Starting phenix.real_space_refine on Tue Mar 19 05:11:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1z_32953/03_2024/7x1z_32953_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1z_32953/03_2024/7x1z_32953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1z_32953/03_2024/7x1z_32953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1z_32953/03_2024/7x1z_32953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1z_32953/03_2024/7x1z_32953_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1z_32953/03_2024/7x1z_32953_updated.pdb" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 90 5.16 5 C 14580 2.51 5 N 4080 2.21 5 O 4506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C GLU 432": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D GLU 444": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E GLU 407": "OE1" <-> "OE2" Residue "E GLU 432": "OE1" <-> "OE2" Residue "F GLU 77": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F GLU 339": "OE1" <-> "OE2" Residue "F GLU 432": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23304 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3820 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 12, 'TRANS': 471} Chain: "B" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3820 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 12, 'TRANS': 471} Chain: "C" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3820 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 12, 'TRANS': 471} Chain: "D" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3820 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 12, 'TRANS': 471} Chain: "E" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3820 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 12, 'TRANS': 471} Chain: "F" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3820 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 12, 'TRANS': 471} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 12.61, per 1000 atoms: 0.54 Number of scatterers: 23304 At special positions: 0 Unit cell: (122.615, 119.875, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 36 15.00 Mg 12 11.99 O 4506 8.00 N 4080 7.00 C 14580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.69 Conformation dependent library (CDL) restraints added in 4.6 seconds 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5328 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 24 sheets defined 27.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'A' and resid 28 through 31 No H-bonds generated for 'chain 'A' and resid 28 through 31' Processing helix chain 'A' and resid 52 through 67 removed outlier: 3.599A pdb=" N GLY A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 90 removed outlier: 3.741A pdb=" N SER A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 123 through 137 removed outlier: 4.132A pdb=" N GLU A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 174 Processing helix chain 'A' and resid 268 through 274 Processing helix chain 'A' and resid 294 through 306 removed outlier: 4.587A pdb=" N ALA A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N CYS A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 329 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.891A pdb=" N LEU A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 406 removed outlier: 3.932A pdb=" N GLU A 406 " --> pdb=" O TYR A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 31 No H-bonds generated for 'chain 'B' and resid 28 through 31' Processing helix chain 'B' and resid 52 through 67 removed outlier: 3.588A pdb=" N GLY B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.797A pdb=" N SER B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 123 through 137 removed outlier: 4.072A pdb=" N GLU B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 174 Processing helix chain 'B' and resid 268 through 274 Processing helix chain 'B' and resid 294 through 306 removed outlier: 4.559A pdb=" N ALA B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N CYS B 306 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 329 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 356 through 370 removed outlier: 4.008A pdb=" N LEU B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 406 removed outlier: 3.929A pdb=" N GLU B 406 " --> pdb=" O TYR B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 31 No H-bonds generated for 'chain 'C' and resid 28 through 31' Processing helix chain 'C' and resid 52 through 67 removed outlier: 3.595A pdb=" N GLY C 63 " --> pdb=" O PHE C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.825A pdb=" N SER C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 123 through 137 removed outlier: 4.221A pdb=" N GLU C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 174 Processing helix chain 'C' and resid 268 through 274 Processing helix chain 'C' and resid 294 through 306 removed outlier: 4.569A pdb=" N ALA C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS C 306 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 329 removed outlier: 4.097A pdb=" N ARG C 326 " --> pdb=" O GLN C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 356 through 370 removed outlier: 3.962A pdb=" N LEU C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 404 Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 52 through 67 removed outlier: 3.599A pdb=" N GLY D 63 " --> pdb=" O PHE D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 removed outlier: 3.824A pdb=" N SER D 89 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE D 90 " --> pdb=" O