Starting phenix.real_space_refine on Tue Aug 6 21:43:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4c_41878/08_2024/8u4c_41878_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4c_41878/08_2024/8u4c_41878.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/8u4c_41878/08_2024/8u4c_41878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4c_41878/08_2024/8u4c_41878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4c_41878/08_2024/8u4c_41878_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4c_41878/08_2024/8u4c_41878_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3510 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 9324 2.51 5 N 2532 2.21 5 O 2730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 142": "OD1" <-> "OD2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "F ASP 52": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14706 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6610 Classifications: {'peptide': 817} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 773} Chain breaks: 6 Chain: "B" Number of atoms: 6610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6610 Classifications: {'peptide': 817} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 773} Chain breaks: 6 Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "D" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Chain: "E" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "F" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Time building chain proxies: 8.99, per 1000 atoms: 0.61 Number of scatterers: 14706 At special positions: 0 Unit cell: (135, 122.04, 170.64, 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 2730 8.00 N 2532 7.00 C 9324 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=2.03 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 872 " distance=2.03 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 807 " 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=2.03 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 872 " distance=2.03 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 807 " 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=2.03 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: 5.57 Conformation dependent library (CDL) restraints added in 2.4 seconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 30 sheets defined 17.1% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 3.584A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.755A 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 132 through 136 removed outlier: 3.664A pdb=" N ARG A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.243A pdb=" N ASN A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.650A 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 323 through 329 removed outlier: 3.893A 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: 3.781A pdb=" N PHE A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.776A 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 Processing helix chain 'A' and resid 874 through 881 Processing helix chain 'B' and resid 16 through 24 removed outlier: 3.580A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.757A 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 132 through 136 removed outlier: 3.663A pdb=" N ARG B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.250A pdb=" N ASN B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.657A 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 323 through 329 removed outlier: 3.900A 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: 3.772A pdb=" N PHE B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.778A 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 removed outlier: 3.562A pdb=" N LEU B 696 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 881 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.518A pdb=" N LEU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.805A pdb=" N THR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 17 removed outlier: 3.863A 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: 3.704A pdb=" N LEU D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.514A pdb=" N LEU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 60 removed outlier: 3.803A pdb=" N THR E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 17 removed outlier: 3.879A 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: 3.675A 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 13 removed outlier: 7.031A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.440A 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 278 through 279 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 293 removed outlier: 3.625A pdb=" N THR A 302 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 321 removed outlier: 9.953A pdb=" N VAL A 335 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N LEU A 315 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N ASN A 337 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLY A 317 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 321 removed outlier: 9.953A pdb=" N VAL A 335 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N LEU A 315 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N ASN A 337 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLY A 317 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB1, first strand: chain 'A' and resid 479 through 480 removed outlier: 4.053A pdb=" N ARG A 479 