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.91 % Favored : 92.87 % Rotamer: Outliers : 3.70 % Allowed : 25.94 % 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: -1.59 (0.20), residues: 1780 helix: -0.04 (0.36), residues: 198 sheet: -0.72 (0.28), residues: 344 loop : -1.40 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 559 HIS 0.002 0.000 HIS A 100 PHE 0.020 0.001 PHE A 572 TYR 0.016 0.001 TYR B 374 ARG 0.005 0.000 ARG B 42 *********************** 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 126 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 65 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7948 (mmt) cc_final: 0.7700 (mmm) REVERT: A 412 TRP cc_start: 0.8861 (OUTLIER) cc_final: 0.7487 (m-90) REVERT: A 442 MET cc_start: 0.8904 (tpp) cc_final: 0.8601 (tpp) REVERT: A 797 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.9016 (p) REVERT: A 831 MET cc_start: 0.9093 (tpp) cc_final: 0.8203 (mmm) REVERT: B 233 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8941 (pt) REVERT: B 412 TRP cc_start: 0.8830 (OUTLIER) cc_final: 0.7425 (m-90) REVERT: B 442 MET cc_start: 0.8956 (tpp) cc_final: 0.8548 (tpp) REVERT: B 797 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.9041 (p) outliers start: 61 outliers final: 29 residues processed: 120 average time/residue: 0.2317 time to fit residues: 44.4835 Evaluate side-chains 95 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 61 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 462 ASN 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 B residue 16 ASN Chi-restraints excluded: chain B residue 212 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 462 ASN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET 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 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL 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: 9.9990 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 109 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 155 optimal weight: 40.0000 chunk 46 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** A 541 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 455 ASN B 541 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 15030 Z= 0.428 Angle : 0.682 10.236 20352 Z= 0.342 Chirality : 0.046 0.148 2214 Planarity : 0.004 0.041 2632 Dihedral : 4.787 43.858 1995 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.49 % Favored : 90.39 % Rotamer: Outliers : 4.06 % Allowed : 26.67 % Favored : 69.27 % 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: -1.88 (0.20), residues: 1780 helix: -0.63 (0.35), residues: 218 sheet: -0.83 (0.28), residues: 358 loop : -1.57 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 551 HIS 0.004 0.001 HIS A 199 PHE 0.016 0.002 PHE B 506 TYR 0.020 0.002 TYR A 374 ARG 0.006 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 127 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 60 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8122 (pp) REVERT: A 38 MET cc_start: 0.8180 (mmt) cc_final: 0.7955 (mmm) REVERT: A 412 TRP cc_start: 0.8985 (OUTLIER) cc_final: 0.7494 (m-90) REVERT: A 442 MET cc_start: 0.9047 (tpp) cc_final: 0.8580 (tpp) REVERT: A 465 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8458 (pm20) REVERT: A 797 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9104 (p) REVERT: A 831 MET cc_start: 0.9142 (tpp) cc_final: 0.8262 (mmm) REVERT: B 2 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8037 (pp) REVERT: B 110 MET cc_start: 0.8414 (mmm) cc_final: 0.8134 (mmm) REVERT: B 412 TRP cc_start: 0.8961 (OUTLIER) cc_final: 0.7521 (m-90) REVERT: B 442 MET cc_start: 0.9068 (tpp) cc_final: 0.8599 (tpp) REVERT: B 465 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8220 (pm20) REVERT: B 797 VAL cc_start: 0.9371 (OUTLIER) cc_final: 0.9132 (p) REVERT: B 831 MET cc_start: 0.8638 (tpt) cc_final: 0.8115 (tpt) outliers start: 67 outliers final: 38 residues processed: 120 average time/residue: 0.2331 time to fit residues: 44.1660 Evaluate side-chains 102 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 56 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 130 THR 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 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 454 ARG 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 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 130 THR 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 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET 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 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 Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 156 optimal weight: 50.0000 chunk 43 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 541 ASN ** 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 589 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: 0.8259 moved from start: 0.1849 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= 0.156 Angle : 0.564 12.964 20352 Z= 0.283 Chirality : 0.043 0.150 2214 Planarity : 0.003 0.040 2632 Dihedral : 4.476 44.718 1995 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.25 % Favored : 92.53 % Rotamer: Outliers : 3.27 % Allowed : 27.52 % Favored : 69.21 % 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: -1.58 (0.20), residues: 1780 helix: -0.09 (0.36), residues: 198 sheet: -0.70 (0.28), residues: 344 loop : -1.38 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 559 HIS 0.002 0.000 HIS A 429 PHE 0.015 0.001 PHE A 705 TYR 0.016 0.001 TYR A 374 ARG 0.014 0.000 ARG F 