Starting phenix.real_space_refine on Sat Oct 12 17:05:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgq_40464/10_2024/8sgq_40464.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgq_40464/10_2024/8sgq_40464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgq_40464/10_2024/8sgq_40464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgq_40464/10_2024/8sgq_40464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgq_40464/10_2024/8sgq_40464.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgq_40464/10_2024/8sgq_40464.cif" } resolution = 3.7 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= 0.005 sd= 0.030 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 384 5.16 5 C 38902 2.51 5 N 10842 2.21 5 O 12027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 62187 Number of models: 1 Model: "" Number of chains: 32 Chain: "z" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3903 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 13, 'TRANS': 494} Chain: "Z" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3903 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 13, 'TRANS': 494} Chain: "a" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3709 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 11, 'TRANS': 478} Chain breaks: 2 Chain: "g" Number of atoms: 3678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3678 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 16, 'TRANS': 460} Chain breaks: 1 Chain: "h" Number of atoms: 3834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3834 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 14, 'TRANS': 485} Chain breaks: 1 Chain: "q" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3692 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 12, 'TRANS': 470} Chain breaks: 1 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3742 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 11, 'TRANS': 482} Chain breaks: 2 Chain: "G" Number of atoms: 3741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3741 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 16, 'TRANS': 468} Chain breaks: 1 Chain: "H" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3825 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 14, 'TRANS': 484} Chain breaks: 1 Chain: "Q" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3692 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 12, 'TRANS': 470} Chain breaks: 1 Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 32.04, per 1000 atoms: 0.52 Number of scatterers: 62187 At special positions: 0 Unit cell: (183.034, 174.57, 188.324, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 384 16.00 P 32 15.00 O 12027 8.00 N 10842 7.00 C 38902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS h 330 " - pdb=" SG CYS h 349 " distance=2.04 Simple disulfide: pdb=" SG CYS H 326 " - pdb=" SG CYS H 345 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.97 Conformation dependent library (CDL) restraints added in 6.9 seconds 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15086 Finding SS restraints... Secondary structure from input PDB file: 315 helices and 90 sheets defined 55.3% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.63 Creating SS restraints... Processing helix chain 'z' and resid 18 through 34 Processing helix chain 'z' and resid 35 through 38 removed outlier: 3.802A pdb=" N LEU z 38 " --> pdb=" O ARG z 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 35 through 38' Processing helix chain 'z' and resid 59 through 67 Processing helix chain 'z' and resid 71 through 86 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.587A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.897A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 157 Processing helix chain 'z' and resid 161 through 180 removed outlier: 4.089A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) Processing helix chain 'z' and resid 181 through 183 No H-bonds generated for 'chain 'z' and resid 181 through 183' Processing helix chain 'z' and resid 187 through 189 No H-bonds generated for 'chain 'z' and resid 187 through 189' Processing helix chain 'z' and resid 254 through 259 Processing helix chain 'z' and resid 263 through 282 removed outlier: 3.729A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 307 Processing helix chain 'z' and resid 317 through 328 removed outlier: 3.771A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 removed outlier: 4.303A pdb=" N CYS z 343 " --> pdb=" O SER z 340 " (cutoff:3.500A) Processing helix chain 'z' and resid 380 through 405 Processing helix chain 'z' and resid 412 through 425 Processing helix chain 'z' and resid 426 through 429 Processing helix chain 'z' and resid 432 through 445 removed outlier: 4.004A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.857A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 removed outlier: 4.028A pdb=" N GLU z 472 " --> pdb=" O ALA z 468 " (cutoff:3.500A) Processing helix chain 'z' and resid 488 through 493 Processing helix chain 'z' and resid 497 through 517 Processing helix chain 'Z' and resid 20 through 35 Processing helix chain 'Z' and resid 59 through 64 Processing helix chain 'Z' and resid 71 through 85 Processing helix chain 'Z' and resid 86 through 88 No H-bonds generated for 'chain 'Z' and resid 86 through 88' Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.619A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 4.253A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL Z 137 " --> pdb=" O PHE Z 133 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS Z 138 " --> pdb=" O LEU Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 158 removed outlier: 3.685A pdb=" N ASP Z 150 " --> pdb=" O GLU Z 146 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Z 151 " --> pdb=" O THR Z 147 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.737A pdb=" N VAL Z 167 " --> pdb=" O GLU Z 163 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP Z 174 " --> pdb=" O GLU Z 170 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER Z 175 " --> pdb=" O ALA Z 171 " (cutoff:3.500A) Processing helix chain 'Z' and resid 252 through 263 Processing helix chain 'Z' and resid 264 through 282 removed outlier: 3.654A pdb=" N GLU Z 268 " --> pdb=" O ARG Z 264 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS Z 273 " --> pdb=" O ASP Z 269 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL Z 281 " --> pdb=" O LEU Z 277 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 308 removed outlier: 3.622A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 319 through 328 removed outlier: 3.529A pdb=" N LEU Z 326 " --> pdb=" O GLU Z 322 " (cutoff:3.500A) Processing helix chain 'Z' and resid 380 through 404 removed outlier: 4.965A pdb=" N GLN Z 386 " --> pdb=" O HIS Z 382 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 425 Processing helix chain 'Z' and resid 432 through 445 removed outlier: 3.709A pdb=" N LEU Z 445 " --> pdb=" O ALA Z 441 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 Processing helix chain 'Z' and resid 458 through 473 removed outlier: 3.507A pdb=" N THR Z 462 " --> pdb=" O ASP Z 458 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU Z 472 " --> pdb=" O ALA Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 498 through 517 removed outlier: 3.653A pdb=" N HIS Z 506 " --> pdb=" O LYS Z 502 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR Z 509 " --> pdb=" O LEU Z 505 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE Z 511 " --> pdb=" O SER Z 507 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 34 removed outlier: 3.617A pdb=" N GLN a 20 " --> pdb=" O THR a 16 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 65 removed outlier: 3.742A pdb=" N ILE a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 87 removed outlier: 3.607A pdb=" N GLU a 85 " --> pdb=" O LEU a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 110 Processing helix chain 'a' and resid 113 through 134 removed outlier: 3.613A pdb=" N VAL a 117 " --> pdb=" O HIS a 113 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN a 133 " --> pdb=" O VAL a 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU a 134 " --> pdb=" O ARG a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 157 Processing helix chain 'a' and resid 159 through 163 Processing helix chain 'a' and resid 164 through 179 Processing helix chain 'a' and resid 191 through 195 removed outlier: 3.692A pdb=" N VAL a 195 " --> pdb=" O VAL a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 272 through 282 removed outlier: 3.640A pdb=" N GLY a 282 " --> pdb=" O ILE a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 295 through 303 removed outlier: 3.921A pdb=" N TYR a 299 " --> pdb=" O MET a 295 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU a 302 " --> pdb=" O LYS a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 324 removed outlier: 3.684A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 385 through 404 removed outlier: 3.607A pdb=" N GLU a 404 " --> pdb=" O LYS a 400 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 429 removed outlier: 3.616A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN a 425 " --> pdb=" O ILE a 421 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 445 Processing helix chain 'a' and resid 447 through 456 Processing helix chain 'a' and resid 459 through 477 removed outlier: 3.806A pdb=" N GLU a 473 " --> pdb=" O ALA a 469 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA a 474 " --> pdb=" O PHE a 470 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN a 475 " --> pdb=" O HIS a 471 " (cutoff:3.500A) Processing helix chain 'a' and resid 478 through 484 removed outlier: 4.744A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS a 484 " --> pdb=" O LYS a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'g' and resid 18 through 35 removed outlier: 4.276A pdb=" N GLN g 22 " --> pdb=" O GLY g 18 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE g 32 " --> pdb=" O ALA g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 61 through 69 Processing helix chain 'g' and resid 73 through 91 removed outlier: 3.822A pdb=" N GLU g 88 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU g 89 " --> pdb=" O THR g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 114 removed outlier: 4.533A pdb=" N HIS g 110 " --> pdb=" O SER g 106 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE g 111 " --> pdb=" O VAL g 107 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN g 114 " --> pdb=" O HIS g 110 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 140 removed outlier: 3.843A pdb=" N VAL g 121 " --> pdb=" O HIS g 117 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER g 134 " --> pdb=" O ASP g 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 147 through 159 Processing helix chain 'g' and resid 164 through 166 No H-bonds generated for 'chain 'g' and resid 164 through 166' Processing helix chain 'g' and resid 167 through 179 removed outlier: 3.897A pdb=" N ALA g 171 " --> pdb=" O TRP g 167 " (cutoff:3.500A) Processing helix chain 'g' and resid 207 through 211 removed outlier: 3.572A pdb=" N SER g 211 " --> pdb=" O ILE g 208 " (cutoff:3.500A) Processing helix chain 'g' and resid 275 through 281 Processing helix chain 'g' and resid 282 through 284 No H-bonds generated for 'chain 'g' and resid 282 through 284' Processing helix chain 'g' and resid 296 through 306 Processing helix chain 'g' and resid 315 through 327 removed outlier: 4.122A pdb=" N ARG g 321 " --> pdb=" O THR g 317 " (cutoff:3.500A) Processing helix chain 'g' and resid 382 through 403 Processing helix chain 'g' and resid 411 through 425 Processing helix chain 'g' and resid 432 through 443 removed outlier: 3.719A pdb=" N ALA g 440 " --> pdb=" O TYR g 436 " (cutoff:3.500A) Processing helix chain 'g' and resid 444 through 453 Processing helix chain 'g' and resid 457 through 472 removed outlier: 3.702A pdb=" N GLN g 471 " --> pdb=" O ALA g 467 " (cutoff:3.500A) Processing helix chain 'g' and resid 489 through 493 Processing helix chain 'g' and resid 498 through 518 removed outlier: 3.545A pdb=" N ILE g 518 " --> pdb=" O LEU g 514 " (cutoff:3.500A) Processing helix chain 'h' and resid 18 through 37 removed outlier: 3.794A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 67 Processing helix chain 'h' and resid 73 through 94 removed outlier: 4.241A pdb=" N ILE h 86 " --> pdb=" O THR h 82 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 117 Proline residue: h 114 - end of helix removed outlier: 4.110A pdb=" N GLU h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) Processing helix chain 'h' and resid 121 through 144 removed outlier: 3.628A pdb=" N ILE h 125 " --> pdb=" O HIS h 121 " (cutoff:3.500A) Processing helix chain 'h' and resid 156 through 165 removed outlier: 3.685A pdb=" N THR h 165 " --> pdb=" O LYS h 161 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 168 No H-bonds generated for 'chain 'h' and resid 166 through 