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 486 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 533 removed outlier: 3.551A pdb=" N LEU A 505 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 599 through 605 removed outlier: 5.560A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 771 through 774 removed outlier: 3.666A pdb=" N GLU A 772 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 630 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 627 " --> pdb=" O CYS A 798 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 827 through 834 removed outlier: 5.092A pdb=" N GLN A 845 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS A 884 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 854 through 863 removed outlier: 3.724A pdb=" N GLY A 892 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 917 " --> pdb=" O GLY A 892 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 12 through 13 removed outlier: 7.031A pdb=" N GLN B 34 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 63 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 36 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG B 65 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.444A 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 278 through 279 Processing sheet with id=AC3, first strand: chain 'B' and resid 292 through 293 removed outlier: 3.624A pdb=" N THR B 302 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 321 removed outlier: 9.946A pdb=" N VAL B 335 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 10.729A pdb=" N LEU B 315 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N ASN B 337 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLY B 317 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 321 removed outlier: 9.946A pdb=" N VAL B 335 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 10.729A pdb=" N LEU B 315 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N ASN B 337 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLY B 317 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC7, first strand: chain 'B' and resid 479 through 480 removed outlier: 4.001A pdb=" N ARG B 479 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 486 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 530 through 533 removed outlier: 3.501A pdb=" N THR B 530 " --> pdb=" O TYR B 507 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 505 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 599 through 605 removed outlier: 5.554A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 771 through 774 removed outlier: 3.604A pdb=" N GLU B 772 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 630 " --> pdb=" O GLU B 772 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 827 through 834 removed outlier: 5.070A pdb=" N GLN B 845 " --> pdb=" O PRO B 829 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 854 through 863 removed outlier: 3.707A pdb=" N GLY B 892 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 917 " --> pdb=" O GLY B 892 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4830 1.34 - 1.46: 3439 1.46 - 1.58: 6637 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 15048 Sorted by residual: bond pdb=" C CYS A 192 " pdb=" N PRO A 193 " ideal model delta sigma weight residual 1.332 1.356 -0.025 1.33e-02 5.65e+03 3.41e+00 bond pdb=" C CYS B 192 " pdb=" N PRO B 193 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.33e-02 5.65e+03 3.11e+00 bond pdb=" CB ARG F 38 " pdb=" CG ARG F 38 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CA ARG D 38 " pdb=" CB ARG D 38 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.59e-02 3.96e+03 1.15e+00 bond pdb=" CB ASP D 52 " pdb=" CG ASP D 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 ... (remaining 15043 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.55: 446 106.55 - 113.56: 8063 113.56 - 120.57: 5825 120.57 - 127.58: 5885 127.58 - 134.59: 155 Bond angle restraints: 20374 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 113.53 108.38 5.15 9.80e-01 1.04e+00 2.77e+01 angle pdb=" CA ARG F 38 " pdb=" CB ARG F 38 " pdb=" CG ARG F 38 " ideal model delta sigma weight residual 114.10 123.50 -9.40 2.00e+00 2.50e-01 2.21e+01 angle pdb=" CA ARG D 38 " pdb=" CB ARG D 38 " pdb=" CG ARG D 38 " ideal model delta sigma weight residual 114.10 123.12 -9.02 2.00e+00 2.50e-01 2.03e+01 angle pdb=" CB MET B 843 " pdb=" CG MET B 843 " pdb=" SD MET B 843 " ideal model delta sigma weight residual 112.70 124.87 -12.17 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CB MET A 843 " pdb=" CG MET A 843 " pdb=" SD MET A 843 " ideal model delta sigma weight residual 112.70 124.32 -11.62 3.00e+00 1.11e-01 1.50e+01 ... (remaining 20369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7713 17.74 - 35.48: 1094 35.48 - 53.22: 249 53.22 - 70.96: 43 70.96 - 88.70: 41 Dihedral angle restraints: 9140 sinusoidal: 3826 harmonic: 5314 Sorted by residual: 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 -170.73 84.73 1 1.00e+01 1.00e-02 8.72e+01 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 -170.51 84.51 1 1.00e+01 1.00e-02 8.68e+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 -163.27 77.27 1 1.00e+01 1.00e-02 7.48e+01 ... (remaining 9137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1378 0.031 - 0.061: 529 0.061 - 0.092: 168 0.092 - 0.122: 129 0.122 - 0.153: 12 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CA THR B 802 " pdb=" N THR B 802 " pdb=" C