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 114 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 60 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.8899 (OUTLIER) cc_final: 0.7375 (m-90) REVERT: A 442 MET cc_start: 0.9019 (tpp) cc_final: 0.8418 (tpp) REVERT: A 797 VAL cc_start: 0.9345 (OUTLIER) cc_final: 0.9113 (p) REVERT: A 831 MET cc_start: 0.9176 (tpp) cc_final: 0.8281 (mmm) REVERT: B 110 MET cc_start: 0.8484 (mmm) cc_final: 0.8243 (mmm) REVERT: B 412 TRP cc_start: 0.8879 (OUTLIER) cc_final: 0.7427 (m-90) REVERT: B 442 MET cc_start: 0.9046 (tpp) cc_final: 0.8444 (tpp) REVERT: B 465 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8280 (pm20) REVERT: B 797 VAL cc_start: 0.9371 (OUTLIER) cc_final: 0.9141 (p) REVERT: B 831 MET cc_start: 0.8414 (tpt) cc_final: 0.8102 (tpt) outliers start: 54 outliers final: 40 residues processed: 107 average time/residue: 0.2340 time to fit residues: 40.7187 Evaluate side-chains 102 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 57 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN 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 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 462 ASN 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 819 THR 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 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 462 ASN Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 541 ASN 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 56 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 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: 20.0000 chunk 156 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 174 optimal weight: 6.9990 chunk 144 optimal weight: 0.0370 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- 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 34 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1960 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= 0.200 Angle : 0.560 13.214 20352 Z= 0.280 Chirality : 0.043 0.145 2214 Planarity : 0.003 0.040 2632 Dihedral : 4.422 46.667 1995 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.92 % Favored : 91.85 % Rotamer: Outliers : 3.45 % Allowed : 27.70 % Favored : 68.85 % 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: -1.59 (0.20), residues: 1780 helix: -0.02 (0.36), residues: 198 sheet: -0.73 (0.28), residues: 358 loop : -1.40 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 559 HIS 0.002 0.000 HIS A 429 PHE 0.022 0.001 PHE A 572 TYR 0.016 0.001 TYR A 374 ARG 0.006 0.000 ARG D 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 115 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 58 time to evaluate : 1.729 Fit side-chains REVERT: A 412 TRP cc_start: 0.8886 (OUTLIER) cc_final: 0.7349 (m-90) REVERT: A 442 MET cc_start: 0.9026 (tpp) cc_final: 0.8499 (tpp) REVERT: A 465 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8407 (pm20) REVERT: A 797 VAL cc_start: 0.9363 (OUTLIER) cc_final: 0.9134 (p) REVERT: A 831 MET cc_start: 0.9228 (tpp) cc_final: 0.8358 (mmm) REVERT: B 2 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8068 (pp) REVERT: B 38 MET cc_start: 0.8110 (mmt) cc_final: 0.7826 (mmm) REVERT: B 110 MET cc_start: 0.8531 (mmm) cc_final: 0.8266 (mmm) REVERT: B 412 TRP cc_start: 0.8865 (OUTLIER) cc_final: 0.7425 (m-90) REVERT: B 442 MET cc_start: 0.9042 (tpp) cc_final: 0.8512 (tpp) REVERT: B 465 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8299 (pm20) REVERT: B 797 VAL cc_start: 0.9389 (OUTLIER) cc_final: 0.9164 (p) REVERT: B 831 MET cc_start: 0.8337 (tpt) cc_final: 0.7983 (tpt) REVERT: B 864 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8547 (pptt) outliers start: 57 outliers final: 41 residues processed: 108 average time/residue: 0.2137 time to fit residues: 38.2688 Evaluate side-chains 106 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 57 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 462 ASN 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 541 ASN 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 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 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 462 ASN Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 541 ASN 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 B residue 864 LYS 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 56 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 42 ILE 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: 0.3980 chunk 19 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 108 optimal weight: 0.4980 chunk 105 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 34 GLN ** 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: 0.8288 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15030 Z= 0.239 Angle : 0.570 12.518 20352 Z= 0.285 Chirality : 0.043 0.144 2214 Planarity : 0.003 0.045 2632 Dihedral : 4.441 47.964 1995 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.20 % Favored : 91.69 % Rotamer: Outliers : 3.88 % Allowed : 27.27 % Favored : 68.85 % 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: -1.58 (0.20), residues: 1780 helix: -0.15 (0.36), residues: 202 sheet: -0.69 (0.28), residues: 354 loop : -1.38 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.002 0.001 HIS A 199 PHE 0.014 0.001 PHE E 19 TYR 0.017 0.001 TYR A 374 ARG 0.006 0.000 ARG E 49 *********************** 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 122 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 58 time to evaluate : 1.692 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8086 (pp) REVERT: A 412 TRP cc_start: 