Starting phenix.real_space_refine on Fri Feb 16 06:19:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi9_4553/02_2024/6qi9_4553_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi9_4553/02_2024/6qi9_4553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi9_4553/02_2024/6qi9_4553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi9_4553/02_2024/6qi9_4553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi9_4553/02_2024/6qi9_4553_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi9_4553/02_2024/6qi9_4553_updated.pdb" } resolution = 4.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 10 5.49 5 S 68 5.16 5 C 9112 2.51 5 N 2538 2.21 5 O 2831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "C GLU 388": "OE1" <-> "OE2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D ARG 330": "NH1" <-> "NH2" Residue "D ARG 353": "NH1" <-> "NH2" Residue "D GLU 381": "OE1" <-> "OE2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E GLU 286": "OE1" <-> "OE2" Residue "E GLU 307": "OE1" <-> "OE2" Residue "E ARG 330": "NH1" <-> "NH2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F GLU 282": "OE1" <-> "OE2" Residue "F GLU 290": "OE1" <-> "OE2" Residue "F GLU 300": "OE1" <-> "OE2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "F GLU 317": "OE1" <-> "OE2" Residue "F ARG 392": "NH1" <-> "NH2" Residue "F ARG 400": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14559 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2423 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2369 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 10, 'TRANS': 299} Chain breaks: 2 Chain: "C" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2401 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 305} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2084 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2585 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2562 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 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: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" 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: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.49, per 1000 atoms: 0.51 Number of scatterers: 14559 At special positions: 0 Unit cell: (135.89, 129.47, 80.25, 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 68 16.00 P 10 15.00 O 2831 8.00 N 2538 7.00 C 9112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.7 seconds 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 11 sheets defined 44.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.615A pdb=" N CYS A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.651A pdb=" N ILE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.961A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 removed outlier: 3.906A pdb=" N ASP A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 246' Processing helix chain 'A' and resid 273 through 289 removed outlier: 3.509A pdb=" N ARG A 276 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY A 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU A 278 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 279 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 281 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 283 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.909A pdb=" N HIS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 352 through 355 No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 370 through 381 removed outlier: 4.027A pdb=" N ILE A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.527A pdb=" N ASN A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 410 through 420 removed outlier: 4.139A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.683A pdb=" N GLU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 removed outlier: 3.623A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 76 through 86 removed outlier: 4.193A pdb=" N ALA B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 116 removed outlier: 3.599A pdb=" N ASN B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 275 through 287 removed outlier: 4.459A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 309 through 318 removed outlier: 3.982A pdb=" N THR B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 368 through 382 removed outlier: 4.071A pdb=" N GLN B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 374 " --> pdb=" O GLU B 370 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 375 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 400 removed outlier: 3.513A pdb=" N GLY B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.887A pdb=" N GLN B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Proline residue: B 412 - end of helix removed outlier: 3.875A pdb=" N ASN B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 430 No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 433 through 436 No H-bonds generated for 'chain 'B' and resid 433 through 436' Processing helix chain 'B' and resid 441 through 451 Processing helix