ASN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 123 through 137 removed outlier: 4.138A pdb=" N GLU D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 268 through 274 Processing helix chain 'D' and resid 294 through 306 removed outlier: 4.574A pdb=" N ALA D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N CYS D 306 " --> pdb=" O VAL D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 356 through 370 removed outlier: 3.848A pdb=" N LEU D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 406 removed outlier: 3.935A pdb=" N GLU D 406 " --> pdb=" O TYR D 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 31 No H-bonds generated for 'chain 'E' and resid 28 through 31' Processing helix chain 'E' and resid 52 through 67 removed outlier: 3.589A pdb=" N GLY E 63 " --> pdb=" O PHE E 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 removed outlier: 3.722A pdb=" N SER E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE E 90 " --> pdb=" O ASN E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 123 through 137 removed outlier: 4.097A pdb=" N GLU E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 174 Processing helix chain 'E' and resid 268 through 274 Processing helix chain 'E' and resid 294 through 306 removed outlier: 4.559A pdb=" N ALA E 305 " --> pdb=" O PHE E 301 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N CYS E 306 " --> pdb=" O VAL E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 329 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 356 through 370 removed outlier: 4.005A pdb=" N LEU E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN E 361 " --> pdb=" O GLU E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 406 removed outlier: 3.918A pdb=" N GLU E 406 " --> pdb=" O TYR E 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 No H-bonds generated for 'chain 'F' and resid 28 through 31' Processing helix chain 'F' and resid 52 through 67 removed outlier: 3.602A pdb=" N GLY F 63 " --> pdb=" O PHE F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 90 removed outlier: 3.865A pdb=" N SER F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 123 through 137 removed outlier: 4.071A pdb=" N GLU F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 174 Processing helix chain 'F' and resid 268 through 274 Processing helix chain 'F' and resid 294 through 306 removed outlier: 3.506A pdb=" N ASN F 304 " --> pdb=" O ARG F 300 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA F 305 " --> pdb=" O PHE F 301 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N CYS F 306 " --> pdb=" O VAL F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 329 Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 356 through 370 removed outlier: 3.822A pdb=" N LEU F 360 " --> pdb=" O LEU F 356 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 404 Processing sheet with id= A, first strand: chain 'A' and resid 180 through 183 removed outlier: 3.780A pdb=" N LYS A 224 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 206 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE A 222 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG A 208 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU A 220 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL A 210 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ARG A 218 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU A 212 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ARG A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 103 through 107 removed outlier: 7.080A pdb=" N GLY A 71 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU A 106 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE A 73 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG A 141 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 74 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER A 143 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N THR A 177 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE A 144 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL A 179 " --> pdb=" O ILE A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= D, first strand: chain 'A' and resid 477 through 479 removed outlier: 4.353A pdb=" N ARG A 451 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 437 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY A 410 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA A 286 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE A 412 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N GLY A 288 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN A 414 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 413 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 376 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS A 345 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 180 through 183 removed outlier: 3.785A pdb=" N LYS B 224 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 206 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE B 222 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG B 208 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU B 220 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL B 210 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ARG B 218 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU B 212 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 103 through 107 removed outlier: 7.118A pdb=" N GLY B 71 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 106 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE B 73 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG B 141 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL B 74 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER B 143 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N THR B 177 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 144 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL B 179 " --> pdb=" O ILE B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 237 through 240 removed outlier: 3.538A pdb=" N THR B 238 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 477 through 479 removed outlier: 4.435A pdb=" N ARG B 451 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 437 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 410 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA B 286 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE B 412 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N GLY B 288 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN B 414 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 413 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 376 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 345 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.788A pdb=" N LYS C 224 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 206 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE C 222 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG C 208 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU C 220 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL C 210 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG C 218 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU C 212 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARG C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 103 through 107 removed outlier: 7.062A pdb=" N GLY C 71 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU C 106 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE C 73 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG C 141 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL C 74 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N SER C 143 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR C 177 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE C 144 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL C 179 " --> pdb=" O ILE C 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 237 through 240 removed outlier: 3.669A pdb=" N THR C 238 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 477 through 479 removed outlier: 4.373A pdb=" N ARG C 451 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 437 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY C 410 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA C 286 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE C 412 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N GLY C 288 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN C 414 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 413 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 376 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS C 345 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 180 through 183 removed outlier: 3.788A pdb=" N LYS D 224 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE D 206 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE D 222 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG D 208 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU D 220 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL D 210 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ARG D 218 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU D 212 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ARG D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 103 through 107 removed outlier: 7.079A pdb=" N GLY D 71 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU D 106 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE D 73 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG D 141 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL D 74 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER D 143 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N THR D 177 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE D 144 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL D 179 " --> pdb=" O ILE D 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 237 through 240 Processing sheet with id= P, first strand: chain 'D' and resid 477 through 479 removed outlier: 4.354A pdb=" N ARG D 451 " --> pdb=" O PHE D 470 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE D 437 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY D 410 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ALA D 286 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE D 412 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N GLY D 288 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN D 414 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR D 413 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 376 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS D 345 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 180 through 183 removed outlier: 3.786A pdb=" N LYS E 224 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE E 206 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE E 222 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ARG E 208 " --> pdb=" O LEU E 220 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LEU E 220 " --> pdb=" O ARG E 208 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL E 210 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ARG E 218 " --> pdb=" O VAL E 210 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 103 through 107 removed outlier: 7.150A pdb=" N GLY E 71 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU E 106 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE E 73 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG E 141 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL E 74 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER E 143 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N THR E 177 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE E 144 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL E 179 " --> pdb=" O ILE E 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 237 through 240 Processing sheet with id= T, first strand: chain 'E' and resid 477 through 479 removed outlier: 4.419A pdb=" N ARG E 451 " --> pdb=" O PHE E 470 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE E 437 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY E 410 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA E 286 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE E 412 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N GLY E 288 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASN E 414 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR E 413 " --> pdb=" O ILE E 377 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA E 376 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS E 345 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 180 through 183 removed outlier: 3.785A pdb=" N LYS F 224 " --> pdb=" O VAL F 204 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE F 206 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE F 222 " --> pdb=" O ILE F 206 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG F 208 " --> pdb=" O LEU F 220 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU F 220 " --> pdb=" O ARG F 208 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL F 210 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ARG F 218 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU F 212 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ARG F 216 " --> pdb=" O GLU F 212 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 103 through 107 removed outlier: 7.096A pdb=" N GLY F 71 " --> pdb=" O PHE F 104 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU F 106 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE F 73 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG F 141 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL F 74 " --> pdb=" O ARG F 141 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N SER F 143 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N THR F 177 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE F 144 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL F 179 " --> pdb=" O ILE F 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 237 through 240 removed outlier: 3.552A pdb=" N THR F 238 " --> pdb=" O ASN F 245 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 477 through 479 removed outlier: 4.374A pdb=" N ARG F 451 " --> pdb=" O PHE F 470 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE F 437 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY F 410 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA F 286 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE F 412 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N GLY F 288 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN F 414 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR F 413 " --> pdb=" O ILE F 377 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA F 376 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS F 345 " --> pdb=" O ALA F 312 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1857 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: 7.54 Time building geometry restraints manager: 9.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7813 1.35 - 1.47: 5322 1.47 - 1.58: 10384 1.58 - 1.70: 25 1.70 - 1.82: 162 Bond restraints: 23706 Sorted by residual: bond pdb=" CA ASN B 245 " pdb=" CB ASN B 245 " ideal model delta sigma weight residual 1.526 1.552 -0.026 1.70e-02 3.46e+03 2.39e+00 bond pdb=" CB PRO B 248 " pdb=" CG PRO B 248 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.28e+00 bond pdb=" CB PRO E 248 " pdb=" CG PRO E 248 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.24e+00 bond pdb=" CG1 ILE A 490 " pdb=" CD1 ILE A 490 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.79e+00 bond pdb=" CA SER D 320 " pdb=" C SER D 320 " ideal model delta sigma weight residual 1.533 1.521 0.013 9.60e-03 1.09e+04 1.71e+00 ... (remaining 23701 not shown) Histogram of bond angle deviations from ideal: 99.35 - 107.43: 771 107.43 - 115.51: 14357 115.51 - 123.59: 16092 123.59 - 131.67: 754 131.67 - 139.75: 60 Bond angle restraints: 32034 Sorted by residual: angle pdb=" N ILE C 433 " pdb=" CA ILE C 433 " pdb=" C ILE C 433 " ideal model delta sigma weight residual 112.96 108.03 4.93 1.00e+00 1.00e+00 2.43e+01 angle pdb=" N ILE F 433 " pdb=" CA ILE F 433 " pdb=" C ILE F 433 " ideal model delta sigma weight residual 112.96 108.07 4.89 1.00e+00 1.00e+00 2.39e+01 angle pdb=" C PHE C 278 " pdb=" N PHE C 279 " pdb=" CA PHE C 279 " ideal model delta sigma weight residual 122.41 132.25 -9.84 2.09e+00 2.29e-01 2.22e+01 angle pdb=" C PHE F 278 " pdb=" N PHE F 279 " pdb=" CA PHE F 279 " ideal model delta sigma weight residual 122.41 132.20 -9.79 2.09e+00 2.29e-01 2.19e+01 angle pdb=" C PHE A 278 " pdb=" N PHE A 279 " pdb=" CA PHE A 279 " ideal model delta