THR B 802 " pdb=" CB THR B 802 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA THR A 802 " pdb=" N THR A 802 " pdb=" C THR A 802 " pdb=" CB THR A 802 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE B 457 " pdb=" N ILE B 457 " pdb=" C ILE B 457 " pdb=" CB ILE B 457 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 2213 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 632 " 0.017 2.00e-02 2.50e+03 1.53e-02 5.84e+00 pdb=" CG TRP B 632 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 632 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 632 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 632 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 632 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 632 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 632 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 632 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 632 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 911 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 912 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 912 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 912 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 911 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 912 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 912 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 912 " -0.023 5.00e-02 4.00e+02 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 34 2.36 - 2.99: 7802 2.99 - 3.63: 22097 3.63 - 4.26: 32555 4.26 - 4.90: 53565 Nonbonded interactions: 116053 Sorted by model distance: nonbonded pdb=" CE1 TYR B 708 " pdb=" NH2 ARG D 37 " model vdw 1.722 3.420 nonbonded pdb=" CE1 TYR A 708 " pdb=" NH2 ARG F 37 " model vdw 1.771 3.420 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.162 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.163 3.040 nonbonded pdb=" O PRO B 716 " pdb=" OH TYR D 27 " model vdw 2.183 3.040 ... (remaining 116048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.580 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.003 0.035 15048 Z= 0.201 Angle : 0.607 12.171 20374 Z= 0.308 Chirality : 0.042 0.153 2216 Planarity : 0.003 0.043 2634 Dihedral : 17.057 88.702 5570 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.79 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 29.12 % Favored : 70.88 % 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: -1.32 (0.20), residues: 1782 helix: 0.44 (0.38), residues: 192 sheet: -0.35 (0.28), residues: 352 loop : -1.32 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 632 HIS 0.008 0.000 HIS A 440 PHE 0.017 0.001 PHE A 572 TYR 0.015 0.001 TYR B 374 ARG 0.004 0.000 ARG A 882 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 843 MET cc_start: 0.8595 (tpp) cc_final: 0.7577 (mmm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3198 time to fit residues: 30.4166 Evaluate side-chains 47 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 46 optimal weight: 0.0370 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 0.0060 chunk 141 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 overall best weight: 1.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15048 Z= 0.260 Angle : 0.608 9.534 20374 Z= 0.311 Chirality : 0.044 0.143 2216 Planarity : 0.004 0.038 2634 Dihedral : 4.344 17.367 1996 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.73 % Favored : 93.04 % Rotamer: Outliers : 1.88 % Allowed : 26.51 % Favored : 71.61 % 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: -1.37 (0.20), residues: 1782 helix: 0.23 (0.37), residues: 200 sheet: -0.54 (0.28), residues: 364 loop : -1.28 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 632 HIS 0.005 0.001 HIS B 440 PHE 0.015 0.001 PHE B 506 TYR 0.014 0.001 TYR A 374 ARG 0.004 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 52 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 843 MET cc_start: 0.8903 (tpp) cc_final: 0.7700 (mmm) outliers start: 31 outliers final: 11 residues processed: 79 average time/residue: 0.2353 time to fit residues: 30.9258 Evaluate side-chains 60 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain C residue 55 LEU 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: 0.8980 chunk 50 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 131 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15048 Z= 0.181 Angle : 0.561 9.244 20374 Z= 0.284 Chirality : 0.042 0.143 2216 Planarity : 0.003 0.040 2634 Dihedral : 4.247 17.668 1996 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.68 % Favored : 93.10 % Rotamer: Outliers : 2.18 % Allowed : 26.69 % Favored : 71.13 % 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: -1.37 (0.20), residues: 1782 helix: 0.06 (0.36), residues: 202 sheet: -0.55 (0.28), residues: 364 loop : -1.24 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 632 HIS 0.003 0.000 HIS A 440 PHE 0.015 0.001 PHE A 705 TYR 0.014 0.001 TYR A 507 ARG 0.003 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 54 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 843 MET cc_start: 0.8808 (tpp) cc_final: 0.7552 (mmm) REVERT: B 412 TRP cc_start: 0.8739 (OUTLIER) cc_final: 0.5804 (m-90) REVERT: F 53 LEU cc_start: 0.9177 (tp) cc_final: 0.8955 (tt) outliers start: 36 outliers final: 20 residues processed: 86 average time/residue: 0.2649 time to fit residues: 36.7380 Evaluate side-chains 70 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 49 