168' Processing helix chain 'h' and resid 172 through 189 removed outlier: 4.251A pdb=" N ALA h 177 " --> pdb=" O SER h 173 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE h 178 " --> pdb=" O GLN h 174 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET h 189 " --> pdb=" O ASP h 185 " (cutoff:3.500A) Processing helix chain 'h' and resid 266 through 281 removed outlier: 3.561A pdb=" N ILE h 270 " --> pdb=" O ASP h 266 " (cutoff:3.500A) Processing helix chain 'h' and resid 282 through 285 removed outlier: 3.909A pdb=" N ILE h 285 " --> pdb=" O LEU h 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 282 through 285' Processing helix chain 'h' and resid 303 through 308 Processing helix chain 'h' and resid 319 through 330 Processing helix chain 'h' and resid 382 through 384 No H-bonds generated for 'chain 'h' and resid 382 through 384' Processing helix chain 'h' and resid 385 through 406 removed outlier: 3.587A pdb=" N HIS h 394 " --> pdb=" O GLU h 390 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP h 395 " --> pdb=" O ARG h 391 " (cutoff:3.500A) Processing helix chain 'h' and resid 415 through 431 removed outlier: 3.827A pdb=" N ARG h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR h 430 " --> pdb=" O ASP h 426 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE h 431 " --> pdb=" O TYR h 427 " (cutoff:3.500A) Processing helix chain 'h' and resid 434 through 446 removed outlier: 4.068A pdb=" N LEU h 438 " --> pdb=" O LYS h 434 " (cutoff:3.500A) Processing helix chain 'h' and resid 447 through 458 removed outlier: 3.691A pdb=" N ARG h 451 " --> pdb=" O GLU h 447 " (cutoff:3.500A) Processing helix chain 'h' and resid 460 through 474 Processing helix chain 'h' and resid 491 through 495 Processing helix chain 'h' and resid 500 through 519 Processing helix chain 'q' and resid 30 through 45 removed outlier: 3.667A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 74 removed outlier: 3.635A pdb=" N ARG q 74 " --> pdb=" O ALA q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 80 through 97 Processing helix chain 'q' and resid 100 through 122 Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 removed outlier: 4.180A pdb=" N VAL q 147 " --> pdb=" O PRO q 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 144 through 147' Processing helix chain 'q' and resid 156 through 164 Processing helix chain 'q' and resid 164 through 172 removed outlier: 4.249A pdb=" N ILE q 168 " --> pdb=" O LEU q 164 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 189 removed outlier: 3.838A pdb=" N LEU q 182 " --> pdb=" O PHE q 178 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS q 187 " --> pdb=" O ILE q 183 " (cutoff:3.500A) Processing helix chain 'q' and resid 198 through 202 Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 263 through 284 Processing helix chain 'q' and resid 298 through 308 Processing helix chain 'q' and resid 319 through 329 removed outlier: 3.890A pdb=" N ARG q 323 " --> pdb=" O TRP q 319 " (cutoff:3.500A) Processing helix chain 'q' and resid 384 through 405 removed outlier: 3.772A pdb=" N THR q 398 " --> pdb=" O ASP q 394 " (cutoff:3.500A) Processing helix chain 'q' and resid 413 through 430 removed outlier: 3.903A pdb=" N GLU q 428 " --> pdb=" O THR q 424 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 446 removed outlier: 4.413A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 455 removed outlier: 4.102A pdb=" N ARG q 450 " --> pdb=" O GLU q 446 " (cutoff:3.500A) Processing helix chain 'q' and resid 459 through 474 removed outlier: 3.573A pdb=" N VAL q 463 " --> pdb=" O LYS q 459 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN q 472 " --> pdb=" O TYR q 468 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU q 473 " --> pdb=" O ALA q 469 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'A' and resid 16 through 34 removed outlier: 3.691A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.970A pdb=" N LEU A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 87 Processing helix chain 'A' and resid 89 through 110 Processing helix chain 'A' and resid 113 through 133 removed outlier: 3.678A pdb=" N VAL A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 157 Processing helix chain 'A' and resid 164 through 179 removed outlier: 3.542A pdb=" N PHE A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 272 through 282 Processing helix chain 'A' and resid 295 through 304 removed outlier: 4.080A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 385 through 404 Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.543A pdb=" N ASN A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 446 removed outlier: 3.925A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.689A pdb=" N ASN A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 477 removed outlier: 3.743A pdb=" N GLU A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'G' and resid 18 through 34 removed outlier: 4.199A pdb=" N GLN G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 37 No H-bonds generated for 'chain 'G' and resid 35 through 37' Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 73 through 90 Processing helix chain 'G' and resid 93 through 114 removed outlier: 4.226A pdb=" N HIS G 110 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE G 111 " --> pdb=" O VAL G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 140 removed outlier: 3.713A pdb=" N VAL G 121 " --> pdb=" O HIS G 117 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 158 Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.669A pdb=" N ALA G 171 " --> pdb=" O TRP G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 211 Processing helix chain 'G' and resid 275 through 285 removed outlier: 3.587A pdb=" N GLU G 279 " --> pdb=" O GLN G 275 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU G 284 " --> pdb=" O ASP G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 Processing helix chain 'G' and resid 315 through 327 removed outlier: 4.745A pdb=" N ARG G 321 " --> pdb=" O THR G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 403 Processing helix chain 'G' and resid 411 through 425 Processing helix chain 'G' and resid 432 through 444 removed outlier: 4.149A pdb=" N ALA G 440 " --> pdb=" O TYR G 436 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU G 444 " --> pdb=" O ALA G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 453 Processing helix chain 'G' and resid 459 through 472 removed outlier: 3.788A pdb=" N GLN G 471 " --> pdb=" O ALA G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 493 Processing helix chain 'G' and resid 498 through 517 Processing helix chain 'H' and resid 17 through 36 removed outlier: 3.573A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 73 through 90 removed outlier: 3.563A pdb=" N GLU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL H 90 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 113 Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 117 through 136 removed outlier: 3.578A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 162 removed outlier: 3.614A pdb=" N ALA H 162 " --> pdb=" O CYS H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 185 removed outlier: 3.970A pdb=" N PHE H 174 " --> pdb=" O GLN H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 263 through 285 removed outlier: 5.176A pdb=" N ASP H 268 " --> pdb=" O GLN H 264 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA H 269 " --> pdb=" O ALA H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 307 removed outlier: 3.793A pdb=" N ARG H 306 " --> pdb=" O PHE H 303 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP H 307 " --> pdb=" O ALA H 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 303 through 307' Processing helix chain 'H' and resid 315 through 321 Processing helix chain 'H' and resid 381 through 402 removed outlier: 4.511A pdb=" N ASP H 391 " --> pdb=" O ARG H 387 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA H 392 " --> pdb=" O SER H 388 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE H 393 " --> pdb=" O LEU H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 425 removed outlier: 3.722A pdb=" N ARG H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 442 removed outlier: 3.964A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 454 removed outlier: 3.609A pdb=" N ARG H 447 " --> pdb=" O GLU H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 471 removed outlier: 3.866A pdb=" N ILE H 460 " --> pdb=" O ASP H 456 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 515 Processing helix chain 'Q' and resid 30 through 45 removed outlier: 3.595A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 Processing helix chain 'Q' and resid 80 through 98 removed outlier: 3.822A pdb=" N GLU Q 96 " --> pdb=" O MET Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 122 removed outlier: 3.624A pdb=" N GLU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY Q 122 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 143 Processing helix chain 'Q' and resid 144 through 146 No H-bonds generated for 'chain 'Q' and resid 144 through 146' Processing helix chain 'Q' and resid 156 through 164 Processing helix chain 'Q' and resid 164 through 172 removed outlier: 4.024A pdb=" N ILE Q 168 " --> pdb=" O LEU Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 189 removed outlier: 3.989A pdb=" N LEU Q 182 " --> pdb=" O PHE Q 178 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS Q 187 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL Q 188 " --> pdb=" O ALA Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 263 through 284 Processing helix chain 'Q' and resid 285 through 288 Processing helix chain 'Q' and resid 298 through 308 removed outlier: 3.708A pdb=" N TYR Q 308 " --> pdb=" O TYR Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 319 through 329 removed outlier: 3.992A pdb=" N ARG Q 323 " --> pdb=" O TRP Q 319 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS Q 325 " --> pdb=" O LEU Q 321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 354 through 358 removed outlier: 3.719A pdb=" N THR Q 358 " --> pdb=" O VAL Q 355 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 405 removed outlier: 4.001A pdb=" N ASP Q 387 " --> pdb=" O ASN Q 383 " (cutoff:3.500A) Processing helix chain 'Q' and resid 413 through 428 removed outlier: 4.276A pdb=" N GLU Q 428 " --> pdb=" O THR Q 424 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 457 removed outlier: 4.396A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE Q 448 " --> pdb=" O ALA Q 444 " (cutoff:3.500A) Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 459 through 472 removed outlier: 3.915A pdb=" N GLN Q 472 " --> pdb=" O TYR Q 468 " (cutoff:3.500A) Processing helix chain 'Q' and resid 501 through 521 removed outlier: 3.816A pdb=" N VAL Q 521 " --> pdb=" O THR Q 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 removed outlier: 3.609A pdb=" N ILE B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 Processing helix chain 'B' and resid 122 through 144 removed outlier: 3.622A pdb=" N SER B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 169 removed outlier: 3.855A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.757A pdb=" N THR B 173 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 174' Processing helix chain 'B' and resid 175 through 190 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 260 through 284 removed outlier: 3.881A pdb=" N VAL B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.733A pdb=" N VAL B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 430 through 453 removed outlier: 3.583A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 28 through 49 removed outlier: 3.611A pdb=" N GLN D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 73 through 81 removed outlier: 3.929A pdb=" N ILE D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 126 removed outlier: 3.536A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.628A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 194 removed outlier: 4.457A pdb=" N SER D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Proline residue: D 185 - end of helix removed outlier: 3.721A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 270 through 294 removed outlier: 3.636A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 removed outlier: 3.807A pdb=" N MET D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 442 Processing helix chain 'D' and resid 445 through 459 removed outlier: 4.342A pdb=" N TYR D 449 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.946A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 21 through 25 Processing helix chain 'E' and resid 30 through 49 Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 73 through 80 removed outlier: 4.459A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 105 through 125 removed outlier: 3.681A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 removed outlier: 3.808A pdb=" N ILE E 133 " --> pdb=" O HIS E 129 