sigma weight residual 122.41 132.07 -9.66 2.09e+00 2.29e-01 2.14e+01 ... (remaining 32029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12616 17.99 - 35.97: 1357 35.97 - 53.95: 343 53.95 - 71.94: 78 71.94 - 89.92: 60 Dihedral angle restraints: 14454 sinusoidal: 6156 harmonic: 8298 Sorted by residual: dihedral pdb=" CA TRP C 462 " pdb=" C TRP C 462 " pdb=" N HIS C 463 " pdb=" CA HIS C 463 " ideal model delta harmonic sigma weight residual 180.00 157.60 22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA TRP F 462 " pdb=" C TRP F 462 " pdb=" N HIS F 463 " pdb=" CA HIS F 463 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA TRP E 462 " pdb=" C TRP E 462 " pdb=" N HIS E 463 " pdb=" CA HIS E 463 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 14451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2412 0.041 - 0.082: 798 0.082 - 0.123: 289 0.123 - 0.163: 43 0.163 - 0.204: 16 Chirality restraints: 3558 Sorted by residual: chirality pdb=" CB VAL A 196 " pdb=" CA VAL A 196 " pdb=" CG1 VAL A 196 " pdb=" CG2 VAL A 196 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL D 196 " pdb=" CA VAL D 196 " pdb=" CG1 VAL D 196 " pdb=" CG2 VAL D 196 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL C 196 " pdb=" CA VAL C 196 " pdb=" CG1 VAL C 196 " pdb=" CG2 VAL C 196 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3555 not shown) Planarity restraints: 4104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 279 " -0.010 2.00e-02 2.50e+03 1.66e-02 4.85e+00 pdb=" CG PHE F 279 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE F 279 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE F 279 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE F 279 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 279 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 279 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 279 " -0.010 2.00e-02 2.50e+03 1.65e-02 4.77e+00 pdb=" CG PHE C 279 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE C 279 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE C 279 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE C 279 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 279 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 279 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 79 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO C 80 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.029 5.00e-02 4.00e+02 ... (remaining 4101 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 397 2.66 - 3.22: 20255 3.22 - 3.78: 34346 3.78 - 4.34: 47783 4.34 - 4.90: 79700 Nonbonded interactions: 182481 Sorted by model distance: nonbonded pdb=" OG1 THR B 295 " pdb="MG MG B 903 " model vdw 2.095 2.170 nonbonded pdb=" OG1 THR E 295 " pdb="MG MG E 903 " model vdw 2.095 2.170 nonbonded pdb=" OG1 THR D 53 " pdb="MG MG D 904 " model vdw 2.101 2.170 nonbonded pdb=" OG1 THR A 53 " pdb="MG MG A 904 " model vdw 2.102 2.170 nonbonded pdb=" OG1 THR E 53 " pdb="MG MG E 904 " model vdw 2.102 2.170 ... (remaining 182476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.500 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 62.440 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 0.076 23706 Z= 0.229 Angle : 0.756 12.268 32034 Z= 0.423 Chirality : 0.048 0.204 3558 Planarity : 0.005 0.069 4104 Dihedral : 17.098 89.925 9126 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.40 % Favored : 93.43 % Rotamer: Outliers : 0.53 % Allowed : 0.44 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.63 (0.14), residues: 2892 helix: -0.74 (0.15), residues: 912 sheet: -1.69 (0.20), residues: 708 loop : -2.49 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 462 HIS 0.009 0.001 HIS F 463 PHE 0.037 0.002 PHE F 279 TYR 0.014 0.001 TYR A 132 ARG 0.015 0.001 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 327 time to evaluate : 2.724 Fit side-chains revert: symmetry clash REVERT: A 490 ILE cc_start: 0.8636 (pt) cc_final: 0.8329 (mt) REVERT: C 167 LEU cc_start: 0.8062 (tp) cc_final: 0.7858 (tp) REVERT: D 490 ILE cc_start: 0.8644 (pt) cc_final: 0.7810 (pt) outliers start: 13 outliers final: 7 residues processed: 339 average time/residue: 0.3650 time to fit residues: 189.0086 Evaluate side-chains 247 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 240 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain D residue 152 GLN Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain E residue 321 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 10.0000 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 168 optimal weight: 0.4980 chunk 261 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS C 230 HIS C 323 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 HIS F 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23706 Z= 0.187 Angle : 0.503 5.884 32034 Z= 0.269 Chirality : 0.042 0.155 3558 Planarity : 0.003 0.043 4104 Dihedral : 11.281 89.972 3631 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.40 % Rotamer: Outliers : 1.54 % Allowed : 7.36 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.15), residues: 2892 helix: 0.27 (0.17), residues: 930 sheet: -1.18 (0.20), residues: 708 loop : -2.42 (0.15), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 462 HIS 0.005 0.001 HIS F 463 PHE 0.021 0.001 PHE F 279 TYR 0.011 0.001 TYR F 132 ARG 0.005 0.000 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 241 time to evaluate : 2.918 Fit side-chains REVERT: B 321 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8064 (tmt90) REVERT: B 352 GLU cc_start: 0.7359 (mp0) cc_final: 0.7062 (mp0) REVERT: B 451 ARG cc_start: 0.8021 (ptp-110) cc_final: 0.7776 (ptp-110) REVERT: D 490 ILE cc_start: 0.8281 (pt) cc_final: 0.7905 (pt) REVERT: E 352 GLU cc_start: 0.7390 (mp0) cc_final: 0.7112 (mp0) REVERT: E 451 ARG cc_start: 0.8030 (ptp-110) cc_final: 0.7752 (ptp-110) REVERT: F 420 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6673 (tpt) outliers start: 38 outliers final: 26 residues processed: 256 average time/residue: 0.3814 time to fit residues: 148.1816 Evaluate side-chains 229 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 434 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 262 optimal weight: 7.9990 chunk 283 optimal weight: 0.2980 chunk 233 optimal weight: 10.0000 chunk 259 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 overall best weight: 6.