Starting phenix.real_space_refine on Mon Jul 22 09:02:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4c_41878/07_2024/8u4c_41878_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4c_41878/07_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_41878/07_2024/8u4c_41878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4c_41878/07_2024/8u4c_41878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4c_41878/07_2024/8u4c_41878_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4c_41878/07_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 9.23, per 1000 atoms: 0.63 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: 5.93 Conformation dependent library (CDL) restraints added in 2.7 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: 2.05 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: 5.07 Time building geometry restraints manager: 6.55 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 2.440 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.163 2.440 nonbonded pdb=" O PRO B 716 " pdb=" OH TYR D 27 " model vdw 2.183 2.440 ... (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 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 43.880 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.460 ------------------------------------------------------------------------------- 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 : 1.781 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: 0.3445 time to fit residues: 32.7434 Evaluate side-chains 47 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 2.011 ------------------------------------------------------------------------------- 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: 10.0000 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 46 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** 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** ** A 893 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15048 Z= 0.350 Angle : 0.626 9.774 20374 Z= 0.317 Chirality : 0.044 0.148 2216 Planarity : 0.004 0.038 2634 Dihedral : 4.448 18.171 1996 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.86 % Favored : 91.92 % Rotamer: Outliers : 3.09 % Allowed : 27.42 % Favored : 69.49 % 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: -1.41 (0.20), residues: 1782 helix: 0.26 (0.37), residues: 196 sheet: -0.48 (0.28), residues: 362 loop : -1.35 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 632 HIS 0.005 0.001 HIS B 440 PHE 0.017 0.002 PHE A 482 TYR 0.014 0.001 TYR A 374 ARG 0.005 0.000 ARG D 40 *********************** 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 102 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 51 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.9533 (OUTLIER) cc_final: 0.8885 (p) REVERT: A 187 HIS cc_start: 0.8828 (OUTLIER) cc_final: 0.8508 (m90) REVERT: A 411 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9335 (tt) REVERT: A 843 MET cc_start: 0.8881 (tpp) cc_final: 0.7599 (mmm) REVERT: B 186 SER cc_start: 0.9502 (OUTLIER) cc_final: 0.8899 (p) REVERT: B 187 HIS cc_start: 0.8835 (OUTLIER) cc_final: 0.8504 (m90) REVERT: B 412 TRP cc_start: 0.8698 (OUTLIER) cc_final: 0.5722 (m-90) REVERT: B 442 MET cc_start: 0.9254 (mmm) cc_final: 0.8788 (mmm) outliers start: 51 outliers final: 17 residues processed: 100 average time/residue: 0.2270 time to fit residues: 36.7353 Evaluate side-chains 73 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 50 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 802 THR 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 122 ASN Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.0570 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 131 optimal weight: 0.0000 overall best weight: 0.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15048 Z= 0.158 Angle : 0.551 9.417 20374 Z= 0.277 Chirality : 0.042 0.145 2216 Planarity : 0.003 0.038 2634 Dihedral : 4.253 17.862 1996 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.68 % Favored : 93.10 % Rotamer: Outliers : 2.60 % Allowed : 27.66 % 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: -1.39 (0.20), residues: 1782 helix: 0.17 (0.36), residues: 200 sheet: -0.50 (0.28), residues: 366 loop : -1.31 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 632 HIS 0.002 0.000 HIS A 440 PHE 0.016 0.001 PHE A 705 TYR 0.014 0.001 TYR A 507 ARG 0.002 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 98 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 55 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8342 (mp-120) REVERT: A 843 MET cc_start: 0.8876 (tpp) cc_final: 0.7582 (mmm) REVERT: B 635 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8377 (mp-120) outliers start: 43 outliers final: 20 residues processed: 94 average time/residue: 0.2408 time to fit residues: 37.4874 Evaluate side-chains 72 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 50 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 635 GLN 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 228 CYS Chi-restraints excluded: chain B residue 459 LEU 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 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 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 42 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 40.0000 chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 0.0040 chunk 155 optimal weight: 30.0000 chunk 46 optimal weight: 0.