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE E 151 " --> pdb=" O HIS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 175 removed outlier: 4.508A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.611A pdb=" N ASN E 179 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 180' Processing helix chain 'E' and resid 181 through 196 removed outlier: 4.165A pdb=" N VAL E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 270 through 296 removed outlier: 3.505A pdb=" N TYR E 274 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY E 296 " --> pdb=" O ILE E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 439 removed outlier: 3.521A pdb=" N ILE E 427 " --> pdb=" O GLY E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 4.301A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 467 removed outlier: 3.895A pdb=" N MET E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER E 466 " --> pdb=" O LEU E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 484 Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 removed outlier: 4.069A pdb=" N ILE b 70 " --> pdb=" O ASP b 66 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 95 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 145 Processing helix chain 'b' and resid 151 through 169 removed outlier: 3.980A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.597A pdb=" N THR b 173 " --> pdb=" O LYS b 170 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 170 through 174' Processing helix chain 'b' and resid 175 through 189 Processing helix chain 'b' and resid 208 through 212 Processing helix chain 'b' and resid 260 through 284 removed outlier: 3.757A pdb=" N VAL b 264 " --> pdb=" O SER b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 308 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 removed outlier: 4.170A pdb=" N VAL b 341 " --> pdb=" O PRO b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 428 Processing helix chain 'b' and resid 430 through 453 removed outlier: 3.655A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) Proline residue: b 447 - end of helix Processing helix chain 'b' and resid 458 through 472 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 Processing helix chain 'd' and resid 73 through 81 removed outlier: 4.008A pdb=" N ILE d 77 " --> pdb=" O ASP d 73 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.782A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS d 126 " --> pdb=" O LYS d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 152 Processing helix chain 'd' and resid 159 through 173 removed outlier: 4.063A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 195 removed outlier: 3.805A pdb=" N MET d 186 " --> pdb=" O LEU d 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 208 removed outlier: 3.649A pdb=" N ILE d 208 " --> pdb=" O LEU d 205 " (cutoff:3.500A) Processing helix chain 'd' and resid 268 through 294 removed outlier: 3.589A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY d 294 " --> pdb=" O ILE d 290 " (cutoff:3.500A) Processing helix chain 'd' and resid 310 through 320 removed outlier: 3.873A pdb=" N MET d 320 " --> pdb=" O PHE d 316 " (cutoff:3.500A) Processing helix chain 'd' and resid 330 through 340 removed outlier: 4.374A pdb=" N GLU d 334 " --> pdb=" O ARG d 330 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE d 335 " --> pdb=" O GLU d 331 " (cutoff:3.500A) Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 394 through 417 removed outlier: 3.645A pdb=" N LYS d 417 " --> pdb=" O ARG d 413 " (cutoff:3.500A) Processing helix chain 'd' and resid 426 through 443 Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.764A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.662A pdb=" N SER d 463 " --> pdb=" O GLU d 459 " (cutoff:3.500A) Processing helix chain 'd' and resid 472 through 487 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.846A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS d 531 " --> pdb=" O ARG d 527 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 Processing helix chain 'e' and resid 50 through 52 No H-bonds generated for 'chain 'e' and resid 50 through 52' Processing helix chain 'e' and resid 73 through 79 Processing helix chain 'e' and resid 85 through 102 removed outlier: 3.531A pdb=" N LYS e 89 " --> pdb=" O HIS e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 126 removed outlier: 3.565A pdb=" N VAL e 109 " --> pdb=" O GLY e 105 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 151 removed outlier: 3.852A pdb=" N ILE e 133 " --> pdb=" O HIS e 129 " (cutoff:3.500A) Processing helix chain 'e' and resid 162 through 175 removed outlier: 4.129A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 180 removed outlier: 4.083A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 181 through 196 removed outlier: 4.090A pdb=" N VAL e 196 " --> pdb=" O ALA e 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 218 through 222 Processing helix chain 'e' and resid 270 through 296 removed outlier: 3.939A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY e 296 " --> pdb=" O ILE e 292 " (cutoff:3.500A) Processing helix chain 'e' and resid 307 through 318 Processing helix chain 'e' and resid 326 through 338 Processing helix chain 'e' and resid 344 through 348 Processing helix chain 'e' and resid 349 through 353 removed outlier: 3.519A pdb=" N LYS e 352 " --> pdb=" O THR e 349 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU e 353 " --> pdb=" O ALA e 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 349 through 353' Processing helix chain 'e' and resid 391 through 415 Processing helix chain 'e' and resid 423 through 439 Processing helix chain 'e' and resid 444 through 456 Processing helix chain 'e' and resid 456 through 467 Processing helix chain 'e' and resid 469 through 484 removed outlier: 3.807A pdb=" N THR e 473 " --> pdb=" O ASN e 469 " (cutoff:3.500A) Processing helix chain 'e' and resid 501 through 505 Processing helix chain 'e' and resid 510 through 529 Processing sheet with id=AA1, first strand: chain 'z' and resid 45 through 48 Processing sheet with id=AA2, first strand: chain 'z' and resid 191 through 194 removed outlier: 6.327A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'z' and resid 210 through 212 removed outlier: 3.670A pdb=" N THR z 361 " --> pdb=" O LEU z 212 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU z 358 " --> pdb=" O LEU z 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'z' and resid 310 through 312 removed outlier: 6.356A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'z' and resid 408 through 409 Processing sheet with id=AA6, first strand: chain 'z' and resid 478 through 479 Processing sheet with id=AA7, first strand: chain 'z' and resid 521 through 523 removed outlier: 3.712A pdb=" N LEU g 50 " --> pdb=" O MET z 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id=AA9, first strand: chain 'Z' and resid 192 through 193 removed outlier: 7.755A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Z' and resid 290 through 293 removed outlier: 7.446A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG Z 224 " --> pdb=" O TYR Z 351 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR Z 351 " --> pdb=" O ARG Z 224 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU Z 226 " --> pdb=" O LEU Z 349 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU Z 349 " --> pdb=" O GLU Z 226 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA Z 347 " --> pdb=" O CYS Z 366 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N CYS Z 366 " --> pdb=" O ALA Z 347 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 478 through 479 Processing sheet with id=AB3, first strand: chain 'Z' and resid 522 through 523 removed outlier: 6.092A pdb=" N MET Z 522 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR G 59 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU G 49 " --> pdb=" O VAL G 57 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 43 through 44 removed outlier: 3.959A pdb=" N THR a 55 " --> pdb=" O LYS a 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 197 through 201 removed outlier: 6.038A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER a 374 " --> pdb=" O ILE a 211 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE a 211 " --> pdb=" O SER a 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'a' and resid 215 through 217 removed outlier: 3.626A pdb=" N LEU a 216 " --> pdb=" O ILE a 362 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU a 361 " --> pdb=" O GLU a 354 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU a 354 " --> pdb=" O LEU a 361 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS a 365 " --> pdb=" O GLU a 350 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS a 233 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU a 287 " --> pdb=" O LYS a 233 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA a 235 " --> pdb=" O LEU a 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'a' and resid 408 through 410 removed outlier: 3.599A pdb=" N GLU a 505 " --> pdb=" O VAL a 409 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 486 through 488 Processing sheet with id=AB9, first strand: chain 'a' and resid 527 through 528 Processing sheet with id=AC1, first strand: chain 'g' and resid 141 through 142 removed outlier: 3.643A pdb=" N ILE g 141 " --> pdb=" O LEU g 406 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'g' and resid 183 through 184 Processing sheet with id=AC3, first strand: chain 'g' and resid 199 through 204 removed outlier: 3.660A pdb=" N GLY g 377 " --> pdb=" O ILE g 203 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 218 through 219 Processing sheet with id=AC5, first strand: chain 'g' and resid 238 through 239 removed outlier: 5.983A pdb=" N VAL g 238 " --> pdb=" O ILE g 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'g' and resid 477 through 479 Processing sheet with id=AC7, first strand: chain 'h' and resid 145 through 146 Processing sheet with id=AC8, first strand: chain 'h' and resid 202 through 203 removed outlier: 7.667A pdb=" N LYS h 202 " --> pdb=" O LEU h 378 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN h 213 " --> pdb=" O ILE h 377 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 220 through 221 Processing sheet with id=AD1, first strand: chain 'h' and resid 313 through 316 removed outlier: 5.888A pdb=" N VAL h 293 " --> pdb=" O ALA h 315 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE h 241 " --> pdb=" O SER h 333 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN h 335 " --> pdb=" O ILE h 241 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU h 243 " --> pdb=" O GLN h 335 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'h' and resid 479 through 482 Processing sheet with id=AD3, first strand: chain 'q' and resid 54 through 56 Processing sheet with id=AD4, first strand: chain 'q' and resid 204 through 208 removed outlier: 3.648A pdb=" N GLY q 379 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'q' and resid 221 through 224 removed outlier: 3.918A pdb=" N TYR q 351 " --> pdb=" O VAL q 362 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'q' and resid 239 through 242 removed outlier: 6.173A pdb=" N ALA q 240 " --> pdb=" O VAL q 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'q' and resid 408 through 410 Processing sheet with id=AD8, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AD9, first strand: chain 'A' and resid 43 through 45 removed outlier: 3.558A pdb=" N THR A 55 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 195 through 199 removed outlier: 3.851A pdb=" N SER A 374 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 211 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 214 through 216 removed outlier: 3.658A pdb=" N TYR A 214 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 216 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 363 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 352 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AE4, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=AE5, first strand: chain 'A' and resid 486 through 488 removed outlier: 3.570A pdb=" N ARG A 496 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AE7, first strand: chain 'G' and resid 183 through 184 Processing sheet with id=AE8, first strand: chain 'G' and resid 199 through 204 removed outlier: 5.858A pdb=" N ARG G 199 " --> pdb=" O ILE G 373 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU G 375 " --> pdb=" O ARG G 199 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLU G 201 " --> pdb=" O LEU G 375 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLY G 377 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE G 203 " --> pdb=" O GLY G 377 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 237 through 239 removed outlier: 6.700A pdb=" N VAL G 238 " --> pdb=" O ILE G 290 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 353 through 354 removed outlier: 3.828A pdb=" N ILE G 354 " --> pdb=" O