chain 'C' and resid 15 through 18 Processing helix chain 'C' and resid 43 through 57 removed outlier: 4.507A pdb=" N GLU C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA C 48 " --> pdb=" O ASN C 44 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 85 removed outlier: 3.660A pdb=" N ALA C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 118 removed outlier: 3.976A pdb=" N VAL C 111 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N MET C 113 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG C 117 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 280 through 289 removed outlier: 4.594A pdb=" N LYS C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 309 through 318 removed outlier: 4.150A pdb=" N THR C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.991A pdb=" N ASP C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 357' Processing helix chain 'C' and resid 368 through 381 removed outlier: 3.651A pdb=" N LYS C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C 374 " --> pdb=" O GLU C 370 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE C 375 " --> pdb=" O MET C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 400 removed outlier: 4.019A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.824A pdb=" N GLN C 408 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 409 " --> pdb=" O TYR C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 419 removed outlier: 3.565A pdb=" N LEU C 415 " --> pdb=" O THR C 411 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU C 416 " --> pdb=" O PRO C 412 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 419' Processing helix chain 'C' and resid 427 through 435 removed outlier: 3.638A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 449 removed outlier: 3.652A pdb=" N LEU C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 65 removed outlier: 4.122A pdb=" N MET D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 removed outlier: 3.691A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 118 No H-bonds generated for 'chain 'D' and resid 115 through 118' Processing helix chain 'D' and resid 121 through 125 Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 272 through 286 removed outlier: 3.609A pdb=" N GLN D 275 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE D 276 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASN D 277 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 281 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU D 282 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ARG D 284 " --> pdb=" O ALA D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.544A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 348 through 351 No H-bonds generated for 'chain 'D' and resid 348 through 351' Processing helix chain 'D' and resid 364 through 376 Processing helix chain 'D' and resid 384 through 394 removed outlier: 3.960A pdb=" N THR D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 391 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG D 392 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 393 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 415 removed outlier: 3.594A pdb=" N LEU D 405 " --> pdb=" O TYR D 401 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 411 " --> pdb=" O THR D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 426 No H-bonds generated for 'chain 'D' and resid 423 through 426' Processing helix chain 'D' and resid 436 through 450 removed outlier: 3.650A pdb=" N GLN D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP D 448 " --> pdb=" O LYS D 444 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE D 450 " --> pdb=" O TYR D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 65 removed outlier: 3.969A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 94 removed outlier: 4.102A pdb=" N GLY E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 117 through 126 removed outlier: 3.725A pdb=" N ARG E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 removed outlier: 3.592A pdb=" N ASP E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN E 251 " --> pdb=" O ILE E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 270 through 283 removed outlier: 3.859A pdb=" N ALA E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 303 No H-bonds generated for 'chain 'E' and resid 301 through 303' Processing helix chain 'E' and resid 306 through 313 removed outlier: 3.683A pdb=" N SER E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'E' and resid 348 through 350 No H-bonds generated for 'chain 'E' and resid 348 through 350' Processing helix chain 'E' and resid 365 through 376 removed outlier: 3.746A pdb=" N ILE E 373 " --> pdb=" O GLN E 369 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 394 removed outlier: 3.845A pdb=" N THR E 391 " --> pdb=" O TYR E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.596A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 432 removed outlier: 4.897A pdb=" N SER E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 451 removed