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 109 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15048 Z= 0.354 Angle : 0.621 9.515 20374 Z= 0.314 Chirality : 0.044 0.172 2216 Planarity : 0.004 0.041 2634 Dihedral : 4.496 17.727 1996 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.41 % Favored : 92.37 % Rotamer: Outliers : 4.36 % Allowed : 24.76 % Favored : 70.88 % 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: -1.50 (0.20), residues: 1782 helix: 0.14 (0.36), residues: 198 sheet: -0.74 (0.28), residues: 368 loop : -1.33 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 632 HIS 0.004 0.001 HIS A 100 PHE 0.021 0.002 PHE B 482 TYR 0.015 0.001 TYR A 374 ARG 0.004 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 56 time to evaluate : 1.740 Fit side-chains revert: symmetry clash REVERT: A 412 TRP cc_start: 0.8835 (OUTLIER) cc_final: 0.5878 (m-90) REVERT: A 442 MET cc_start: 0.8862 (tpp) cc_final: 0.8386 (tpp) REVERT: A 635 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8273 (mp-120) REVERT: A 843 MET cc_start: 0.8828 (tpp) cc_final: 0.7558 (mmm) REVERT: B 412 TRP cc_start: 0.8781 (OUTLIER) cc_final: 0.5653 (m-10) REVERT: B 477 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8632 (p90) REVERT: B 635 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8384 (mp-120) REVERT: B 843 MET cc_start: 0.8999 (tpp) cc_final: 0.8732 (tpp) REVERT: F 40 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.7990 (mtm180) REVERT: F 53 LEU cc_start: 0.9217 (tp) cc_final: 0.8987 (tt) outliers start: 72 outliers final: 36 residues processed: 124 average time/residue: 0.2208 time to fit residues: 43.8149 Evaluate side-chains 93 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 52 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU 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 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.3980 chunk 98 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS A 589 GLN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15048 Z= 0.222 Angle : 0.569 9.232 20374 Z= 0.289 Chirality : 0.043 0.174 2216 Planarity : 0.003 0.041 2634 Dihedral : 4.380 18.142 1996 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.62 % Favored : 93.15 % Rotamer: Outliers : 3.75 % Allowed : 25.42 % Favored : 70.82 % 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: -1.47 (0.20), residues: 1782 helix: 0.14 (0.36), residues: 198 sheet: -0.77 (0.28), residues: 356 loop : -1.29 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 632 HIS 0.006 0.001 HIS A 185 PHE 0.016 0.001 PHE B 705 TYR 0.015 0.001 TYR B 374 ARG 0.007 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 55 time to evaluate : 1.536 Fit side-chains revert: symmetry clash REVERT: A 223 THR cc_start: 0.9417 (OUTLIER) cc_final: 0.9178 (p) REVERT: A 412 TRP cc_start: 0.8804 (OUTLIER) cc_final: 0.5987 (m-90) REVERT: A 442 MET cc_start: 0.8841 (tpp) cc_final: 0.8407 (tpp) REVERT: A 582 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8206 (mttp) REVERT: A 635 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8288 (mp-120) REVERT: A 843 MET cc_start: 0.8888 (tpp) cc_final: 0.7638 (mmm) REVERT: B 223 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9131 (p) REVERT: B 412 TRP cc_start: 0.8795 (OUTLIER) cc_final: 0.5792 (m-90) REVERT: B 477 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8752 (p90) REVERT: B 635 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8334 (mp-120) REVERT: B 843 MET cc_start: 0.9035 (tpp) cc_final: 0.8562 (tpp) REVERT: F 40 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8027 (mtm180) REVERT: F 53 LEU cc_start: 0.9118 (tp) cc_final: 0.8853 (tt) outliers start: 62 outliers final: 37 residues processed: 115 average time/residue: 0.2226 time to fit residues: 41.0782 Evaluate side-chains 93 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 48 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU 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 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.0670 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 80 optimal weight: 40.0000 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15048 Z= 0.282 Angle : 0.590 9.374 20374 Z= 0.296 Chirality : 0.044 0.184 2216 Planarity : 0.003 0.041 2634 Dihedral : 4.394 17.910 1996 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.79 % Favored : 92.99 % Rotamer: Outliers : 4.30 % Allowed : 25.24 % Favored : 70.46 % 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: -1.49 (0.20), residues: 1782 helix: 0.24 (0.36), residues: 196 sheet: -0.78 (0.28), residues: 346 loop : -1.32 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 632 HIS 0.003 0.001 HIS A 440 PHE 0.017 0.001 PHE A 482 TYR 0.015 0.001 TYR A 374 ARG 0.004 0.000 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 52 time to evaluate : 1.672 Fit side-chains REVERT: A 223 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.9182 (p) REVERT: A 412 TRP cc_start: 0.8789 (OUTLIER) cc_final: 0.5948 (m-10) REVERT: A 442 MET cc_start: 0.8939 (tpp) cc_final: 0.8462 (tpp) REVERT: A 635 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8233 (mp-120) REVERT: A 698 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8729 (mm-30) REVERT: A 843 MET cc_start: 0.8923 (tpp) cc_final: 0.7454 (mmm) REVERT: B 223 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9135 (p) REVERT: B 412 TRP cc_start: 0.8811 (OUTLIER) cc_final: 0.5822 (m-10) REVERT: B 477 