GLU G 357 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 49 through 50 Processing sheet with id=AF3, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AF4, first strand: chain 'H' and resid 196 through 201 removed outlier: 7.695A pdb=" N GLY H 196 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU H 374 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LYS H 198 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLY H 376 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL H 200 " --> pdb=" O GLY H 376 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL H 211 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 310 through 312 removed outlier: 5.949A pdb=" N VAL H 289 " --> pdb=" O ALA H 311 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE H 237 " --> pdb=" O SER H 329 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLN H 331 " --> pdb=" O ILE H 237 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU H 239 " --> pdb=" O GLN H 331 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 352 through 353 Processing sheet with id=AF7, first strand: chain 'H' and resid 475 through 477 Processing sheet with id=AF8, first strand: chain 'H' and resid 516 through 520 removed outlier: 6.025A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 202 through 205 removed outlier: 3.572A pdb=" N ARG Q 203 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL Q 376 " --> pdb=" O SER Q 216 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 221 through 223 removed outlier: 3.581A pdb=" N TYR Q 351 " --> pdb=" O VAL Q 362 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS Q 364 " --> pdb=" O SER Q 349 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 311 through 313 removed outlier: 6.818A pdb=" N VAL Q 291 " --> pdb=" O VAL Q 313 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ALA Q 240 " --> pdb=" O VAL Q 292 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU Q 333 " --> pdb=" O ILE Q 239 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL Q 241 " --> pdb=" O LEU Q 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'B' and resid 63 through 64 removed outlier: 3.810A pdb=" N THR B 64 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 50 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AG5, first strand: chain 'B' and resid 199 through 201 removed outlier: 3.585A pdb=" N ILE B 373 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 372 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 204 through 205 removed outlier: 6.547A pdb=" N LYS B 204 " --> pdb=" O GLY B 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'B' and resid 218 through 220 removed outlier: 3.662A pdb=" N ASP B 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 310 through 312 removed outlier: 6.176A pdb=" N PHE B 290 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU B 238 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ALA B 332 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B 239 " --> pdb=" O ALA B 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'D' and resid 262 through 263 removed outlier: 9.269A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG B 255 " --> pdb=" O VAL E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'B' and resid 476 through 478 Processing sheet with id=AH2, first strand: chain 'B' and resid 517 through 522 removed outlier: 4.262A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS E 59 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR E 71 " --> pdb=" O LYS E 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.832A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 297 through 301 removed outlier: 3.612A pdb=" N ILE D 325 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE D 300 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP D 327 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 363 through 366 Processing sheet with id=AH6, first strand: chain 'D' and resid 421 through 423 Processing sheet with id=AH7, first strand: chain 'E' and resid 28 through 29 removed outlier: 3.945A pdb=" N ILE E 533 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AH9, first strand: chain 'E' and resid 223 through 225 removed outlier: 4.187A pdb=" N LYS E 223 " --> pdb=" O PHE E 386 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE E 386 " --> pdb=" O LYS E 223 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 229 through 230 removed outlier: 3.513A pdb=" N LEU E 372 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET E 371 " --> pdb=" O ILE E 362 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 321 through 322 removed outlier: 6.636A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'b' and resid 62 through 64 removed outlier: 6.136A pdb=" N ASP b 49 " --> pdb=" O ILE d 532 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP d 534 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE b 51 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL d 536 " --> pdb=" O ILE b 51 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AI5, first strand: chain 'b' and resid 200 through 201 removed outlier: 7.002A pdb=" N HIS b 200 " --> pdb=" O ILE b 373 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'b' and resid 204 through 205 removed outlier: 6.048A pdb=" N LYS b 204 " --> pdb=" O GLY b 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'b' and resid 218 through 220 removed outlier: 3.789A pdb=" N ASP b 357 " --> pdb=" O ILE b 354 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE b 354 " --> pdb=" O ASP b 357 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LYS b 236 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE b 291 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU b 238 " --> pdb=" O ILE b 291 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE b 290 " --> pdb=" O ILE b 312 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'b' and resid 218 through 220 removed outlier: 3.789A pdb=" N ASP b 357 " --> pdb=" O ILE b 354 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE b 354 " --> pdb=" O ASP b 357 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N ALA b 332 " --> pdb=" O ILE b 237 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE b 239 " --> pdb=" O ALA b 332 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'd' and resid 262 through 264 removed outlier: 10.065A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'b' and resid 517 through 522 removed outlier: 3.982A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AJ3, first strand: chain 'd' and resid 209 through 212 Processing sheet with id=AJ4, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.658A pdb=" N LEU d 374 " --> pdb=" O LEU d 229 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N CYS d 379 " --> pdb=" O ALA d 359 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ALA d 359 " --> pdb=" O CYS d 379 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'd' and resid 246 through 249 removed outlier: 3.750A pdb=" N ASP d 327 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AJ7, first strand: chain 'e' and resid 153 through 154 removed outlier: 3.681A pdb=" N VAL e 418 " --> pdb=" O ASP e 153 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'e' and resid 223 through 225 Processing sheet with id=AJ9, first strand: chain 'e' and resid 227 through 230 removed outlier: 3.533A pdb=" N MET e 371 " --> pdb=" O ILE e 362 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU e 358 " --> pdb=" O GLU e 244 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLU e 244 " --> pdb=" O LEU e 358 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA e 300 " --> pdb=" O VAL e 322 " (cutoff:3.500A) 3310 hydrogen bonds defined for protein. 9561 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: 25.99 Time building geometry restraints manager: 14.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16089 1.33 - 1.46: 10140 1.46 - 1.58: 36011 1.58 - 1.70: 48 1.70 - 1.82: 632 Bond restraints: 62920 Sorted by residual: bond pdb=" C LYS E 439 " pdb=" N CYS E 440 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.59e-02 3.96e+03 8.63e+00 bond pdb=" CG ARG E 478 " pdb=" CD ARG E 478 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CA GLY Z 345 " pdb=" C GLY Z 345 " ideal model delta sigma weight residual 1.520 1.512 0.009 7.30e-03 1.88e+04 1.38e+00 bond pdb=" N MET h 231 " pdb=" CA MET h 231 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.34e+00 bond pdb=" C4 ADP Q5000 " pdb=" C5 ADP Q5000 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.32e+00 ... (remaining 62915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 83407 2.04 - 4.07: 1226 4.07 - 6.11: 306 6.11 - 8.15: 38 8.15 - 10.18: 6 Bond angle restraints: 84983 Sorted by residual: angle pdb=" N VAL Z 62 " pdb=" CA VAL Z 62 " pdb=" C VAL Z 62 " ideal model delta sigma weight residual 112.96 109.21 3.75 1.00e+00 1.00e+00 1.40e+01 angle pdb=" C GLU E 121 " pdb=" N GLN E 122 " pdb=" CA GLN E 122 " ideal model delta sigma weight residual 121.58 114.39 7.19 1.95e+00 2.63e-01 1.36e+01 angle pdb=" C VAL E 477 " pdb=" N ARG E 478 " pdb=" CA ARG E 478 " ideal model delta sigma weight residual 121.14 115.05 6.09 1.75e+00 3.27e-01 1.21e+01 angle pdb=" CA GLN E 122 " pdb=" CB GLN E 122 " pdb=" CG GLN E 122 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA LYS a 111 " pdb=" CB LYS a 111 " pdb=" CG LYS a 111 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 ... (remaining 84978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.00: 37686 31.00 - 62.00: 1113 62.00 - 93.00: 94 93.00 - 124.00: 13 124.00 - 155.00: 9 Dihedral angle restraints: 38915 sinusoidal: 15629 harmonic: 23286 Sorted by residual: dihedral pdb=" C5' ADP q5000 " pdb=" O5' ADP q5000 " pdb=" PA ADP q5000 " pdb=" O2A ADP q5000 " ideal model delta sinusoidal sigma weight residual -60.00 95.00 -155.00 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP b 601 " pdb=" O3A ADP b 601 " pdb=" PA ADP b 601 " pdb=" PB ADP b 601 " ideal model delta sinusoidal sigma weight residual 300.00 154.95 145.05 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O2A ADP e 601 " pdb=" O3A ADP e 601 " pdb=" PA ADP e 601 " pdb=" PB ADP e 601 " ideal model delta sinusoidal sigma weight residual 300.00 162.01 137.99 1 2.00e+01 2.50e-03 4.18e+01 ... (remaining 38912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 8288 0.055 - 0.110: 1652 0.110 - 0.165: 217 0.165 - 0.219: 10 0.219 - 0.274: 1 Chirality restraints: 10168 Sorted by residual: chirality pdb=" CB ILE A 531 " pdb=" CA ILE A 531 " pdb=" CG1 ILE A 531 " pdb=" CG2 ILE A 531 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE Q 497 " pdb=" CA ILE Q 497 " pdb=" CG1 ILE Q 497 " pdb=" CG2 ILE Q 497 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CG LEU A 530 " pdb=" CB LEU A 530 " pdb=" CD1 LEU A 530 " pdb=" CD2 LEU A 530 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 10165 not shown) Planarity restraints: 10833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO Q 338 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO Q 339 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO Q 339 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO Q 339 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO e 441 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU b 108 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C GLU b 108 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU b 108 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU b 109 " -0.012 2.00e-02 2.50e+03 ... (remaining 10830 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 899 2.60 - 3.18: 57763 3.18 - 3.75: 103753 3.75 - 4.33: 133998 4.33 - 4.90: 216349 Nonbonded interactions: 512762 Sorted by model distance: nonbonded pdb=" OG1 THR D 69 " pdb=" OE1 GLN D 80 " model vdw 2.031 3.040 nonbonded pdb=" O ASN g 156 " pdb=" OG1 THR g 160 " model vdw 2.145 3.040 nonbonded pdb=" OG1 THR D 71 " pdb=" OE1 GLU D 400 " model vdw 2.157 3.040 nonbonded pdb=" NH2 ARG G 229 " pdb=" OD1 ASN G 307 " model vdw 2.168 3.120 nonbonded pdb=" O LYS Q 400 " pdb=" OG1 THR Q 403 " model vdw 2.177 3.040 ... (remaining 512757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 528 or resid 601)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601)) } ncs_group { reference = (chain 'G' and (resid 17 through 241 or resid 274 through 525 or resid 601)) selection = chain 'g' } ncs_group { reference = chain 'H' selection = (chain 'h' and (resid 12 through 250 or resid 266 through 529 or resid 601)) } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 2.020 Check model and map are aligned: 0.350 Set scattering table: 0.470 Process input model: 116.080 Find NCS groups from input model: 5.110 Set up NCS constraints: 0.440 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: 0.030 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 0.047 62920 Z= 0.175 Angle : 0.645 10.183 84983 Z= 0.325 Chirality : 0.043 0.274 10168 Planarity : 0.003 0.081 10833 Dihedral : 14.793 155.001 23823 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.34 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 0.13 (0.10), residues: 8047 helix: 1.38 (0.08), residues: 4072 sheet: -1.01 (0.22), residues: 622 loop : -1.34 (0.11), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 506 HIS 0.009 0.001 HIS E 182 PHE 0.025 0.001 PHE B 317 TYR 0.025 0.001 TYR h 267 ARG 0.006 0.000 ARG E 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 558 time to evaluate : 5.