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 323 GLN A 327 ASN B 62 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 ASN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 HIS D 327 ASN E 327 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23706 Z= 0.419 Angle : 0.599 5.752 32034 Z= 0.322 Chirality : 0.045 0.166 3558 Planarity : 0.004 0.040 4104 Dihedral : 11.039 89.391 3614 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.71 % Favored : 92.12 % Rotamer: Outliers : 2.35 % Allowed : 11.00 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.78 (0.15), residues: 2892 helix: 0.40 (0.17), residues: 930 sheet: -1.32 (0.20), residues: 720 loop : -2.32 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 92 HIS 0.005 0.001 HIS F 463 PHE 0.017 0.002 PHE B 237 TYR 0.023 0.002 TYR F 132 ARG 0.005 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 180 time to evaluate : 2.856 Fit side-chains REVERT: A 352 GLU cc_start: 0.7631 (mp0) cc_final: 0.7404 (mp0) REVERT: B 321 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7867 (tmt90) REVERT: D 490 ILE cc_start: 0.8625 (pt) cc_final: 0.8377 (pt) REVERT: E 490 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8332 (pt) outliers start: 58 outliers final: 37 residues processed: 224 average time/residue: 0.3753 time to fit residues: 130.1829 Evaluate side-chains 208 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 425 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 249 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 62 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN D 323 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23706 Z= 0.181 Angle : 0.481 8.589 32034 Z= 0.259 Chirality : 0.042 0.149 3558 Planarity : 0.003 0.041 4104 Dihedral : 10.556 88.841 3610 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.84 % Favored : 93.98 % Rotamer: Outliers : 1.94 % Allowed : 12.82 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 2892 helix: 0.81 (0.18), residues: 918 sheet: -1.15 (0.20), residues: 708 loop : -2.34 (0.15), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 462 HIS 0.004 0.001 HIS F 463 PHE 0.023 0.001 PHE F 419 TYR 0.015 0.001 TYR E 132 ARG 0.005 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 199 time to evaluate : 2.800 Fit side-chains REVERT: A 262 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6406 (mtp85) REVERT: A 352 GLU cc_start: 0.7512 (mp0) cc_final: 0.7300 (mp0) REVERT: B 262 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6605 (mtp85) REVERT: B 321 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7865 (tmt90) REVERT: B 352 GLU cc_start: 0.7436 (mp0) cc_final: 0.7216 (mp0) REVERT: C 247 PHE cc_start: 0.8430 (m-10) cc_final: 0.8017 (m-10) REVERT: C 357 GLU cc_start: 0.7670 (tp30) cc_final: 0.7231 (tp30) REVERT: D 262 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6411 (mtp85) REVERT: D 352 GLU cc_start: 0.7544 (mp0) cc_final: 0.7282 (mp0) REVERT: E 262 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6612 (mtp85) REVERT: E 352 GLU cc_start: 0.7518 (mp0) cc_final: 0.7316 (mp0) outliers start: 48 outliers final: 32 residues processed: 237 average time/residue: 0.3833 time to fit residues: 138.4601 Evaluate side-chains 222 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 237 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 62 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN C 62 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23706 Z= 0.298 Angle : 0.525 8.418 32034 Z= 0.283 Chirality : 0.043 0.156 3558 Planarity : 0.003 0.039 4104 Dihedral : 10.516 89.430 3610 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.68 % Favored : 92.15 % Rotamer: Outliers : 2.27 % Allowed : 14.40 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.16), residues: 2892 helix: 0.76 (0.18), residues: 930 sheet: -1.28 (0.20), residues: 732 loop : -2.24 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 92 HIS 0.004 0.001 HIS F 463 PHE 0.013 0.002 PHE B 237 TYR 0.017 0.001 TYR F 132 ARG 0.003 0.000 ARG E 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 184 time to evaluate : 2.764 Fit side-chains REVERT: A 262 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6504 (mtp85) REVERT: B 262 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6646 (mtp85) REVERT: B 321 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7759 (tmt90) REVERT: C 352 GLU cc_start: 0.7593 (mp0) cc_final: 0.7372 (mp0) REVERT: C 357 GLU cc_start: 0.7748 (tp30) cc_final: 0.7411 (tp30) REVERT: D 262 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6480 (mtp85) REVERT: D 488 ARG cc_start: 0.8280 (ptp90) cc_final: 0.8042 (ptp90) REVERT: E 262 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6634 (mtp85) REVERT: F 338 MET cc_start: 0.7978 (mmt) cc_final: 0.7303 (mmt) REVERT: F 420 MET cc_start: 0.8370 (tpp) cc_final: 0.7796 (tpp) outliers start: 56 outliers final: 38 residues processed: 231 average time/residue: 0.4013 time to fit residues: 140.1627 Evaluate side-chains 223 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 180 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 350 TYR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 3.9990 chunk 250 optimal weight: 40.0000 chunk 55 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23706 Z= 0.306 Angle : 0.532 7.834 32034 Z= 0.286 Chirality : 0.043 0.155 3558 Planarity : 0.003 0.039 4104 Dihedral : 10.469 89.065 3610 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.16 % Favored : 92.67 % Rotamer: Outliers : 2.14 % Allowed : 15.57 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2892 helix: 0.77 (0.18), residues: 930 sheet: -1.31 (0.20), residues: 720 loop : -2.24 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 92 HIS 0.004 0.001 HIS F 463 PHE 0.013 0.002 PHE D 59 TYR 0.021 0.002 TYR C 132 ARG 0.003 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 179 time to evaluate : 2.850 Fit side-chains revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6571 (mtp85) REVERT: A 352 GLU cc_start: 0.7606 (mp0) cc_final: 0.7360 (mp0) REVERT: B 249 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7998 (mm) REVERT: B 262 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6680 (mtp85) REVERT: C 319 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7472 (mm-30) REVERT: D 262 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.6480 (mtp85) REVERT: D 352 GLU cc_start: 0.7625 (mp0) cc_final: 0.7364 (mp0) REVERT: D 488 ARG cc_start: 0.8325 (ptp90) cc_final: 0.8092 (ptp90) REVERT: E 262 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6699 (mtp85) REVERT: F 338 MET cc_start: 0.7972 (mmt) cc_final: 0.7671 (mmt) REVERT: F 420 MET cc_start: 0.8453 (tpp) cc_final: 0.7884 (tpp) outliers start: 53 outliers final: 41 residues processed: 226 average time/residue: 0.3957 time to fit residues: 135.3221 Evaluate side-chains 220 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 174 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN E 15 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 23706 Z= 0.467 Angle : 0.629 7.586 32034 Z= 0.337 Chirality : 0.046 0.165 3558 Planarity : 0.004 0.037 4104 Dihedral : 10.683 84.901 3606 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.47 % Favored : 91.36 % Rotamer: Outliers : 2.55 % Allowed : 16.79 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.78 (0.15), residues: 2892 helix: 0.60 (0.17), residues: 930 sheet: -1.56 (0.19), residues: 732 loop : -2.32 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 92 HIS 0.005 0.001 HIS F 463 PHE 0.018 0.002 PHE B 237 TYR 0.025 0.002 TYR C 132 ARG 0.004 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 181 time to evaluate : 2.641 Fit side-chains REVERT: A 262 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.6634 (mtp85) REVERT: C 262 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7219 (mtt180) REVERT: C 319 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7427 (mm-30) REVERT: C 357 GLU cc_start: 0.7929 (tp30) cc_final: 0.7594 (tp30) REVERT: D 262 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.6628 (mtp85) REVERT: D 488 ARG cc_start: 0.8381 (ptp90) cc_final: 0.8108 (ptt-90) REVERT: E 262 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6776 (mtt90) REVERT: F 420 MET cc_start: 0.8489 (tpp) cc_final: 0.7979 (tpp) outliers start: 63 outliers final: 46 residues processed: 239 average time/residue: 0.3756 time to fit residues: 136.7247 Evaluate side-chains 227 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 177 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 350 TYR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 15 HIS Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23706 Z= 0.309 Angle : 0.555 7.318 32034 Z= 0.297 Chirality : 0.044 0.158 3558 Planarity : 0.003 0.038 4104 Dihedral : 10.484 88.293 3606 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.23 % Favored : 92.63 % Rotamer: Outliers : 2.18 % Allowed : 17.03 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.73 (0.16), residues: 2892 helix: 0.45 (0.17), residues: 966 sheet: -1.51 (0.19), residues: 720 loop : -2.20 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 92 HIS 0.005 0.001 HIS F 463 PHE 0.013 0.002 PHE D 59 TYR 0.028 0.002 TYR E 132 ARG 0.005 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 189 time to evaluate : 2.797 Fit side-chains REVERT: A 262 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6661 (mtp85) REVERT: A 352 GLU cc_start: 0.7659 (mp0) cc_final: 0.7380 (mp0) REVERT: B 262 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.6732 (mtp85) REVERT: C 319 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7398 (mm-30) REVERT: C 352 GLU cc_start: 0.7628 (mp0) cc_final: 0.7421 (mp0) REVERT: D 152 GLN cc_start: 0.7169 (pp30) cc_final: 0.6959 (pp30) REVERT: D 262 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6695 (mtp85) REVERT: D 352 GLU cc_start: 0.7633 (mp0) cc_final: 0.7344 (mp0) REVERT: D 488 ARG cc_start: 0.8372 (ptp90) cc_final: 0.8105 (ptt-90) REVERT: E 262 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.6775 (mtp85) REVERT: F 352 GLU cc_start: 0.7743 (mp0) cc_final: 0.7483 (mp0) REVERT: F 420 MET cc_start: 0.8501 (tpp) cc_final: 0.7927 (tpp) outliers start: 54 outliers final: 44 residues processed: 242 average time/residue: 0.3974 time to fit residues: 144.8989 Evaluate side-chains 231 