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.8658 (p90) REVERT: B 635 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8370 (mp-120) REVERT: D 40 ARG cc_start: 0.8343 (tpp80) cc_final: 0.8037 (tpp80) REVERT: D 45 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6357 (mp0) REVERT: F 40 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.8099 (mtm180) REVERT: F 53 LEU cc_start: 0.9151 (tp) cc_final: 0.8878 (tt) outliers start: 71 outliers final: 46 residues processed: 121 average time/residue: 0.2179 time to fit residues: 42.6569 Evaluate side-chains 104 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 49 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain E residue 13 LEU 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 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 146 optimal weight: 0.3980 chunk 97 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 80 optimal weight: 20.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 513 GLN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS B 513 GLN ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 15048 Z= 0.487 Angle : 0.699 9.331 20374 Z= 0.351 Chirality : 0.047 0.192 2216 Planarity : 0.004 0.043 2634 Dihedral : 4.854 19.243 1996 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.47 % Favored : 91.30 % Rotamer: Outliers : 4.84 % Allowed : 25.42 % Favored : 69.73 % 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: -1.82 (0.20), residues: 1782 helix: -0.59 (0.33), residues: 228 sheet: -0.83 (0.28), residues: 352 loop : -1.52 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 632 HIS 0.004 0.001 HIS B 548 PHE 0.029 0.002 PHE B 482 TYR 0.017 0.002 TYR A 374 ARG 0.006 0.001 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 56 time to evaluate : 1.699 Fit side-chains REVERT: A 223 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.9215 (p) REVERT: A 412 TRP cc_start: 0.8771 (OUTLIER) cc_final: 0.6140 (m-10) REVERT: A 442 MET cc_start: 0.9059 (tpp) cc_final: 0.8599 (tpp) REVERT: A 477 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8656 (p90) REVERT: A 482 PHE cc_start: 0.7801 (t80) cc_final: 0.7594 (t80) REVERT: A 635 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8301 (mp-120) REVERT: B 223 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9168 (p) REVERT: B 410 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8589 (pp30) REVERT: B 412 TRP cc_start: 0.8854 (OUTLIER) cc_final: 0.5761 (m-10) REVERT: B 477 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8468 (p90) REVERT: B 482 PHE cc_start: 0.7750 (t80) cc_final: 0.7539 (t80) REVERT: B 635 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8395 (mp-120) REVERT: D 45 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: F 38 ARG cc_start: 0.7631 (tmm-80) cc_final: 0.7331 (tpp-160) REVERT: F 40 ARG cc_start: 0.8600 (mmm-85) cc_final: 0.8379 (tpp-160) REVERT: F 53 LEU cc_start: 0.9223 (tp) cc_final: 0.8950 (tt) outliers start: 80 outliers final: 49 residues processed: 134 average time/residue: 0.2671 time to fit residues: 55.1477 Evaluate side-chains 107 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 48 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain E residue 13 LEU 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 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 34 optimal weight: 0.0050 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15048 Z= 0.165 Angle : 0.590 10.508 20374 Z= 0.297 Chirality : 0.044 0.179 2216 Planarity : 0.003 0.042 2634 Dihedral : 4.468 18.339 1996 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.78 % Favored : 94.00 % Rotamer: Outliers : 3.63 % Allowed : 26.15 % Favored : 70.22 % 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: -1.60 (0.20), residues: 1782 helix: -0.14 (0.35), residues: 208 sheet: -0.67 (0.29), residues: 312 loop : -1.41 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 632 HIS 0.004 0.001 HIS A 429 PHE 0.020 0.001 PHE A 705 TYR 0.016 0.001 TYR A 507 ARG 0.006 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 51 time to evaluate : 1.777 Fit side-chains REVERT: A 223 THR cc_start: 0.9455 (OUTLIER) cc_final: 0.9239 (p) REVERT: A 412 TRP cc_start: 0.8709 (OUTLIER) cc_final: 0.6021 (m-10) REVERT: A 442 MET cc_start: 0.8950 (tpp) cc_final: 0.8393 (tpp) REVERT: A 635 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8184 (mp-120) REVERT: A 843 MET cc_start: 0.8100 (tpp) cc_final: 0.7634 (tpp) REVERT: B 410 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8704 (pp30) REVERT: B 412 TRP cc_start: 0.8793 (OUTLIER) cc_final: 0.5872 (m-90) REVERT: B 477 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8720 (p90) REVERT: B 635 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8250 (mp-120) REVERT: C 53 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8381 (tt) REVERT: D 45 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: F 53 LEU cc_start: 0.9085 (tp) cc_final: 0.8783 (tt) outliers start: 60 outliers final: 38 residues processed: 109 average time/residue: 0.2692 time to fit residues: 45.8608 Evaluate side-chains 95 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 48 time to evaluate : 1.807 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU 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 241 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 151 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 chunk 97 optimal weight: 0.5980 chunk 70 