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 321 MET cc_start: 0.7891 (mpp) cc_final: 0.7686 (mpp) REVERT: Z 520 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6708 (tm-30) REVERT: a 20 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7730 (tm-30) REVERT: a 76 CYS cc_start: 0.9235 (m) cc_final: 0.8990 (m) REVERT: a 225 MET cc_start: 0.2353 (mmt) cc_final: 0.1867 (mmt) REVERT: a 306 MET cc_start: 0.6270 (ptp) cc_final: 0.6025 (ttp) REVERT: a 430 MET cc_start: 0.8027 (tmm) cc_final: 0.7760 (tmm) REVERT: q 385 MET cc_start: 0.8328 (mmp) cc_final: 0.7975 (mmm) REVERT: A 78 LEU cc_start: 0.8975 (mm) cc_final: 0.8625 (mm) REVERT: A 156 MET cc_start: 0.6858 (tpt) cc_final: 0.6295 (tpp) REVERT: H 323 MET cc_start: 0.6556 (mpp) cc_final: 0.6088 (pmm) REVERT: Q 116 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7688 (tm-30) REVERT: Q 344 MET cc_start: 0.2367 (tpt) cc_final: 0.2063 (tpt) REVERT: D 32 GLN cc_start: 0.7922 (pt0) cc_final: 0.7689 (pt0) REVERT: D 122 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8205 (pttt) REVERT: E 214 LYS cc_start: 0.7271 (pttt) cc_final: 0.7065 (pttm) REVERT: b 48 MET cc_start: 0.8526 (mtm) cc_final: 0.8289 (mtm) REVERT: b 52 LEU cc_start: 0.9115 (tp) cc_final: 0.8891 (tp) REVERT: b 93 ASP cc_start: 0.8622 (m-30) cc_final: 0.7797 (p0) REVERT: b 275 MET cc_start: 0.6111 (tpt) cc_final: 0.5806 (tpp) REVERT: b 417 MET cc_start: 0.8830 (mtt) cc_final: 0.8567 (mtt) REVERT: d 35 PHE cc_start: 0.8707 (m-10) cc_final: 0.8364 (m-10) REVERT: d 533 ASP cc_start: 0.8717 (p0) cc_final: 0.8135 (p0) REVERT: e 199 MET cc_start: 0.0415 (mpp) cc_final: 0.0086 (tmm) REVERT: e 448 MET cc_start: 0.6410 (mmm) cc_final: 0.5555 (mmm) outliers start: 0 outliers final: 0 residues processed: 558 average time/residue: 0.5271 time to fit residues: 515.9635 Evaluate side-chains 449 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 5.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 678 optimal weight: 50.0000 chunk 608 optimal weight: 6.9990 chunk 337 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 410 optimal weight: 9.9990 chunk 325 optimal weight: 7.9990 chunk 629 optimal weight: 8.9990 chunk 243 optimal weight: 9.9990 chunk 382 optimal weight: 1.9990 chunk 468 optimal weight: 5.9990 chunk 729 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 386 GLN ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 434 GLN ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 450 ASN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 ASN Q 53 ASN ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 HIS ** Q 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN b 65 ASN ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 290 GLN e 403 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 62920 Z= 0.266 Angle : 0.677 12.212 84983 Z= 0.338 Chirality : 0.045 0.221 10168 Planarity : 0.004 0.079 10833 Dihedral : 7.910 166.284 8763 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.70 % Favored : 94.25 % Rotamer: Outliers : 0.74 % Allowed : 7.87 % Favored : 91.39 % 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: -0.03 (0.10), residues: 8047 helix: 1.25 (0.08), residues: 4105 sheet: -1.32 (0.22), residues: 581 loop : -1.38 (0.11), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 495 HIS 0.011 0.001 HIS Q 365 PHE 0.038 0.001 PHE e 364 TYR 0.020 0.001 TYR d 439 ARG 0.009 0.000 ARG h 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 476 time to evaluate : 5.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 196 MET cc_start: 0.7280 (ppp) cc_final: 0.5851 (ppp) REVERT: z 221 MET cc_start: 0.4611 (ptt) cc_final: 0.4306 (mmt) REVERT: Z 520 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6733 (tm-30) REVERT: a 20 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7650 (tm-30) REVERT: a 225 MET cc_start: 0.3052 (mmt) cc_final: 0.2452 (mmt) REVERT: a 266 ARG cc_start: 0.4792 (mpp-170) cc_final: 0.4539 (mpt180) REVERT: a 306 MET cc_start: 0.6268 (ptp) cc_final: 0.6059 (ttp) REVERT: a 430 MET cc_start: 0.7967 (tmm) cc_final: 0.7656 (tmm) REVERT: q 385 MET cc_start: 0.8151 (mmp) cc_final: 0.7945 (mmm) REVERT: A 77 GLU cc_start: 0.7111 (pp20) cc_final: 0.6760 (pp20) REVERT: A 78 LEU cc_start: 0.8968 (mm) cc_final: 0.8713 (mm) REVERT: A 156 MET cc_start: 0.7024 (tpt) cc_final: 0.6168 (tpp) REVERT: G 46 MET cc_start: 0.8444 (ttt) cc_final: 0.8233 (mtp) REVERT: H 109 LYS cc_start: 0.8793 (mmmt) cc_final: 0.7958 (tttt) REVERT: H 184 MET cc_start: 0.3067 (mpp) cc_final: 0.2801 (mpp) REVERT: Q 116 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7737 (tm-30) REVERT: Q 344 MET cc_start: 0.2557 (tpt) cc_final: 0.2297 (tpt) REVERT: B 25 ARG cc_start: 0.7598 (mmm160) cc_final: 0.7174 (mmm160) REVERT: D 32 GLN cc_start: 0.7939 (pt0) cc_final: 0.7099 (pt0) REVERT: D 35 PHE cc_start: 0.7989 (m-80) cc_final: 0.7097 (m-80) REVERT: D 78 LEU cc_start: 0.9142 (mm) cc_final: 0.8754 (mm) REVERT: E 364 PHE cc_start: 0.4824 (m-10) cc_final: 0.4581 (m-10) REVERT: b 48 MET cc_start: 0.8464 (mtm) cc_final: 0.8223 (mtm) REVERT: b 112 GLU cc_start: 0.8921 (mp0) cc_final: 0.8687 (mp0) REVERT: b 275 MET cc_start: 0.6155 (tpt) cc_final: 0.5853 (tpp) REVERT: b 417 MET cc_start: 0.8873 (mtt) cc_final: 0.8466 (mtt) REVERT: d 35 PHE cc_start: 0.8631 (m-10) cc_final: 0.8358 (m-10) REVERT: d 260 MET cc_start: 0.1177 (mtt) cc_final: 0.0663 (mtp) REVERT: d 533 ASP cc_start: 0.8752 (p0) cc_final: 0.8279 (p0) REVERT: e 61 MET cc_start: 0.5649 (ppp) cc_final: 0.5425 (ppp) REVERT: e 199 MET cc_start: 0.0910 (mpp) cc_final: 0.0514 (tmm) REVERT: e 448 MET cc_start: 0.6873 (mmm) cc_final: 0.6182 (mmm) outliers start: 50 outliers final: 33 residues processed: 507 average time/residue: 0.5213 time to fit residues: 465.7528 Evaluate side-chains 468 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 435 time to evaluate : 5.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 394 MET Chi-restraints excluded: chain g residue 511 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 484 ASN Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 120 CYS Chi-restraints excluded: chain d residue 529 ILE Chi-restraints excluded: chain e residue 403 HIS Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain e residue 457 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 405 optimal weight: 50.0000 chunk 226 optimal weight: 50.0000 chunk 606 optimal weight: 0.8980 chunk 496 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 730 optimal weight: 30.0000 chunk 789 optimal weight: 40.0000 chunk 650 optimal weight: 10.0000 chunk 724 optimal weight: 10.0000 chunk 249 optimal weight: 8.9990 chunk 586 optimal weight: 1.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 37 ASN ** z 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 436 GLN ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS G 220 ASN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 62920 Z= 0.252 Angle : 0.656 10.241 84983 Z= 0.325 Chirality : 0.044 0.294 10168 Planarity : 0.004 0.078 10833 Dihedral : 7.847 176.822 8763 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.59 % Rotamer: Outliers : 1.38 % Allowed : 11.07 % Favored : 87.55 % 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: -0.09 (0.09), residues: 8047 helix: 1.19 (0.08), residues: 4114 sheet: -1.36 (0.22), residues: 602 loop : -1.41 (0.11), residues: 3331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 495 HIS 0.019 0.001 HIS e 403 PHE 0.021 0.001 PHE D 35 TYR 0.028 0.001 TYR d 439 ARG 0.010 0.000 ARG h 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 466 time to evaluate : 6.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 196 MET cc_start: 0.7500 (ppp) cc_final: 0.6290 (ppp) REVERT: z 221 MET cc_start: 0.4634 (ptt) cc_final: 0.4294 (mmt) REVERT: Z 196 MET cc_start: 0.6843 (pmm) cc_final: 0.6329 (pmm) REVERT: Z 520 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6655 (tm-30) REVERT: a 20 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7691 (tm-30) REVERT: a 225 MET cc_start: 0.3228 (mmt) cc_final: 0.2690 (mmt) REVERT: a 266 ARG cc_start: 0.4761 (mpp-170) cc_final: 0.4415 (mpt180) REVERT: a 306 MET cc_start: 0.6217 (ptp) cc_final: 0.5871 (ptm) REVERT: a 430 MET cc_start: 0.8108 (tmm) cc_final: 0.7843 (tmm) REVERT: g 53 MET cc_start: 0.6309 (ptp) cc_final: 0.6063 (ppp) REVERT: h 306 TYR cc_start: 0.2629 (t80) cc_final: 0.2280 (m-10) REVERT: q 311 MET cc_start: 0.0870 (pmm) cc_final: 0.0500 (pmm) REVERT: A 78 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8822 (mm) REVERT: A 156 MET cc_start: 0.7110 (tpt) cc_final: 0.6032 (tpp) REVERT: G 228 MET cc_start: 0.2998 (ppp) cc_final: 0.2619 (ppp) REVERT: G 231 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.6910 (p90) REVERT: H 194 MET cc_start: 0.3539 (mtp) cc_final: 0.3257 (mpp) REVERT: Q 116 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7668 (tm-30) REVERT: Q 344 MET cc_start: 0.3197 (tpt) cc_final: 0.2929 (tpp) REVERT: B 488 MET cc_start: 0.7451 (mmp) cc_final: 0.7034 (mmt) REVERT: D 35 PHE cc_start: 0.7984 (m-80) cc_final: 0.7400 (m-80) REVERT: D 122 LYS cc_start: 0.8780 (mmtm) cc_final: 0.8458 (pttt) REVERT: E 48 MET cc_start: 0.8359 (tpp) cc_final: 0.8019 (tpp) REVERT: E 364 PHE cc_start: 0.4719 (m-10) cc_final: 0.4115 (m-10) REVERT: b 112 GLU cc_start: 0.8976 (mp0) cc_final: 0.8711 (mp0) REVERT: b 275 MET cc_start: 0.6353 (tpt) cc_final: 0.6009 (tpp) REVERT: b 417 MET cc_start: 0.8894 (mtt) cc_final: 0.8503 (mtt) REVERT: d 35 PHE cc_start: 0.8627 (m-10) cc_final: 0.8355 (m-10) REVERT: d 122 LYS cc_start: 0.8695 (mptt) cc_final: 0.8067 (tppt) REVERT: d 260 MET cc_start: 0.1195 (mtt) cc_final: 0.0695 (mtp) REVERT: d 533 ASP cc_start: 0.8755 (p0) cc_final: 0.8524 (p0) REVERT: e 48 MET cc_start: 0.8642 (tmm) cc_final: 0.8251 (tmm) REVERT: e 199 MET cc_start: 0.0971 (mpp) cc_final: 0.0533 (tmm) REVERT: e 448 MET cc_start: 0.7039 (mmm) cc_final: 0.6212 (mmm) REVERT: e 460 MET cc_start: 0.8356 (tpt) cc_final: 0.8069 (tpt) outliers start: 93 outliers final: 51 residues processed: 530 average time/residue: 0.5397 time to fit residues: 502.4994 Evaluate side-chains 487 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 434 time to evaluate : 5.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 276 GLU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 197 TYR Chi-restraints excluded: chain g residue 394 MET Chi-restraints excluded: chain g residue 511 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 68 LEU Chi-restraints excluded: chain h residue 481 VAL Chi-restraints excluded: chain h residue 484 ASN Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain G residue 231 TYR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 360 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain d residue 38 ILE Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 120 CYS Chi-restraints excluded: chain d residue 529 ILE Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain e residue 457 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 721 optimal weight: 0.4980 chunk 549 optimal weight: 0.8980 chunk 379 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 348 optimal weight: 1.9990 chunk 490 optimal weight: 8.9990 chunk 733 optimal weight: 0.0070 chunk 776 optimal weight: 6.9990 chunk 383 optimal weight: 0.0000 chunk 694 optimal weight: 7.9990 chunk 209 optimal weight: 0.9990 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 470 HIS ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN D 406 HIS D 502 ASN E 72 ASN b 65 ASN ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 178 HIS ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 498 GLN ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 62920 Z= 0.163 Angle : 0.621 12.550 84983 Z= 0.302 Chirality : 0.043 0.351 10168 Planarity : 0.003 0.079 10833 Dihedral : 7.553 175.368 8763 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.99 % Favored : 94.96 % Rotamer: Outliers : 1.28 % Allowed : 12.81 % Favored : 85.92 % 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: 0.08 (0.10), residues: 8047 helix: 1.36 (0.08), residues: 4126 sheet: -1.27 (0.21), residues: 617 loop : -1.38 (0.11), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP h 497 HIS 0.006 0.001 HIS E 37 PHE 0.027 0.001 PHE d 351 TYR 0.030 0.001 TYR d 439 ARG 0.010 0.000 ARG h 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 495 time to evaluate : 5.