outlier: 3.981A pdb=" N GLN E 441 " --> pdb=" O SER E 437 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS E 444 " --> pdb=" O THR E 440 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 64 removed outlier: 3.769A pdb=" N ALA F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 94 removed outlier: 3.986A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN F 92 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA F 93 " --> pdb=" O GLY F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 108 Processing helix chain 'F' and resid 115 through 126 removed outlier: 3.655A pdb=" N LEU F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 249 Processing helix chain 'F' and resid 259 through 262 Processing helix chain 'F' and resid 271 through 282 removed outlier: 3.772A pdb=" N GLN F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F 280 " --> pdb=" O ILE F 276 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.998A pdb=" N SER F 310 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU F 317 " --> pdb=" O ASN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 353 removed outlier: 4.674A pdb=" N ARG F 353 " --> pdb=" O ASP F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 378 removed outlier: 3.505A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG F 372 " --> pdb=" O LYS F 368 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 373 " --> pdb=" O GLN F 369 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG F 374 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 396 removed outlier: 3.708A pdb=" N THR F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 416 removed outlier: 3.807A pdb=" N ILE F 403 " --> pdb=" O LEU F 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU F 405 " --> pdb=" O TYR F 401 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG F 414 " --> pdb=" O SER F 410 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS F 415 " --> pdb=" O LEU F 411 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG F 416 " --> pdb=" O VAL F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 432 removed outlier: 3.523A pdb=" N ARG F 428 " --> pdb=" O ASP F 424 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 451 removed outlier: 3.977A pdb=" N MET F 443 " --> pdb=" O SER F 439 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 93 through 96 removed outlier: 7.068A pdb=" N VAL A 298 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N MET A 96 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE A 300 " --> pdb=" O MET A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 358 through 362 removed outlier: 6.547A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 66 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS B 94 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 300 " --> pdb=" O CYS B 94 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 335 through 337 Processing sheet with id= D, first strand: chain 'C' and resid 358 through 363 removed outlier: 6.579A pdb=" N ALA C 65 " --> pdb=" O MET C 359 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE C 361 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 67 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR C 363 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA C 69 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 328 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 73 through 76 removed outlier: 6.451A pdb=" N LEU D 355 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA D 76 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL D 357 " --> pdb=" O ALA D 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.754A pdb=" N VAL D 295 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE D 103 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE D 297 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL D 323 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ILE D 298 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE D 325 " --> pdb=" O ILE D 298 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 354 through 357 removed outlier: 6.258A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR E 101 " --> pdb=" O VAL E 295 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 127 through 129 Processing sheet with id= I, first strand: chain 'E' and resid 332 through 334 Processing sheet with id= J, first strand: chain 'F' and resid 354 through 358 removed outlier: 6.523A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 332 through 334 removed outlier: 3.590A pdb=" N THR F 333 " --> pdb=" O SER F 342 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 951 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: 3.44 Time building geometry restraints manager: 5.