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 ASN B 34 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15048 Z= 0.425 Angle : 0.654 9.802 20374 Z= 0.327 Chirality : 0.045 0.177 2216 Planarity : 0.004 0.039 2634 Dihedral : 4.590 18.551 1996 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.26 % Favored : 90.52 % Rotamer: Outliers : 5.02 % Allowed : 26.09 % Favored : 68.89 % 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: 0.03 (0.36), residues: 198 sheet: -0.69 (0.28), residues: 376 loop : -1.43 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 632 HIS 0.005 0.001 HIS A 440 PHE 0.021 0.002 PHE A 482 TYR 0.015 0.001 TYR A 374 ARG 0.004 0.000 ARG A 86 *********************** 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 135 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 52 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.9540 (OUTLIER) cc_final: 0.8899 (p) REVERT: A 187 HIS cc_start: 0.8824 (OUTLIER) cc_final: 0.8521 (m90) REVERT: A 412 TRP cc_start: 0.8782 (OUTLIER) cc_final: 0.5710 (m-10) REVERT: A 442 MET cc_start: 0.8869 (tpp) cc_final: 0.8437 (tpp) REVERT: A 635 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8351 (mp-120) REVERT: A 843 MET cc_start: 0.8937 (tpp) cc_final: 0.7644 (mmm) REVERT: B 186 SER cc_start: 0.9509 (OUTLIER) cc_final: 0.8883 (p) REVERT: B 187 HIS cc_start: 0.8808 (OUTLIER) cc_final: 0.8474 (m90) REVERT: B 223 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.9124 (p) REVERT: B 412 TRP cc_start: 0.8804 (OUTLIER) cc_final: 0.5736 (m-10) REVERT: B 477 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8916 (p90) REVERT: B 482 PHE cc_start: 0.7386 (t80) cc_final: 0.7049 (t80) REVERT: B 541 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.7287 (p0) REVERT: B 635 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8530 (mp-120) REVERT: B 843 MET cc_start: 0.9059 (tpp) cc_final: 0.8717 (tpp) outliers start: 83 outliers final: 42 residues processed: 131 average time/residue: 0.2608 time to fit residues: 55.3763 Evaluate side-chains 103 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 50 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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 186 SER Chi-restraints excluded: chain A residue 187 HIS 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 412 TRP 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 802 THR 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 122 ASN Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 187 HIS 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 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 477 TYR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 578 THR 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 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 42 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 56 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 Chi-restraints excluded: chain F residue 56 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 156 optimal weight: 40.0000 chunk 43 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1583 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= 0.210 Angle : 0.565 9.491 20374 Z= 0.282 Chirality : 0.043 0.177 2216 Planarity : 0.003 0.043 2634 Dihedral : 4.413 18.625 1996 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.79 % Favored : 92.99 % Rotamer: Outliers : 3.51 % Allowed : 27.36 % Favored : 69.13 % 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: -1.50 (0.20), residues: 1782 helix: 0.08 (0.36), residues: 198 sheet: -0.72 (0.28), residues: 376 loop : -1.33 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 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 0.007 0.000 ARG F 38 *********************** 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 113 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 55 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9219 (p) REVERT: A 411 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9237 (mt) REVERT: A 412 TRP cc_start: 0.8768 (OUTLIER) cc_final: 0.5810 (m-10) REVERT: A 442 MET cc_start: 0.8918 (tpp) cc_final: 0.8437 (tpp) REVERT: A 635 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8277 (mp-120) REVERT: A 843 MET cc_start: 0.8949 (tpp) cc_final: 0.7661 (mmm) REVERT: B 412 TRP cc_start: 0.8812 (OUTLIER) cc_final: 0.5809 (m-10) REVERT: B 635 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8475 (mp-120) REVERT: B 843 MET cc_start: 0.9137 (tpp) cc_final: 0.8845 (tpp) outliers start: 58 outliers final: 36 residues processed: 109 average time/residue: 0.2200 time to fit residues: 39.2381 Evaluate side-chains 95 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 53 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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 459 LEU 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 185 HIS 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 412 TRP Chi-restraints excluded: chain B residue 472 LEU 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 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 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 56 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 9.9990 chunk 156 optimal weight: 30.0000 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.0030 chunk 42 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1678 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= 0.169 Angle : 0.543 9.701 20374 Z= 0.269 Chirality : 0.042 0.177 2216 Planarity : 0.003 0.038 2634 Dihedral : 4.200 18.067 1996 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.62 % Favored : 93.15 % Rotamer: Outliers : 4.12 % Allowed : 27.00 % Favored : 68.89 % 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: -1.44 (0.20), residues: 1782 helix: 0.18 (0.36), residues: 200 sheet: -0.54 (0.29), residues: 344 loop : -1.34 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 632 HIS 0.003 0.000 HIS A 185 PHE 0.017 0.001 PHE C 28 TYR 0.014 0.001 TYR A 374 ARG 0.007 0.000 ARG D 38 *********************** 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: 68 poor density : 55 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9198 (p) REVERT: A 411 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9146 (tt) REVERT: A 412 TRP cc_start: 0.8750 (OUTLIER) cc_final: 0.5834 (m-10) REVERT: A 442 MET cc_start: 0.8945 (tpp) cc_final: 0.8385 (tpp) REVERT: A 843 MET cc_start: 0.8971 (tpp) cc_final: 0.7428 (mmm) REVERT: B 410 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8678 (pp30) REVERT: B 412 TRP cc_start: 0.8808 (OUTLIER) cc_final: 0.5901 (m-10) REVERT: B 635 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8426 (mp-120) outliers start: 68 outliers final: 40 residues processed: 120 average time/residue: 0.2266 time to fit residues: 43.9169 Evaluate side-chains 98 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 52 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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 158 ILE 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 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 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 158 ILE 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 268 ASN 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 472 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 578 THR 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 C residue 13 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 55 LEU 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: 0.0980 chunk 19 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 80 optimal weight: 40.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 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: 0.8161 moved from start: 0.1780 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= 0.196 Angle : 0.562 9.822 20374 Z= 0.276 Chirality : 0.043 0.243 2216 Planarity : 0.003 0.038 2634 Dihedral : 4.201 18.418 1996 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.96 % Favored : 92.82 % Rotamer: Outliers : 3.87 % Allowed : 27.66 % Favored : 68.46 % 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: -1.47 (0.20), residues: 1782 helix: 0.18 (0.36), residues: 200 sheet: -0.66 (0.28), residues: 344 loop : -1.33 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 632 HIS 0.002 0.000 HIS A 185 PHE 0.014 0.001 PHE A 705 TYR 0.013 0.001 TYR A 374 ARG 0.005 0.000 ARG F 38 *********************** 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 118 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 54 time to evaluate : 1.798 Fit side-chains revert: symmetry clash REVERT: A 410 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8586 (pp30) REVERT: A 411 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9139 (tt) REVERT: A 412 TRP cc_start: 0.8714 (OUTLIER) cc_final: 0.5725 (m-10) REVERT: A 442 MET cc_start: 0.8895 (tpp) cc_final: 0.8282 (tpp) REVERT: A 635 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8232 (mp-120) REVERT: A 843 MET cc_start: 0.8798 (tpp) cc_final: 0.7430 (mmm) REVERT: B 410 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8674 (pp30) REVERT: B 412 TRP cc_start: 0.8787 (OUTLIER) cc_final: 0.5837 (m-10) REVERT: B 635 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8429 (mp-120) outliers start: 64 outliers final: 43 residues processed: 116 average time/residue: 0.2136 time to fit residues: 40.9108 Evaluate side-chains 100 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 50 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 158 ILE Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 410 GLN 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 635 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 158 ILE 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 472 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 578 THR 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 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 44 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: 8.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 0.0370 chunk 16 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1894 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= 0.186 Angle : 0.559 9.949 20374 Z= 0.273 Chirality : 0.043 0.229 2216 Planarity : 0.003 0.039 2634 Dihedral : 4.151 17.958 1996 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.79 % Favored : 92.99 % Rotamer: Outliers : 3.93 % Allowed : 27.97 % Favored : 68.10 % 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: -1.43 (0.20), residues: 1782 helix: 0.27 (0.36), residues: 200 sheet: -0.61 (0.28), residues: 340 loop : -1.32 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 632 HIS 0.003 0.000 HIS A 429 PHE 0.018 0.001 PHE E 28 TYR 0.013 0.001 TYR B 374 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 117 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 52 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: A 410 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8477 (pp30) REVERT: A 411 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9109 (tt) REVERT: A 412 TRP cc_start: 0.8732 (OUTLIER) cc_final: 0.5701 (m-10) REVERT: A 442 MET cc_start: 0.8887 (tpp) cc_final: 0.8222 (tpp) REVERT: A 635 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8217 (mp-120) REVERT: A 843 MET cc_start: 0.8859 (tpp) cc_final: 0.7562 (mmm) REVERT: B 410 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8665 (pp30) REVERT: B 412 TRP cc_start: 0.8784 (OUTLIER) cc_final: 0.5809 (m-10) REVERT: B 635 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8410 (mp-120) REVERT: D 40 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8086 (tpp80) outliers start: 65 outliers final: 48 residues processed: 115 average time/residue: 0.2209 time to fit residues: 42.4117 Evaluate side-chains 105 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 50 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 158 ILE Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 410 GLN 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 B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 158 ILE 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 348 ASN 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 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 609 SER 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 B residue 864 TYR 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 44 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 7.9990 chunk 166 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 152 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8178 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15048 Z= 0.235 Angle : 0.578 9.996 20374 Z= 0.283 Chirality : 