0.8910 (OUTLIER) cc_final: 0.7422 (m-90) REVERT: A 442 MET cc_start: 0.9031 (tpp) cc_final: 0.8520 (tpp) REVERT: A 452 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8176 (mm-40) REVERT: A 465 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8432 (pm20) REVERT: A 797 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9152 (p) REVERT: A 831 MET cc_start: 0.9252 (tpp) cc_final: 0.8381 (mmm) REVERT: B 2 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8073 (pp) REVERT: B 38 MET cc_start: 0.8070 (mmt) cc_final: 0.7868 (mmm) REVERT: B 110 MET cc_start: 0.8553 (mmm) cc_final: 0.8274 (mmm) REVERT: B 412 TRP cc_start: 0.8889 (OUTLIER) cc_final: 0.7407 (m-90) REVERT: B 442 MET cc_start: 0.9048 (tpp) cc_final: 0.8673 (tpp) REVERT: B 465 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8264 (pm20) REVERT: B 797 VAL cc_start: 0.9400 (OUTLIER) cc_final: 0.9165 (p) REVERT: B 831 MET cc_start: 0.8263 (tpt) cc_final: 0.7862 (tpt) outliers start: 64 outliers final: 41 residues processed: 116 average time/residue: 0.2484 time to fit residues: 45.6328 Evaluate side-chains 107 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 57 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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 452 GLN Chi-restraints excluded: chain A residue 462 ASN 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 516 THR Chi-restraints excluded: chain A residue 541 ASN 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 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 462 ASN Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 541 ASN 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 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 42 ILE Chi-restraints excluded: chain F residue 53 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 833 GLN ** 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: 0.8283 moved from start: 0.2221 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= 0.222 Angle : 0.570 12.493 20352 Z= 0.286 Chirality : 0.043 0.144 2214 Planarity : 0.003 0.040 2632 Dihedral : 4.441 48.872 1995 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.03 % Favored : 91.85 % Rotamer: Outliers : 3.76 % Allowed : 27.45 % Favored : 68.79 % 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: -1.58 (0.20), residues: 1780 helix: -0.23 (0.36), residues: 202 sheet: -0.67 (0.28), residues: 354 loop : -1.38 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.002 0.001 HIS B 865 PHE 0.012 0.001 PHE A 506 TYR 0.017 0.001 TYR A 374 ARG 0.004 0.000 ARG A 454 *********************** 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 119 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 57 time to evaluate : 1.770 Fit side-chains revert: symmetry clash REVERT: A 412 TRP cc_start: 0.8912 (OUTLIER) cc_final: 0.7463 (m-90) REVERT: A 442 MET cc_start: 0.9020 (tpp) cc_final: 0.8608 (tpp) REVERT: A 452 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8220 (mm-40) REVERT: A 465 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: A 797 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9177 (p) REVERT: A 831 MET cc_start: 0.9263 (tpp) cc_final: 0.8231 (mmm) REVERT: B 2 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8086 (pp) REVERT: B 110 MET cc_start: 0.8540 (mmm) cc_final: 0.8245 (mmm) REVERT: B 412 TRP cc_start: 0.8882 (OUTLIER) cc_final: 0.7412 (m-90) REVERT: B 442 MET cc_start: 0.9027 (tpp) cc_final: 0.8615 (tpp) REVERT: B 465 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8240 (pm20) REVERT: B 797 VAL cc_start: 0.9405 (OUTLIER) cc_final: 0.9172 (p) REVERT: B 831 MET cc_start: 0.8278 (tpt) cc_final: 0.7869 (tpt) outliers start: 62 outliers final: 42 residues processed: 113 average time/residue: 0.2135 time to fit residues: 40.7754 Evaluate side-chains 107 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 57 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 378 SER Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 462 ASN 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 516 THR Chi-restraints excluded: chain A residue 541 ASN 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 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 378 SER Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 541 ASN 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 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: 3.9990 chunk 166 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 146 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8320 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15030 Z= 0.342 Angle : 0.626 12.333 20352 Z= 0.313 Chirality : 0.044 0.146 2214 Planarity : 0.004 0.040 2632 Dihedral : 4.632 49.474 1995 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.16 % Favored : 90.73 % Rotamer: Outliers : 3.58 % Allowed : 27.70 % Favored : 68.73 % 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: -0.65 (0.35), residues: 218 sheet: -0.67 (0.27), residues: 364 loop : -1.48 (0.19), residues: 1198 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 A 506 TYR 0.018 0.001 TYR A 374 ARG 0.006 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 118 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 59 time to evaluate : 1.742 Fit side-chains revert: symmetry clash REVERT: A 412 TRP cc_start: 0.8972 (OUTLIER) cc_final: 0.7551 (m-90) REVERT: A 442 MET cc_start: 0.9109 (tpp) cc_final: 0.8687 (tpp) REVERT: A 452 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8235 (mm-40) REVERT: A 465 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: A 797 VAL cc_start: 0.9446 (OUTLIER) cc_final: 0.9225 (p) REVERT: A 831 MET cc_start: 0.9192 (tpp) cc_final: 0.8272 (mmm) REVERT: B 110 MET cc_start: 0.8494 (mmm) cc_final: 0.8260 (mmm) REVERT: B 412 TRP cc_start: 0.8959 (OUTLIER) cc_final: 0.7545 (m-90) REVERT: B 442 MET cc_start: 0.9126 (tpp) cc_final: 0.8694 (tpp) REVERT: B 452 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8258 (mm-40) REVERT: B 465 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: B 797 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9240 (p) REVERT: B 831 MET cc_start: 0.8336 (tpt) cc_final: 0.7943 (tpt) outliers start: 59 outliers final: 44 residues processed: 112 average time/residue: 0.1932 time to fit residues: 36.9569 Evaluate side-chains 110 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 58 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN 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 378 SER Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 462 ASN 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 516 THR Chi-restraints excluded: chain A residue 541 ASN 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 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 378 SER Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 541 ASN 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 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 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: 2.9990 chunk 104 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 179 optimal weight: 0.3980 chunk 165 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 0.0770 overall best weight: 0.8944 ------------------------------------------------------------------------------- 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 34 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2449 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= 0.157 Angle : 0.569 12.215 20352 Z= 0.286 Chirality : 0.043 0.146 2214 Planarity : 0.003 0.040 2632 Dihedral : 4.468 49.675 1995 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.47 % Favored : 92.30 % Rotamer: Outliers : 3.03 % Allowed : 28.18 % Favored : 68.79 % 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: -0.21 (0.36), residues: 200 sheet: -0.40 (0.28), residues: 340 loop : -1.41 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 632 HIS 0.002 0.000 HIS A 429 PHE 0.013 0.001 PHE E 19 TYR 0.015 0.001 TYR A 374 ARG 0.007 0.000 ARG E 49 ********************** 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 112 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 62 time to evaluate : 1.656 Fit side-chains REVERT: A 110 MET cc_start: 0.8325 (mmm) cc_final: 0.8033 (mmm) REVERT: A 412 TRP cc_start: 0.8883 (OUTLIER) cc_final: 0.7467 (m-90) REVERT: A 442 MET cc_start: 0.9049 (tpp) cc_final: 0.8518 (tpp) REVERT: A 465 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8311 (pm20) REVERT: A 797 VAL cc_start: 0.9431 (OUTLIER) cc_final: 0.9223 (p) REVERT: A 831 MET cc_start: 0.9217 (tpp) cc_final: 0.8346 (mmm) REVERT: B 110 MET cc_start: 0.8505 (mmm) cc_final: 0.8226 (mmm) REVERT: B 412 TRP cc_start: 0.8876 (OUTLIER) cc_final: 0.7461 (m-90) REVERT: B 442 MET cc_start: 0.9069 (tpp) cc_final: 0.8525 (tpp) REVERT: B 465 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: B 797 VAL cc_start: 0.9449 (OUTLIER) cc_final: 0.9247 (p) REVERT: B 831 MET cc_start: 0.8311 (tpt) cc_final: 0.7912 (tpt) outliers start: 50 outliers final: 43 residues processed: 106 average time/residue: 0.2176 time to fit residues: 38.6291 Evaluate side-chains 106 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 57 time to evaluate : 1.849 ------------------------------------------------------------------------------- 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 378 SER Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 462 ASN 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 516 THR Chi-restraints excluded: chain A residue 541 ASN 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 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 462 ASN Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 541 ASN 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 819 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 852 TYR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 40.0000 chunk 43 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 59 optimal weight: 0.0370 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 0.0870 overall best weight: 1.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.079917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.051345 restraints weight = 64216.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.053131 restraints weight = 32761.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.054223 restraints weight = 22443.555| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2529 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= 0.203 Angle : 0.576 12.187 20352 Z= 0.288 Chirality : 0.044 0.151 2214 Planarity : 0.003 0.041 2632 Dihedral : 4.474 50.589 1995 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.98 % Favored : 91.80 % Rotamer: Outliers : 3.15 % Allowed : 28.06 % Favored : 68.79 % 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: -0.10 (0.36), residues: 202 sheet: -0.59 (0.28), residues: 364 loop : -1.37 (0.19), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 559 HIS 0.002 0.000 HIS A 429 PHE 0.012 0.001 PHE A 506 TYR 0.016 0.001 TYR A 374 ARG 0.005 0.000 ARG E 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.27 seconds wall clock time: 47 minutes 34.02 seconds (2854.02 seconds total)