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4880 1.34 - 1.46: 2501 1.46 - 1.58: 7226 1.58 - 1.69: 15 1.69 - 1.81: 118 Bond restraints: 14740 Sorted by residual: bond pdb=" C VAL F 10 " pdb=" N PRO F 11 " ideal model delta sigma weight residual 1.332 1.365 -0.033 8.20e-03 1.49e+04 1.59e+01 bond pdb=" N THR F 419 " pdb=" CA THR F 419 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.01e+00 bond pdb=" C THR F 359 " pdb=" N THR F 360 " ideal model delta sigma weight residual 1.329 1.302 0.027 1.21e-02 6.83e+03 4.91e+00 bond pdb=" N THR E 419 " pdb=" CA THR E 419 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.62e+00 bond pdb=" CA GLU C 5 " pdb=" CB GLU C 5 " ideal model delta sigma weight residual 1.528 1.559 -0.030 1.67e-02 3.59e+03 3.29e+00 ... (remaining 14735 not shown) Histogram of bond angle deviations from ideal: 98.27 - 105.86: 304 105.86 - 113.46: 8501 113.46 - 121.05: 7064 121.05 - 128.64: 3979 128.64 - 136.24: 62 Bond angle restraints: 19910 Sorted by residual: angle pdb=" C ILE F 306 " pdb=" CA ILE F 306 " pdb=" CB ILE F 306 " ideal model delta sigma weight residual 111.29 103.31 7.98 1.64e+00 3.72e-01 2.37e+01 angle pdb=" C ILE E 291 " pdb=" N ILE E 292 " pdb=" CA ILE E 292 " ideal model delta sigma weight residual 123.33 119.37 3.96 8.70e-01 1.32e+00 2.07e+01 angle pdb=" C GLU E 378 " pdb=" N ASP E 379 " pdb=" CA ASP E 379 " ideal model delta sigma weight residual 122.46 128.83 -6.37 1.41e+00 5.03e-01 2.04e+01 angle pdb=" N ASP D 379 " pdb=" CA ASP D 379 " pdb=" C ASP D 379 " ideal model delta sigma weight residual 111.24 117.31 -6.07 1.38e+00 5.25e-01 1.93e+01 angle pdb=" C ILE F 13 " pdb=" N ARG F 14 " pdb=" CA ARG F 14 " ideal model delta sigma weight residual 121.19 128.11 -6.92 1.59e+00 3.96e-01 1.90e+01 ... (remaining 19905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 8295 23.42 - 46.84: 670 46.84 - 70.26: 81 70.26 - 93.68: 20 93.68 - 117.10: 6 Dihedral angle restraints: 9072 sinusoidal: 3677 harmonic: 5395 Sorted by residual: dihedral pdb=" O1B ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PB ADP B 501 " pdb=" PA ADP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 -177.10 117.10 1 2.00e+01 2.50e-03 3.49e+01 dihedral pdb=" CA VAL E 10 " pdb=" C VAL E 10 " pdb=" N PRO E 11 " pdb=" CA PRO E 11 " ideal model delta harmonic sigma weight residual 180.00 150.82 29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ARG E 416 " pdb=" C ARG E 416 " pdb=" N LYS E 417 " pdb=" CA LYS E 417 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 9069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1965 0.077 - 0.154: 360 0.154 - 0.230: 33 0.230 - 0.307: 3 0.307 - 0.384: 1 Chirality restraints: 2362 Sorted by residual: chirality pdb=" CB ILE D 332 " pdb=" CA ILE D 332 " pdb=" CG1 ILE D 332 " pdb=" CG2 ILE D 332 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB ILE D 298 " pdb=" CA ILE D 298 " pdb=" CG1 ILE D 298 " pdb=" CG2 ILE D 298 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA THR C 10 " pdb=" N THR C 10 " pdb=" C THR C 10 " pdb=" CB THR C 10 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2359 not shown) Planarity restraints: 2538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 346 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO B 347 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 347 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 347 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 292 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO D 293 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 293 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 293 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 10 " 0.041 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO E 11 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 11 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 11 " 0.035 5.00e-02 4.00e+02 ... (remaining 2535 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 241 2.57 - 3.16: 11945 3.16 - 3.74: 23098 3.74 - 4.32: 30282 4.32 - 4.90: 46787 Nonbonded interactions: 112353 Sorted by model distance: nonbonded pdb=" OD2 ASP E 435 " pdb=" NH1 ARG E 438 " model vdw 1.993 2.520 nonbonded pdb=" OG SER E 383 " pdb=" OD1 ASP E 385 " model vdw 2.230 2.440 nonbonded pdb=" OG1 THR A 104 " pdb=" OG1 THR F 116 " model vdw 2.260 2.440 nonbonded pdb=" O SER E 339 " pdb=" OG SER E 339 " model vdw 2.261 2.440 nonbonded pdb=" O SER A 17 " pdb=" OG SER A 17 " model vdw 2.265 2.440 ... (remaining 112348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 120 or resid 239 through 248 or (resid 274 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 thr \ ough 452 or resid 501)) selection = (chain 'B' and (resid 2 through 120 or resid 239 through 248 or (resid 274 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 thr \ ough 452 or resid 501)) selection = (chain 'C' and (resid 2 through 120 or resid 239 through 248 or resid 274 throug \ h 452 or resid 501)) } ncs_group { reference = (chain 'E' and (resid 8 through 127 or resid 129 or resid 243 through 269 or (re \ sid 270 and (name N or name CA or name C or name O or name CB )) or resid 271 th \ rough 282 or (resid 283 and (name N or name CA or name C or name O or name CB )) \ or resid 284 through 453 or resid 501)) selection = (chain 'F' and (resid 8 through 127 or resid 242 through 453 or resid 