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15048 Z= 0.255 Angle : 0.604 10.075 20374 Z= 0.301 Chirality : 0.044 0.191 2216 Planarity : 0.004 0.042 2634 Dihedral : 4.440 18.443 1996 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.79 % Favored : 92.99 % Rotamer: Outliers : 3.57 % Allowed : 26.03 % Favored : 70.40 % 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: 1782 helix: -0.05 (0.35), residues: 208 sheet: -0.73 (0.29), residues: 332 loop : -1.38 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 632 HIS 0.003 0.001 HIS A 429 PHE 0.016 0.001 PHE B 482 TYR 0.014 0.001 TYR A 374 ARG 0.013 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 49 time to evaluate : 1.569 Fit side-chains REVERT: A 223 THR cc_start: 0.9457 (OUTLIER) cc_final: 0.9235 (p) REVERT: A 412 TRP cc_start: 0.8757 (OUTLIER) cc_final: 0.6181 (m-10) REVERT: A 442 MET cc_start: 0.8987 (tpp) cc_final: 0.8527 (tpp) REVERT: A 635 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8197 (mp-120) REVERT: A 843 MET cc_start: 0.8261 (tpp) cc_final: 0.7840 (tpp) REVERT: B 410 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8626 (pp30) REVERT: B 412 TRP cc_start: 0.8827 (OUTLIER) cc_final: 0.6040 (m-90) REVERT: B 477 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.8471 (p90) REVERT: B 635 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8272 (mp-120) REVERT: D 45 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6594 (mp0) REVERT: F 53 LEU cc_start: 0.9119 (tp) cc_final: 0.8833 (tt) outliers start: 59 outliers final: 45 residues processed: 106 average time/residue: 0.2123 time to fit residues: 36.9293 Evaluate side-chains 100 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 47 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU 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 241 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 13 LEU 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 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 0.1980 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15048 Z= 0.179 Angle : 0.600 11.453 20374 Z= 0.299 Chirality : 0.044 0.192 2216 Planarity : 0.003 0.042 2634 Dihedral : 4.380 18.327 1996 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.89 % Favored : 93.88 % Rotamer: Outliers : 3.33 % Allowed : 26.03 % Favored : 70.64 % 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: -1.54 (0.20), residues: 1782 helix: -0.05 (0.36), residues: 208 sheet: -0.48 (0.30), residues: 302 loop : -1.41 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 632 HIS 0.003 0.001 HIS A 429 PHE 0.025 0.001 PHE B 482 TYR 0.014 0.001 TYR B 374 ARG 0.011 0.000 ARG A 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 49 time to evaluate : 1.628 Fit side-chains REVERT: A 103 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8649 (pm20) REVERT: A 223 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9234 (p) REVERT: A 412 TRP cc_start: 0.8694 (OUTLIER) cc_final: 0.6238 (m-10) REVERT: A 442 MET cc_start: 0.8963 (tpp) cc_final: 0.8449 (tpp) REVERT: A 635 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8160 (mp-120) REVERT: A 843 MET cc_start: 0.8181 (tpp) cc_final: 0.7812 (tpp) REVERT: B 410 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8640 (pp30) REVERT: B 412 TRP cc_start: 0.8794 (OUTLIER) cc_final: 0.5819 (m-10) REVERT: B 442 MET cc_start: 0.9227 (mmm) cc_final: 0.8766 (mmm) REVERT: B 477 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.8664 (p90) REVERT: B 635 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8232 (mp-120) REVERT: B 843 MET cc_start: 0.8719 (tpp) cc_final: 0.8463 (tpp) REVERT: D 40 ARG cc_start: 0.8032 (tpp80) cc_final: 0.7665 (tpp80) REVERT: D 45 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6222 (mp0) REVERT: F 53 LEU cc_start: 0.9092 (tp) cc_final: 0.8799 (tt) outliers start: 55 outliers final: 42 residues processed: 102 average time/residue: 0.2194 time to fit residues: 36.7516 Evaluate side-chains 97 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 46 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU 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 241 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 chunk 59 optimal weight: 0.0050 chunk 146 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 0.4980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 GLN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.081084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.051098 restraints weight = 63519.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.052805 restraints weight = 33074.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.053876 restraints weight = 22914.019| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15048 Z= 0.167 Angle : 0.594 13.094 20374 Z= 0.292 Chirality : 0.043 0.187 2216 Planarity : 0.003 0.042 2634 Dihedral : 4.238 17.786 1996 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.29 % Favored : 93.49 % Rotamer: Outliers : 3.27 % Allowed : 26.45 % Favored : 70.28 % 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: -1.50 (0.20), residues: 1782 helix: -0.05 (0.36), residues: 210 sheet: -0.44 (0.29), residues: 302 loop : -1.38 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 632 HIS 0.003 0.000 HIS A 429 PHE 0.017 0.001 PHE A 705 TYR 0.014 0.001 TYR A 374 ARG 0.010 0.000 ARG A 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2634.52 seconds wall clock time: 48 minutes 24.28 seconds (2904.28 seconds total)