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 183 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 350 TYR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 8.9990 chunk 265 optimal weight: 8.9990 chunk 242 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 23706 Z= 0.406 Angle : 0.607 7.988 32034 Z= 0.324 Chirality : 0.045 0.166 3558 Planarity : 0.004 0.039 4104 Dihedral : 10.534 84.179 3606 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.54 % Favored : 91.32 % Rotamer: Outliers : 2.10 % Allowed : 17.19 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2892 helix: 0.35 (0.17), residues: 966 sheet: -1.64 (0.19), residues: 732 loop : -2.25 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 92 HIS 0.005 0.001 HIS F 463 PHE 0.022 0.002 PHE A 247 TYR 0.031 0.002 TYR C 132 ARG 0.008 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 179 time to evaluate : 2.886 Fit side-chains REVERT: A 262 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.6685 (mtp85) REVERT: A 352 GLU cc_start: 0.7681 (mp0) cc_final: 0.7412 (mp0) REVERT: B 262 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.6725 (mtp85) REVERT: C 319 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7367 (mm-30) REVERT: D 262 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.6703 (mtp85) REVERT: D 352 GLU cc_start: 0.7645 (mp0) cc_final: 0.7375 (mp0) REVERT: D 488 ARG cc_start: 0.8400 (ptp90) cc_final: 0.8125 (ptt-90) REVERT: E 262 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.6814 (mtp85) REVERT: F 338 MET cc_start: 0.7718 (mmt) cc_final: 0.7250 (mmt) REVERT: F 420 MET cc_start: 0.8506 (tpp) cc_final: 0.7966 (tpp) outliers start: 52 outliers final: 42 residues processed: 230 average time/residue: 0.3853 time to fit residues: 134.8837 Evaluate side-chains 221 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 175 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 350 TYR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 15 HIS Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 190 optimal weight: 0.5980 chunk 286 optimal weight: 8.9990 chunk 264 optimal weight: 0.0770 chunk 228 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 140 optimal weight: 0.0970 overall best weight: 2.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 HIS ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23706 Z= 0.197 Angle : 0.516 7.624 32034 Z= 0.274 Chirality : 0.043 0.154 3558 Planarity : 0.003 0.038 4104 Dihedral : 10.204 88.262 3606 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.22 % Favored : 93.64 % Rotamer: Outliers : 1.78 % Allowed : 17.52 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.16), residues: 2892 helix: 0.53 (0.17), residues: 966 sheet: -1.35 (0.20), residues: 714 loop : -2.12 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 92 HIS 0.012 0.001 HIS E 15 PHE 0.019 0.001 PHE A 247 TYR 0.032 0.001 TYR C 132 ARG 0.009 0.000 ARG B 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 201 time to evaluate : 2.502 Fit side-chains revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6764 (mtp85) REVERT: A 352 GLU cc_start: 0.7621 (mp0) cc_final: 0.7347 (mp0) REVERT: B 152 GLN cc_start: 0.7301 (pp30) cc_final: 0.6986 (pp30) REVERT: B 247 PHE cc_start: 0.8199 (m-10) cc_final: 0.7870 (m-10) REVERT: B 262 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6723 (mtp85) REVERT: B 338 MET cc_start: 0.7565 (mmt) cc_final: 0.7279 (mmp) REVERT: B 488 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7413 (ttm110) REVERT: C 319 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7397 (mm-30) REVERT: C 432 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6855 (mm-30) REVERT: D 152 GLN cc_start: 0.7325 (pp30) cc_final: 0.7094 (pp30) REVERT: D 262 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.6739 (mtp85) REVERT: D 352 GLU cc_start: 0.7574 (mp0) cc_final: 0.7308 (mp0) REVERT: D 488 ARG cc_start: 0.8351 (ptp90) cc_final: 0.8084 (ptt-90) REVERT: E 262 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6763 (mtp85) REVERT: F 338 MET cc_start: 0.7555 (mmt) cc_final: 0.7083 (mmt) REVERT: F 420 MET cc_start: 0.8465 (tpp) cc_final: 0.7796 (tpp) REVERT: F 432 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6898 (mm-30) outliers start: 44 outliers final: 39 residues processed: 244 average time/residue: 0.3823 time to fit residues: 142.3891 Evaluate side-chains 231 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 188 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 350 TYR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 350 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 350 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 228 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086677 restraints weight = 44127.601| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.96 r_work: 0.2989 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23706 Z= 0.231 Angle : 0.526 8.179 32034 Z= 0.279 Chirality : 0.043 0.165 3558 Planarity : 0.003 0.042 4104 Dihedral : 10.077 89.784 3606 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.64 % Favored : 92.22 % Rotamer: Outliers : 2.06 % Allowed : 17.56 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2892 helix: 0.63 (0.17), residues: 960 sheet: -1.31 (0.20), residues: 714 loop : -2.06 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 92 HIS 0.005 0.001 HIS F 463 PHE 0.026 0.001 PHE A 247 TYR 0.031 0.001 TYR C 132 ARG 0.010 0.000 ARG B 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4373.40 seconds wall clock time: 80 minutes 11.81 seconds (4811.81 seconds total)