0.044 0.317 2216 Planarity : 0.003 0.039 2634 Dihedral : 4.199 18.592 1996 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.41 % Favored : 92.37 % Rotamer: Outliers : 3.87 % Allowed : 27.66 % Favored : 68.46 % 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: -1.44 (0.20), residues: 1782 helix: 0.33 (0.37), residues: 198 sheet: -0.62 (0.28), residues: 340 loop : -1.34 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 632 HIS 0.003 0.000 HIS B 440 PHE 0.015 0.001 PHE C 19 TYR 0.013 0.001 TYR B 374 ARG 0.005 0.000 ARG F 38 *********************** 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 117 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 53 time to evaluate : 1.931 Fit side-chains revert: symmetry clash REVERT: A 410 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8591 (pp30) REVERT: A 411 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9269 (mt) REVERT: A 412 TRP cc_start: 0.8743 (OUTLIER) cc_final: 0.5921 (m-10) REVERT: A 442 MET cc_start: 0.8908 (tpp) cc_final: 0.8329 (tpp) REVERT: A 635 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8265 (mp-120) REVERT: A 843 MET cc_start: 0.8883 (tpp) cc_final: 0.7586 (mmm) REVERT: B 410 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8664 (pp30) REVERT: B 412 TRP cc_start: 0.8775 (OUTLIER) cc_final: 0.5798 (m-90) REVERT: B 635 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8425 (mp-120) REVERT: D 40 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8131 (tpp80) outliers start: 64 outliers final: 52 residues processed: 115 average time/residue: 0.2135 time to fit residues: 40.8537 Evaluate side-chains 110 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 51 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 158 ILE Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 410 GLN 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 609 SER 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 B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 158 ILE 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 348 ASN 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 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 609 SER 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 B residue 864 TYR 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 44 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 0.1980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2087 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 : 0.573 13.014 20374 Z= 0.280 Chirality : 0.044 0.244 2216 Planarity : 0.003 0.039 2634 Dihedral : 4.181 18.247 1996 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.96 % Favored : 92.82 % Rotamer: Outliers : 3.39 % Allowed : 28.09 % Favored : 68.52 % 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: -1.45 (0.20), residues: 1782 helix: 0.39 (0.37), residues: 198 sheet: -0.68 (0.28), residues: 344 loop : -1.35 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 632 HIS 0.003 0.000 HIS A 429 PHE 0.020 0.001 PHE E 28 TYR 0.013 0.001 TYR B 374 ARG 0.004 0.000 ARG F 38 ********************** 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 112 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 56 time to evaluate : 1.880 Fit side-chains revert: symmetry clash REVERT: A 410 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8494 (pp30) REVERT: A 411 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9133 (tt) REVERT: A 412 TRP cc_start: 0.8717 (OUTLIER) cc_final: 0.5683 (m-10) REVERT: A 442 MET cc_start: 0.8899 (tpp) cc_final: 0.8223 (tpp) REVERT: A 635 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8254 (mp-120) REVERT: A 843 MET cc_start: 0.8911 (tpp) cc_final: 0.7610 (mmm) REVERT: B 410 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8675 (pp30) REVERT: B 412 TRP cc_start: 0.8792 (OUTLIER) cc_final: 0.5891 (m-10) REVERT: B 442 MET cc_start: 0.9231 (mmm) cc_final: 0.8783 (mmm) REVERT: B 635 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8422 (mp-120) REVERT: D 40 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8162 (tpp80) outliers start: 56 outliers final: 48 residues processed: 110 average time/residue: 0.2445 time to fit residues: 42.8025 Evaluate side-chains 107 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 52 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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 158 ILE Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 410 GLN 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 635 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 158 ILE 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 348 ASN 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 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 609 SER 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 864 TYR 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 44 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 125 optimal weight: 0.0870 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.080624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050216 restraints weight = 64393.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.051858 restraints weight = 34201.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.052894 restraints weight = 24002.524| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15048 Z= 0.254 Angle : 0.590 12.385 20374 Z= 0.289 Chirality : 0.044 0.249 2216 Planarity : 0.003 0.039 2634 Dihedral : 4.268 18.625 1996 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.74 % Favored : 92.03 % Rotamer: Outliers : 3.75 % Allowed : 27.85 % Favored : 68.40 % 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: -1.54 (0.20), residues: 1782 helix: 0.34 (0.37), residues: 198 sheet: -0.83 (0.28), residues: 354 loop : -1.37 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 632 HIS 0.003 0.001 HIS B 440 PHE 0.016 0.001 PHE A 482 TYR 0.014 0.001 TYR B 374 ARG 0.004 0.000 ARG F 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2643.94 seconds wall clock time: 48 minutes 23.45 seconds (2903.45 seconds total)