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 196 MET cc_start: 0.7230 (ppp) cc_final: 0.6184 (ppp) REVERT: z 221 MET cc_start: 0.4518 (ptt) cc_final: 0.4074 (mmt) REVERT: Z 24 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9033 (tt) REVERT: Z 196 MET cc_start: 0.6865 (pmm) cc_final: 0.6522 (pmm) REVERT: Z 321 MET cc_start: 0.8115 (mpp) cc_final: 0.7763 (mpp) REVERT: Z 520 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6636 (tm-30) REVERT: a 20 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7777 (tm-30) REVERT: a 225 MET cc_start: 0.3170 (mmt) cc_final: 0.2483 (mmt) REVERT: a 266 ARG cc_start: 0.4863 (mpp-170) cc_final: 0.4503 (mpt180) REVERT: a 306 MET cc_start: 0.6295 (ptp) cc_final: 0.6006 (ptm) REVERT: h 306 TYR cc_start: 0.2548 (t80) cc_final: 0.2199 (m-10) REVERT: q 73 LEU cc_start: 0.9255 (mm) cc_final: 0.8980 (pp) REVERT: q 385 MET cc_start: 0.8486 (mmm) cc_final: 0.8012 (mmm) REVERT: A 77 GLU cc_start: 0.7051 (pp20) cc_final: 0.6589 (pp20) REVERT: A 78 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8778 (mm) REVERT: A 156 MET cc_start: 0.7104 (tpt) cc_final: 0.5972 (tpp) REVERT: G 228 MET cc_start: 0.2632 (ppp) cc_final: 0.2420 (ppp) REVERT: G 231 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.6983 (p90) REVERT: H 109 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8471 (mmtt) REVERT: H 184 MET cc_start: 0.3172 (mpp) cc_final: 0.2923 (mpp) REVERT: Q 344 MET cc_start: 0.2707 (tpt) cc_final: 0.2455 (tpp) REVERT: B 488 MET cc_start: 0.7518 (mmp) cc_final: 0.7183 (mmt) REVERT: D 35 PHE cc_start: 0.8079 (m-80) cc_final: 0.7301 (m-80) REVERT: D 122 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8267 (pttp) REVERT: E 48 MET cc_start: 0.8298 (tpp) cc_final: 0.7975 (tpp) REVERT: E 364 PHE cc_start: 0.4811 (m-10) cc_final: 0.4607 (m-10) REVERT: b 48 MET cc_start: 0.8468 (mtt) cc_final: 0.7965 (mtm) REVERT: b 93 ASP cc_start: 0.8514 (m-30) cc_final: 0.8308 (m-30) REVERT: b 275 MET cc_start: 0.6353 (tpt) cc_final: 0.6022 (tpp) REVERT: b 416 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7656 (mm) REVERT: d 35 PHE cc_start: 0.8666 (m-10) cc_final: 0.8356 (m-10) REVERT: d 122 LYS cc_start: 0.8661 (mptt) cc_final: 0.7916 (tppt) REVERT: d 533 ASP cc_start: 0.8729 (p0) cc_final: 0.8135 (p0) REVERT: e 48 MET cc_start: 0.8593 (tmm) cc_final: 0.8197 (tmm) REVERT: e 199 MET cc_start: 0.1087 (mpp) cc_final: 0.0636 (tmm) REVERT: e 288 MET cc_start: 0.3642 (mmt) cc_final: 0.3114 (ttt) REVERT: e 448 MET cc_start: 0.6955 (mmm) cc_final: 0.6235 (mmm) REVERT: e 449 ARG cc_start: 0.6760 (mtt90) cc_final: 0.5685 (mmt180) REVERT: e 460 MET cc_start: 0.8318 (tpt) cc_final: 0.8046 (tpt) REVERT: e 523 MET cc_start: 0.8927 (mmp) cc_final: 0.8611 (mmt) outliers start: 86 outliers final: 44 residues processed: 554 average time/residue: 0.5346 time to fit residues: 521.4229 Evaluate side-chains 497 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 448 time to evaluate : 5.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 276 GLU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 110 GLN Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 394 MET Chi-restraints excluded: chain h residue 68 LEU Chi-restraints excluded: chain h residue 481 VAL Chi-restraints excluded: chain h residue 484 ASN Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 337 THR Chi-restraints excluded: chain q residue 376 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 231 TYR Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 360 VAL Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain Q residue 417 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 120 CYS Chi-restraints excluded: chain d residue 529 ILE Chi-restraints excluded: chain e residue 440 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 646 optimal weight: 0.9990 chunk 440 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 577 optimal weight: 10.0000 chunk 320 optimal weight: 4.9990 chunk 662 optimal weight: 40.0000 chunk 536 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 396 optimal weight: 0.2980 chunk 696 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 62920 Z= 0.169 Angle : 0.623 14.552 84983 Z= 0.302 Chirality : 0.043 0.360 10168 Planarity : 0.003 0.081 10833 Dihedral : 7.441 172.036 8763 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 1.40 % Allowed : 14.23 % Favored : 84.37 % 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: 0.12 (0.10), residues: 8047 helix: 1.40 (0.08), residues: 4133 sheet: -1.27 (0.22), residues: 608 loop : -1.38 (0.11), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 493 HIS 0.008 0.001 HIS E 85 PHE 0.020 0.001 PHE d 137 TYR 0.025 0.001 TYR d 439 ARG 0.010 0.000 ARG h 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 472 time to evaluate : 5.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 196 MET cc_start: 0.7280 (ppp) cc_final: 0.6399 (ppp) REVERT: z 221 MET cc_start: 0.4348 (ptt) cc_final: 0.3791 (mmt) REVERT: Z 24 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9103 (tt) REVERT: Z 86 ASP cc_start: 0.8598 (m-30) cc_final: 0.8288 (m-30) REVERT: Z 196 MET cc_start: 0.6945 (pmm) cc_final: 0.6656 (pmm) REVERT: Z 321 MET cc_start: 0.8148 (mpp) cc_final: 0.7814 (mpp) REVERT: Z 487 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7721 (ppp) REVERT: a 20 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7791 (tm-30) REVERT: a 225 MET cc_start: 0.3395 (mmt) cc_final: 0.2738 (mmt) REVERT: a 266 ARG cc_start: 0.4884 (mpp-170) cc_final: 0.4592 (mpt180) REVERT: g 228 MET cc_start: 0.1928 (ppp) cc_final: 0.1717 (ppp) REVERT: g 402 LEU cc_start: 0.7403 (mt) cc_final: 0.6935 (tt) REVERT: h 306 TYR cc_start: 0.2549 (t80) cc_final: 0.2196 (m-10) REVERT: q 73 LEU cc_start: 0.9296 (mm) cc_final: 0.8987 (pp) REVERT: q 385 MET cc_start: 0.8502 (mmm) cc_final: 0.8077 (mmm) REVERT: A 77 GLU cc_start: 0.7224 (pp20) cc_final: 0.6883 (pp20) REVERT: A 78 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8725 (mm) REVERT: A 156 MET cc_start: 0.7084 (tpt) cc_final: 0.5902 (tpp) REVERT: G 46 MET cc_start: 0.8171 (mtp) cc_final: 0.7948 (mtp) REVERT: G 231 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7055 (p90) REVERT: H 109 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8621 (mmtt) REVERT: H 184 MET cc_start: 0.3229 (OUTLIER) cc_final: 0.3010 (mpp) REVERT: B 62 MET cc_start: 0.7620 (mmm) cc_final: 0.7330 (mmp) REVERT: B 89 ARG cc_start: 0.9083 (ttp80) cc_final: 0.8794 (tmm-80) REVERT: B 488 MET cc_start: 0.7557 (mmp) cc_final: 0.7244 (mmt) REVERT: D 35 PHE cc_start: 0.8097 (m-80) cc_final: 0.7260 (m-80) REVERT: D 78 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8874 (mm) REVERT: D 122 LYS cc_start: 0.8722 (mmtm) cc_final: 0.8227 (pttp) REVERT: E 72 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7512 (t0) REVERT: E 364 PHE cc_start: 0.4716 (m-10) cc_final: 0.4201 (m-10) REVERT: b 48 MET cc_start: 0.8498 (mtt) cc_final: 0.8073 (mtm) REVERT: b 93 ASP cc_start: 0.8604 (m-30) cc_final: 0.7827 (p0) REVERT: b 275 MET cc_start: 0.6345 (tpt) cc_final: 0.6036 (tpp) REVERT: b 416 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7611 (mm) REVERT: b 417 MET cc_start: 0.8795 (mtt) cc_final: 0.8307 (mtt) REVERT: d 35 PHE cc_start: 0.8666 (m-10) cc_final: 0.8375 (m-10) REVERT: d 533 ASP cc_start: 0.8746 (p0) cc_final: 0.8271 (p0) REVERT: e 48 MET cc_start: 0.8692 (tmm) cc_final: 0.8317 (tmm) REVERT: e 199 MET cc_start: 0.1074 (mpp) cc_final: 0.0618 (tmm) REVERT: e 288 MET cc_start: 0.3652 (mmt) cc_final: 0.3121 (ttt) REVERT: e 364 PHE cc_start: 0.3711 (t80) cc_final: 0.3122 (t80) REVERT: e 448 MET cc_start: 0.6997 (mmm) cc_final: 0.6294 (mmm) REVERT: e 449 ARG cc_start: 0.6842 (mtt90) cc_final: 0.5772 (mmt180) REVERT: e 460 MET cc_start: 0.8287 (tpt) cc_final: 0.8007 (tpt) outliers start: 94 outliers final: 53 residues processed: 535 average time/residue: 0.5411 time to fit residues: 509.5687 Evaluate side-chains 509 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 447 time to evaluate : 5.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 276 GLU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 444 LEU Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 110 GLN Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 197 TYR Chi-restraints excluded: chain g residue 394 MET Chi-restraints excluded: chain h residue 481 VAL Chi-restraints excluded: chain h residue 484 ASN Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 337 THR Chi-restraints excluded: chain q residue 376 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 231 TYR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 360 VAL Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 120 CYS Chi-restraints excluded: chain d residue 529 ILE Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain e residue 440 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 261 optimal weight: 5.9990 chunk 698 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 455 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 776 optimal weight: 8.9990 chunk 644 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 chunk 64 optimal weight: 0.0040 chunk 257 optimal weight: 7.9990 chunk 407 optimal weight: 8.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS E 72 ASN E 317 ASN ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 486 GLN ** e 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 62920 Z= 0.237 Angle : 0.656 12.411 84983 Z= 0.321 Chirality : 0.044 0.339 10168 Planarity : 0.004 0.079 10833 Dihedral : 7.451 168.629 8763 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.35 % Favored : 94.61 % Rotamer: Outliers : 1.65 % Allowed : 15.54 % Favored : 82.81 % 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: 0.04 (0.10), residues: 8047 helix: 1.32 (0.08), residues: 4123 sheet: -1.44 (0.22), residues: 597 loop : -1.35 (0.11), residues: 3327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 324 HIS 0.008 0.001 HIS G 469 PHE 0.027 0.001 PHE d 137 TYR 0.023 0.001 TYR G 302 ARG 0.012 0.000 ARG h 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 454 time to evaluate : 5.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 196 MET cc_start: 0.7446 (ppp) cc_final: 0.6542 (ppp) REVERT: z 221 MET cc_start: 0.4516 (ptt) cc_final: 0.3950 (mmt) REVERT: Z 86 ASP cc_start: 0.8641 (m-30) cc_final: 0.8346 (m-30) REVERT: Z 196 MET cc_start: 0.7093 (pmm) cc_final: 0.6780 (pmm) REVERT: Z 487 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7710 (ppp) REVERT: Z 520 GLU cc_start: 0.7168 (tp30) cc_final: 0.6907 (tp30) REVERT: a 266 ARG cc_start: 0.4734 (mpp-170) cc_final: 0.4418 (mpt180) REVERT: g 184 PHE cc_start: 0.7683 (m-80) cc_final: 0.6785 (m-80) REVERT: g 443 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8828 (tt) REVERT: h 306 TYR cc_start: 0.2548 (t80) cc_final: 0.2199 (m-10) REVERT: q 385 MET cc_start: 0.8348 (mmm) cc_final: 0.7941 (mmm) REVERT: q 492 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7642 (mmm) REVERT: A 78 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 156 MET cc_start: 0.7009 (tpt) cc_final: 0.5809 (tpp) REVERT: G 231 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.6920 (p90) REVERT: H 109 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8756 (mmtt) REVERT: H 178 MET cc_start: 0.5834 (ttt) cc_final: 0.5377 (ttt) REVERT: B 89 ARG cc_start: 0.9099 (ttp80) cc_final: 0.8792 (tmm-80) REVERT: B 488 MET cc_start: 0.7697 (mmp) cc_final: 0.7419 (mmt) REVERT: D 35 PHE cc_start: 0.8127 (m-80) cc_final: 0.7255 (m-80) REVERT: D 57 MET cc_start: 0.5905 (tpt) cc_final: 0.5567 (tpt) REVERT: D 78 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8856 (mm) REVERT: D 122 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8241 (pttp) REVERT: E 42 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8381 (mmmt) REVERT: b 48 MET cc_start: 0.8488 (mtt) cc_final: 0.8011 (mtm) REVERT: b 275 MET cc_start: 0.6196 (tpt) cc_final: 0.5888 (tpp) REVERT: b 416 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7728 (mm) REVERT: b 417 MET cc_start: 0.8805 (mtt) cc_final: 0.8306 (mtt) REVERT: d 35 PHE cc_start: 0.8630 (m-10) cc_final: 0.8266 (m-10) REVERT: d 533 ASP cc_start: 0.8783 (p0) cc_final: 0.8238 (p0) REVERT: e 48 MET cc_start: 0.8681 (tmm) cc_final: 0.8442 (tmm) REVERT: e 199 MET cc_start: 0.1106 (mpp) cc_final: 0.0632 (tmm) REVERT: e 288 MET cc_start: 0.3711 (mmt) cc_final: 0.3185 (ttt) REVERT: e 448 MET cc_start: 0.7218 (mmm) cc_final: 0.6296 (mmm) REVERT: e 449 ARG cc_start: 0.6907 (mtt90) cc_final: 0.5735 (mmt180) REVERT: e 460 MET cc_start: 0.8348 (tpt) cc_final: 0.8064 (tpt) REVERT: e 523 MET cc_start: 0.8903 (mmp) cc_final: 0.8594 (mmt) outliers start: 111 outliers final: 67 residues processed: 531 average time/residue: 0.5454 time to fit residues: 509.5308 Evaluate side-chains 508 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 433 time to evaluate : 5.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 101 GLU Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 276 GLU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 444 LEU Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 110 GLN Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain g residue 110 HIS Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 197 TYR Chi-restraints excluded: chain g residue 394 MET Chi-restraints excluded: chain g residue 443 LEU Chi-restraints excluded: chain h residue 481 VAL Chi-restraints excluded: chain h residue 484 ASN Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 337 THR Chi-restraints excluded: chain q residue 376 VAL Chi-restraints excluded: chain q residue 429 THR Chi-restraints excluded: chain q residue 492 MET Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 231 TYR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 118 LEU Chi-restraints excluded: chain Q residue 360 VAL Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 120 CYS Chi-restraints excluded: chain d residue 529 ILE Chi-restraints excluded: chain e residue 80 MET Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain e residue 457 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 749 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 442 optimal weight: 7.9990 chunk 567 optimal weight: 30.0000 chunk 439 optimal weight: 10.0000 chunk 654 optimal weight: 20.0000 chunk 433 optimal weight: 0.9990 chunk 773 optimal weight: 50.0000 chunk 484 optimal weight: 10.0000 chunk 471 optimal weight: 5.9990 chunk 357 optimal weight: 40.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 526 ASN ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 435 GLN Q 477 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 62920 Z= 0.230 Angle : 0.662 12.751 84983 Z= 0.323 Chirality : 0.044 0.355 10168 Planarity : 0.004 0.079 10833 Dihedral : 7.405 165.839 8763 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 1.60 % Allowed : 16.84 % Favored : 81.55 % 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: -0.01 (0.10), residues: 8047 helix: 1.28 (0.08), residues: 4120 sheet: -1.40 (0.21), residues: 610 loop : -1.39 (0.11), residues: 3317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 324 HIS 0.006 0.001 HIS g 469 PHE 0.030 0.001 PHE d 137 TYR 0.022 0.001 TYR d 439 ARG 0.016 0.000 ARG h 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 456 time to evaluate : 5.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 101 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: z 196 MET cc_start: 0.7575 (ppp) cc_final: 0.6783 (ppp) REVERT: z 221 MET cc_start: 0.3985 (ptt) cc_final: 0.3642 (mmt) REVERT: z 326 LEU cc_start: 0.8259 (pp) cc_final: 0.7890 (pp) REVERT: Z 86 ASP cc_start: 0.8634 (m-30) cc_final: 0.8332 (m-30) REVERT: Z 196 MET cc_start: 0.7103 (pmm) cc_final: 0.6844 (pmm) REVERT: Z 487 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7732 (ppp) REVERT: Z 520 GLU cc_start: 0.7112 (tp30) cc_final: 0.6658 (tp30) REVERT: a 266 ARG cc_start: 0.4760 (mpp-170) cc_final: 0.4474 (mpt180) REVERT: a 306 MET cc_start: 0.3942 (tmm) cc_final: 0.3514 (tmm) REVERT: g 228 MET cc_start: 0.2121 (ppp) cc_final: 0.1338 (ppp) REVERT: g 443 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8834 (tt) REVERT: h 306 TYR cc_start: 0.2546 (t80) cc_final: 0.2184 (m-10) REVERT: q 385 MET cc_start: 0.8368 (mmm) cc_final: 0.7965 (mmm) REVERT: q 492 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7613 (mmm) REVERT: A 156 MET cc_start: 0.6957 (tpt) cc_final: 0.5734 (tpp) REVERT: A 225 MET cc_start: 0.0761 (OUTLIER) cc_final: 0.0044 (tmm) REVERT: G 231 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.6906 (p90) REVERT: H 109 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8784 (mmtt) REVERT: H 382 MET cc_start: -0.1875 (mtt) cc_final: -0.2796 (tpt) REVERT: H 394 MET cc_start: 0.4052 (mmm) cc_final: 0.3851 (mmt) REVERT: Q 311 MET cc_start: 0.0197 (pmm) cc_final: -0.0300 (pmm) REVERT: B 62 MET cc_start: 0.7672 (mmm) cc_final: 0.7381 (mmp) REVERT: B 89 ARG cc_start: 0.9113 (ttp80) cc_final: 0.8857 (tmm-80) REVERT: B 488 MET cc_start: 0.7806 (mmp) cc_final: 0.7552 (mmt) REVERT: D 35 PHE cc_start: 0.8247 (m-80) cc_final: 0.7499 (m-80) REVERT: D 57 MET cc_start: 0.5848 (tpt) cc_final: 0.5547 (tpt) REVERT: D 78 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8946 (mm) REVERT: D 122 LYS cc_start: 0.8705 (mmtm) cc_final: 0.8342 (pttp) REVERT: E 39 MET cc_start: 0.8718 (tmm) cc_final: 0.8459 (tmm) REVERT: b 275 MET cc_start: 0.6193 (tpt) cc_final: 0.5854 (tpt) REVERT: b 310 MET cc_start: 0.1049 (mpp) cc_final: 0.0765 (mpp) REVERT: b 416 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7722 (mm) REVERT: b 417 MET cc_start: 0.8776 (mtt) cc_final: 0.8268 (mtt) REVERT: d 35 PHE cc_start: 0.8584 (m-10) cc_final: 0.8227 (m-10) REVERT: e 199 MET cc_start: 0.1195 (mpp) cc_final: 0.0762 (tmm) REVERT: e 448 MET cc_start: 0.7270 (mmm) cc_final: 0.6362 (mmm) REVERT: e 449 ARG cc_start: 0.6942 (mtt90) cc_final: 0.5753 (mmt180) REVERT: e 460 MET cc_start: 0.8339 (tpt) cc_final: 0.8050 (tpt) outliers start: 108 outliers final: 73 residues processed: 535 average time/residue: 0.5294 time to fit residues: 496.5861 Evaluate side-chains 516 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 434 time to evaluate : 5.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 101 GLU Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 276 GLU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 444 LEU Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain Z residue 518 VAL Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 110 GLN Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 197 TYR Chi-restraints excluded: chain g residue 394 MET Chi-restraints excluded: chain g residue 443 LEU Chi-restraints excluded: chain h residue 481 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 337 THR Chi-restraints excluded: chain q residue 376 VAL Chi-restraints excluded: chain q residue 429 THR Chi-restraints excluded: chain q residue 471 HIS Chi-restraints excluded: chain q residue 492 MET Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 231 TYR Chi-restraints excluded: chain G residue 372 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 442 LEU Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 118 LEU Chi-restraints excluded: chain Q residue 360 VAL Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 445 PHE Chi-restraints excluded: chain Q residue 492 MET Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 120 CYS Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 529 ILE Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain e residue 457 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 478 optimal weight: 2.9990 chunk 309 optimal weight: 20.0000 chunk 462 optimal weight: 6.9990 chunk 233 optimal weight: 30.0000 chunk 152 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 492 optimal weight: 6.9990 chunk 527 optimal weight: 8.9990 chunk 382 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 608 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 62920 Z= 0.227 Angle : 0.669 13.494 84983 Z= 0.324 Chirality : 0.044 0.362 10168 Planarity : 0.004 0.079 10833 Dihedral : 7.361 163.481 8763 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 1.63 % Allowed : 17.42 % Favored : 80.94 % 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: -0.05 (0.10), residues: 8047 helix: 1.26 (0.08), residues: 4120 sheet: -1.41 (0.21), residues: 622 loop : -1.41 (0.11), residues: 3305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 324 HIS 0.006 0.001 HIS G 469 PHE 0.034 0.001 PHE e 364 TYR 0.018 0.001 TYR d 439 ARG 0.013 0.000 ARG h 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 449 time to evaluate : 5.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 101 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: z 196 MET cc_start: 0.7533 (ppp) cc_final: 0.6757 (ppp) REVERT: z 221 MET cc_start: 0.4067 (ptt) cc_final: 0.3382 (mmm) REVERT: z 326 LEU cc_start: 0.8216 (pp) cc_final: 0.7855 (pp) REVERT: Z 86 ASP cc_start: 0.8640 (m-30) cc_final: 0.8357 (m-30) REVERT: Z 196 MET cc_start: 0.6926 (pmm) cc_final: 0.6690 (pmm) REVERT: Z 487 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7735 (ppp) REVERT: Z 520 GLU cc_start: 0.7138 (tp30) cc_final: 0.6602 (tp30) REVERT: a 20 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7511 (tm-30) REVERT: a 266 ARG cc_start: 0.4751 (mpp-170) cc_final: 0.4466 (mpt180) REVERT: a 306 MET cc_start: 0.3936 (tmm) cc_final: 0.3273 (tmm) REVERT: g 443 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8834 (tt) REVERT: h 188 MET cc_start: 0.7594 (ptt) cc_final: 0.7317 (ptt) REVERT: h 189 MET cc_start: 0.8843 (ppp) cc_final: 0.8577 (mmt) REVERT: h 306 TYR cc_start: 0.2551 (t80) cc_final: 0.2174 (m-10) REVERT: q 385 MET cc_start: 0.8388 (mmm) cc_final: 0.8009 (mmm) REVERT: A 156 MET cc_start: 0.6986 (tpt) cc_final: 0.5689 (tpp) REVERT: A 225 MET cc_start: 0.0728 (OUTLIER) cc_final: 0.0052 (tmm) REVERT: H 109 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8852 (mmtt) REVERT: H 382 MET cc_start: -0.1827 (mtt) cc_final: -0.2748 (tpt) REVERT: B 62 MET cc_start: 0.7794 (mmm) cc_final: 0.7500 (mmp) REVERT: B 89 ARG cc_start: 0.9128 (ttp80) cc_final: 0.8860 (tmm-80) REVERT: B 488 MET cc_start: 0.7829 (mmp) cc_final: 0.7603 (mmt) REVERT: D 35 PHE cc_start: 0.8159 (m-80) cc_final: 0.7301 (m-80) REVERT: D 57 MET cc_start: 0.5817 (tpt) cc_final: 0.5543 (tpt) REVERT: D 78 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8951 (mm) REVERT: D 122 LYS cc_start: 0.8740 (mmtm) cc_final: 0.8437 (pttt) REVERT: E 39 MET cc_start: 0.8701 (tmm) cc_final: 0.8391 (tmm) REVERT: E 42 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8469 (mmmt) REVERT: b 275 MET cc_start: 0.6192 (tpt) cc_final: 0.5852 (tpt) REVERT: b 310 MET cc_start: 0.1065 (mpp) cc_final: 0.0770 (mpp) REVERT: b 416 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7725 (mm) REVERT: b 417 MET cc_start: 0.8796 (mtt) cc_final: 0.8292 (mtt) REVERT: b 480 MET cc_start: 0.8447 (ppp) cc_final: 0.8163 (ppp) REVERT: d 35 PHE cc_start: 0.8574 (m-10) cc_final: 0.8229 (m-10) REVERT: e 199 MET cc_start: 0.1220 (mpp) cc_final: 0.0781 (tmm) REVERT: e 239 MET cc_start: 0.2104 (tpt) cc_final: 0.1292 (ttt) REVERT: e 288 MET cc_start: 0.3636 (mmt) cc_final: 0.3123 (ttt) REVERT: e 448 MET cc_start: 0.7245 (mmm) cc_final: 0.6329 (mmm) REVERT: e 449 ARG cc_start: 0.6950 (mtt90) cc_final: 0.5839 (mmt180) REVERT: e 460 MET cc_start: 0.8405 (tpt) cc_final: 0.8119 (tpt) REVERT: e 523 MET cc_start: 0.8873 (mmp) cc_final: 0.8538 (mmt) outliers start: 110 outliers final: 82 residues processed: 526 average time/residue: 0.5265 time to fit residues: 488.4411 Evaluate side-chains 530 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 441 time to evaluate : 5.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 101 GLU Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 444 LEU Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain Z residue 518 VAL Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 110 GLN Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 197 TYR Chi-restraints excluded: chain g residue 394 MET Chi-restraints excluded: chain g residue 443 LEU Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 481 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 337 THR Chi-restraints excluded: chain q residue 376 VAL Chi-restraints excluded: chain q residue 429 THR Chi-restraints excluded: chain q residue 471 HIS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 231 TYR Chi-restraints excluded: chain G residue 372 THR Chi-restraints excluded: chain G residue 428 MET Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 442 LEU Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 118 LEU Chi-restraints excluded: chain Q residue 360 VAL Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain Q residue 445 PHE Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 492 MET Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 120 CYS Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 529 ILE Chi-restraints excluded: chain e residue 80 MET Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain e residue 457 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 704 optimal weight: 9.9990 chunk 741 optimal weight: 8.9990 chunk 676 optimal weight: 30.0000 chunk 721 optimal weight: 40.0000 chunk 434 optimal weight: 0.9990 chunk 314 optimal weight: 5.9990 chunk 566 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 651 optimal weight: 9.9990 chunk 682 optimal weight: 40.0000 chunk 718 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 237 HIS ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 32 ASN ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 ASN ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 62920 Z= 0.313 Angle : 0.732 13.092 84983 Z= 0.360 Chirality : 0.046 0.386 10168 Planarity : 0.004 0.079 10833 Dihedral : 7.553 163.611 8763 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.03 % Favored : 93.93 % Rotamer: Outliers : 1.72 % Allowed : 17.72 % Favored : 80.56 % 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: -0.34 (0.09), residues: 8047 helix: 0.97 (0.08), residues: 4128 sheet: -1.54 (0.21), residues: 609 loop : -1.50 (0.11), residues: 3310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 324 HIS 0.009 0.001 HIS G 469 PHE 0.036 0.002 PHE d 137 TYR 0.018 0.002 TYR G 302 ARG 0.019 0.001 ARG h 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 433 time to evaluate : 5.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 101 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: z 196 MET cc_start: 0.7511 (ppp) cc_final: 0.6713 (ppp) REVERT: z 326 LEU cc_start: 0.8507 (pp) cc_final: 0.8179 (pp) REVERT: Z 487 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7703 (ppp) REVERT: Z 520 GLU cc_start: 0.7242 (tp30) cc_final: 0.6623 (tp30) REVERT: a 20 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7588 (tm-30) REVERT: a 76 CYS cc_start: 0.9237 (p) cc_final: 0.9012 (p) REVERT: a 306 MET cc_start: 0.3742 (tmm) cc_final: 0.2937 (tmm) REVERT: a 385 CYS cc_start: 0.3088 (OUTLIER) cc_final: 0.2316 (m) REVERT: g 132 MET cc_start: 0.8084 (mmm) cc_final: 0.7650 (mmm) REVERT: g 443 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8981 (tt) REVERT: h 189 MET cc_start: 0.8860 (ppp) cc_final: 0.8645 (mmt) REVERT: h 306 TYR cc_start: 0.2592 (t80) cc_final: 0.2237 (m-10) REVERT: q 385 MET cc_start: 0.8329 (mmm) cc_final: 0.7960 (mmm) REVERT: q 526 MET cc_start: 0.5782 (ppp) cc_final: 0.5470 (tmm) REVERT: A 156 MET cc_start: 0.6993 (tpt) cc_final: 0.5751 (tpp) REVERT: A 209 MET cc_start: 0.5225 (ppp) cc_final: 0.5018 (pmm) REVERT: A 225 MET cc_start: 0.1080 (OUTLIER) cc_final: 0.0321 (tmm) REVERT: G 218 MET cc_start: -0.1126 (mmt) cc_final: -0.1903 (mtm) REVERT: H 109 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8904 (tttt) REVERT: H 382 MET cc_start: -0.1753 (mtt) cc_final: -0.2684 (tpt) REVERT: Q 311 MET cc_start: 0.0276 (pmm) cc_final: -0.0192 (pmm) REVERT: B 488 MET cc_start: 0.7973 (mmp) cc_final: 0.7740 (mmt) REVERT: D 32 GLN cc_start: 0.7829 (pt0) cc_final: 0.7445 (pm20) REVERT: D 35 PHE cc_start: 0.8199 (m-80) cc_final: 0.7416 (m-80) REVERT: D 57 MET cc_start: 0.5468 (tpt) cc_final: 0.5196 (tpt) REVERT: D 78 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9027 (mm) REVERT: D 122 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8637 (pttt) REVERT: D 192 MET cc_start: 0.1692 (mpp) cc_final: 0.0962 (mpp) REVERT: D 450 CYS cc_start: 0.8409 (m) cc_final: 0.7846 (t) REVERT: E 39 MET cc_start: 0.8693 (tmm) cc_final: 0.8343 (tmm) REVERT: E 42 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8572 (mmmt) REVERT: b 48 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8142 (mtm) REVERT: b 275 MET cc_start: 0.6230 (tpt) cc_final: 0.5852 (tpt) REVERT: b 416 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7784 (mm) REVERT: b 417 MET cc_start: 0.8832 (mtt) cc_final: 0.8327 (mtt) REVERT: b 480 MET cc_start: 0.8337 (ppp) cc_final: 0.8106 (ppp) REVERT: d 35 PHE cc_start: 0.8502 (m-10) cc_final: 0.8173 (m-10) REVERT: d 81 MET cc_start: 0.8621 (ptt) cc_final: 0.7861 (ppp) REVERT: e 199 MET cc_start: 0.1358 (mpp) cc_final: 0.0840 (tmm) REVERT: e 239 MET cc_start: 0.2253 (tpt) cc_final: 0.1577 (ttt) REVERT: e 448 MET cc_start: 0.7333 (mmm) cc_final: 0.6627 (mmm) REVERT: e 449 ARG cc_start: 0.7156 (mtt90) cc_final: 0.5941 (mmt180) REVERT: e 460 MET cc_start: 0.8462 (tpt) cc_final: 0.8169 (tpt) REVERT: e 523 MET cc_start: 0.8918 (mmp) cc_final: 0.8585 (mmt) outliers start: 116 outliers final: 81 residues processed: 516 average time/residue: 0.5292 time to fit residues: 481.3176 Evaluate side-chains 512 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 422 time to evaluate : 5.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 99 ILE Chi-restraints excluded: chain z residue 101 GLU Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 444 LEU Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain Z residue 518 VAL Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 446 LEU Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain g residue 46 MET Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 197 TYR Chi-restraints excluded: chain g residue 394 MET Chi-restraints excluded: chain g residue 443 LEU Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 481 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 376 VAL Chi-restraints excluded: chain q residue 429 THR Chi-restraints excluded: chain q residue 458 VAL Chi-restraints excluded: chain q residue 471 HIS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 231 TYR Chi-restraints excluded: chain G residue 428 MET Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 442 LEU Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 118 LEU Chi-restraints excluded: chain Q residue 360 VAL Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain Q residue 445 PHE Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 492 MET Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain b residue 9 VAL Chi-restraints excluded: chain b residue 48 MET Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 120 CYS Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 529 ILE Chi-restraints excluded: chain d residue 533 ASP Chi-restraints excluded: chain e residue 80 MET Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain e residue 457 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 473 optimal weight: 40.0000 chunk 762 optimal weight: 0.9980 chunk 465 optimal weight: 0.0170 chunk 361 optimal weight: 7.9990 chunk 530 optimal weight: 6.9990 chunk 799 optimal weight: 1.9990 chunk 736 optimal weight: 9.9990 chunk 637 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 492 optimal weight: 5.9990 chunk 390 optimal weight: 2.9990 overall best weight: 0.8218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 319 ASN ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 32 ASN ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN D 406 HIS ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 62920 Z= 0.174 Angle : 0.679 14.329 84983 Z= 0.327 Chirality : 0.044 0.405 10168 Planarity : 0.004 0.078 10833 Dihedral : 7.273 162.710 8763 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 1.11 % Allowed : 18.60 % Favored : 80.29 % 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: -0.06 (0.10), residues: 8047 helix: 1.23 (0.08), residues: 4127 sheet: -1.45 (0.22), residues: 601 loop : -1.40 (0.11), residues: 3319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP h 497 HIS 0.006 0.001 HIS z 218 PHE 0.030 0.001 PHE e 364 TYR 0.024 0.001 TYR h 267 ARG 0.013 0.000 ARG h 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 464 time to evaluate : 5.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 101 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7584 (mm-30) REVERT: z 196 MET cc_start: 0.7238 (ppp) cc_final: 0.6474 (ppp) REVERT: z 326 LEU cc_start: 0.8502 (pp) cc_final: 0.8175 (pp) REVERT: Z 86 ASP cc_start: 0.8586 (m-30) cc_final: 0.8297 (m-30) REVERT: Z 487 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7624 (ppp) REVERT: Z 520 GLU cc_start: 0.6948 (tp30) cc_final: 0.6395 (tp30) REVERT: a 20 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7528 (tm-30) REVERT: a 306 MET cc_start: 0.3965 (tmm) cc_final: 0.3228 (tmm) REVERT: a 385 CYS cc_start: 0.3093 (OUTLIER) cc_final: 0.2420 (m) REVERT: a 408 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8373 (t) REVERT: g 132 MET cc_start: 0.7674 (mmm) cc_final: 0.7245 (mmm) REVERT: g 184 PHE cc_start: 0.7436 (m-80) cc_final: 0.6712 (m-80) REVERT: g 228 MET cc_start: 0.2149 (ppp) cc_final: 0.0824 (ppp) REVERT: h 188 MET cc_start: 0.7560 (ptt) cc_final: 0.7247 (ptt) REVERT: h 189 MET cc_start: 0.8802 (ppp) cc_final: 0.8562 (mmt) REVERT: h 306 TYR cc_start: 0.2546 (t80) cc_final: 0.2152 (m-10) REVERT: q 385 MET cc_start: 0.8459 (mmm) cc_final: 0.8151 (mmm) REVERT: q 526 MET cc_start: 0.5676 (ppp) cc_final: 0.5242 (tmm) REVERT: A 156 MET cc_start: 0.6967 (tpt) cc_final: 0.5690 (tpp) REVERT: A 209 MET cc_start: 0.5446 (ppp) cc_final: 0.5204 (pmm) REVERT: A 225 MET cc_start: 0.0660 (OUTLIER) cc_final: -0.0085 (tmm) REVERT: G 218 MET cc_start: -0.1008 (mmt) cc_final: -0.2053 (mtm) REVERT: G 394 MET cc_start: 0.7034 (mmt) cc_final: 0.6115 (mmt) REVERT: H 160 MET cc_start: 0.6308 (mmm) cc_final: 0.5806 (mmt) REVERT: H 382 MET cc_start: -0.1787 (mtt) cc_final: -0.2739 (tpt) REVERT: Q 300 MET cc_start: 0.4979 (ppp) cc_final: 0.4368 (ppp) REVERT: Q 311 MET cc_start: 0.0089 (pmm) cc_final: -0.0336 (pmm) REVERT: D 35 PHE cc_start: 0.8149 (m-80) cc_final: 0.7365 (m-80) REVERT: D 57 MET cc_start: 0.5429 (tpt) cc_final: 0.5079 (tpt) REVERT: D 60 MET cc_start: -0.3541 (tpt) cc_final: -0.6118 (pmm) REVERT: D 78 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8952 (mm) REVERT: D 122 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8499 (pttt) REVERT: D 192 MET cc_start: 0.1182 (mpp) cc_final: 0.0638 (mpp) REVERT: D 446 MET cc_start: 0.7833 (tpt) cc_final: 0.7582 (mmm) REVERT: E 39 MET cc_start: 0.8651 (tmm) cc_final: 0.8355 (tmm) REVERT: E 42 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8504 (mmmt) REVERT: b 48 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8041 (mtm) REVERT: b 275 MET cc_start: 0.6156 (tpt) cc_final: 0.5797 (tpp) REVERT: b 310 MET cc_start: 0.1100 (mpp) cc_final: 0.0823 (mpp) REVERT: b 416 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7727 (mm) REVERT: b 417 MET cc_start: 0.8709 (mtt) cc_final: 0.8195 (mtt) REVERT: b 480 MET cc_start: 0.8378 (ppp) cc_final: 0.8161 (ppp) REVERT: d 35 PHE cc_start: 0.8530 (m-10) cc_final: 0.8187 (m-10) REVERT: d 81 MET cc_start: 0.8730 (ptt) cc_final: 0.8092 (ppp) REVERT: e 199 MET cc_start: 0.1462 (mpp) cc_final: 0.1024 (tmm) REVERT: e 239 MET cc_start: 0.2263 (tpt) cc_final: 0.1584 (ttt) REVERT: e 288 MET cc_start: 0.3597 (mmt) cc_final: 0.3062 (ttt) REVERT: e 448 MET cc_start: 0.7051 (mmm) cc_final: 0.6159 (mmm) REVERT: e 449 ARG cc_start: 0.6916 (mtt90) cc_final: 0.5900 (mmt180) REVERT: e 501 MET cc_start: 0.7998 (mmm) cc_final: 0.7646 (tpp) outliers start: 75 outliers final: 54 residues processed: 513 average time/residue: 0.5344 time to fit residues: 482.8127 Evaluate side-chains 504 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 442 time to evaluate : 5.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 101 GLU Chi-restraints excluded: chain z residue 148 LEU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 444 LEU Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 408 VAL Chi-restraints excluded: chain g residue 197 TYR Chi-restraints excluded: chain g residue 394 MET Chi-restraints excluded: chain h residue 481 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 376 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 458 VAL Chi-restraints excluded: chain q residue 471 HIS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 231 TYR Chi-restraints excluded: chain H residue 390 HIS Chi-restraints excluded: chain H residue 442 LEU Chi-restraints excluded: chain H residue 521 LYS Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 445 PHE Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 492 MET Chi-restraints excluded: chain Q residue 526 MET Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain b residue 48 MET Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 448 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 120 CYS Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 529 ILE Chi-restraints excluded: chain d residue 533 ASP Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain e residue 440 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 506 optimal weight: 40.0000 chunk 678 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 587 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 177 optimal weight: 40.0000 chunk 638 optimal weight: 0.9990 chunk 267 optimal weight: 40.0000 chunk 655 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 300 GLN ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 461 ASN ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.119352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.085733 restraints weight = 324734.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.086215 restraints weight = 211628.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.086535 restraints weight = 130538.037| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 62920 Z= 0.263 Angle : 0.706 14.674 84983 Z= 0.344 Chirality : 0.045 0.360 10168 Planarity : 0.004 0.081 10833 Dihedral : 7.337 162.409 8763 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 1.19 % Allowed : 18.85 % Favored : 79.96 % 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: -0.18 (0.10), residues: 8047 helix: 1.11 (0.08), residues: 4138 sheet: -1.54 (0.21), residues: 607 loop : -1.44 (0.11), residues: 3302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 495 HIS 0.008 0.001 HIS q 59 PHE 0.031 0.001 PHE d 137 TYR 0.023 0.001 TYR h 267 ARG 0.017 0.000 ARG h 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10629.77 seconds wall clock time: 190 minutes 6.03 seconds (11406.03 seconds total)