501)) } 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=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.390 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.540 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.007 0.068 14740 Z= 0.452 Angle : 1.088 8.955 19910 Z= 0.622 Chirality : 0.059 0.384 2362 Planarity : 0.007 0.067 2538 Dihedral : 17.097 117.097 5580 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.39 % Allowed : 13.56 % Favored : 86.05 % 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: -4.28 (0.16), residues: 1847 helix: -3.86 (0.11), residues: 717 sheet: -1.70 (0.36), residues: 196 loop : -2.15 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 283 HIS 0.010 0.002 HIS A 18 PHE 0.026 0.003 PHE B 300 TYR 0.025 0.003 TYR B 314 ARG 0.016 0.001 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 314 time to evaluate : 1.656 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: A 286 TYR cc_start: 0.8320 (m-10) cc_final: 0.7745 (m-10) REVERT: A 300 PHE cc_start: 0.8661 (t80) cc_final: 0.8430 (t80) REVERT: A 303 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6470 (tm-30) REVERT: A 369 GLN cc_start: 0.9292 (tt0) cc_final: 0.8655 (tm-30) REVERT: A 373 GLN cc_start: 0.9640 (mp10) cc_final: 0.9307 (mp10) REVERT: B 53 VAL cc_start: 0.9067 (t) cc_final: 0.8847 (t) REVERT: B 61 MET cc_start: 0.9096 (tpp) cc_final: 0.8896 (tpp) REVERT: B 66 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7671 (p) REVERT: B 337 VAL cc_start: 0.8888 (t) cc_final: 0.8661 (p) REVERT: C 112 LEU cc_start: 0.9298 (mt) cc_final: 0.9055 (mm) REVERT: C 317 ARG cc_start: 0.9080 (tmm160) cc_final: 0.8478 (ttp80) REVERT: C 371 MET cc_start: 0.9116 (ttm) cc_final: 0.8447 (mtp) REVERT: C 384 ILE cc_start: 0.9590 (mt) cc_final: 0.9345 (mm) REVERT: D 117 GLU cc_start: 0.9177 (tp30) cc_final: 0.8907 (tp30) REVERT: D 125 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7457 (tpt90) REVERT: D 311 PHE cc_start: 0.9395 (t80) cc_final: 0.8735 (t80) REVERT: D 320 MET cc_start: 0.3982 (mtt) cc_final: 0.2871 (ptt) REVERT: D 326 MET cc_start: 0.7138 (mmp) cc_final: 0.6478 (mmp) REVERT: E 25 HIS cc_start: 0.8544 (m-70) cc_final: 0.8172 (m90) REVERT: E 324 LEU cc_start: 0.8715 (tp) cc_final: 0.8172 (tp) REVERT: E 404 GLN cc_start: 0.8361 (tt0) cc_final: 0.8024 (tm-30) REVERT: E 430 TYR cc_start: 0.9079 (t80) cc_final: 0.8874 (t80) REVERT: F 29 ARG cc_start: 0.9196 (mpp80) cc_final: 0.8982 (mpt-90) REVERT: F 62 MET cc_start: 0.9360 (mtp) cc_final: 0.9089 (mtp) REVERT: F 67 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8792 (mmmt) REVERT: F 317 GLU cc_start: 0.8801 (tp30) cc_final: 0.8382 (tp30) REVERT: F 326 MET cc_start: 0.9181 (ptp) cc_final: 0.8876 (mtm) outliers start: 6 outliers final: 1 residues processed: 320 average time/residue: 0.3072 time to fit residues: 136.4283 Evaluate side-chains 214 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 212 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS B 42 GLN B 85 GLN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN B 385 ASN B 393 HIS B 451 GLN C 42 GLN C 115 ASN C 247 ASN C 348 HIS ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN F 453 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14740 Z= 0.188 Angle : 0.659 10.263 19910 Z= 0.329 Chirality : 0.044 0.188 2362 Planarity : 0.005 0.056 2538 Dihedral : 8.995 110.114 2070 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.13 % Allowed : 5.53 % Favored : 94.34 % 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: -3.34 (0.18), residues: 1847 helix: -2.47 (0.15), residues: 822 sheet: -1.21 (0.37), residues: 193 loop : -2.05 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 283 HIS 0.003 0.001 HIS F 25 PHE 0.021 0.001 PHE D 309 TYR 0.023 0.002 TYR E 387 ARG 0.006 0.000 ARG F 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 295 time to evaluate : 1.800 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: A 64 ARG cc_start: 0.7465 (mtt180) cc_final: 0.6789 (mmm-85) REVERT: A 94 CYS cc_start: 0.8185 (t) cc_final: 0.7922 (t) REVERT: A 106 ILE cc_start: 0.8956 (tt) cc_final: 0.8752 (tt) REVERT: A 115 ASN cc_start: 0.9272 (m-40) cc_final: 0.9061 (m-40) REVERT: A 300 PHE cc_start: 0.8507 (t80) cc_final: 0.8181 (t80) REVERT: A 369 GLN cc_start: 0.9354 (tt0) cc_final: 0.8634 (tm-30) REVERT: A 373 GLN cc_start: 0.9576 (mp10) cc_final: 0.9202 (mp10) REVERT: B 44 ASN cc_start: 0.9014 (t0) cc_final: 0.8206 (t0) REVERT: B 61 MET cc_start: 0.9075 (tpp) cc_final: 0.8779 (tpp) REVERT: B 359 MET cc_start: 0.8058 (mtm) cc_final: 0.7855 (mpp) REVERT: B 364 MET cc_start: 0.8324 (mmp) cc_final: 0.8029 (mmp) REVERT: B 420 ASN cc_start: 0.8867 (m-40) cc_final: 0.8532 (t0) REVERT: C 113 MET cc_start: 0.9066 (tpt) cc_final: 0.8730 (ttm) REVERT: C 317 ARG cc_start: 0.8854 (tmm160) cc_final: 0.8246 (ttp80) REVERT: C 371 MET cc_start: 0.9168 (ttm) cc_final: 0.8660 (mtm) REVERT: C 384 ILE cc_start: 0.9545 (mt) cc_final: 0.9279 (mm) REVERT: C 410 LEU cc_start: 0.9317 (mt) cc_final: 0.8962 (tt) REVERT: C 428 GLU cc_start: 0.9002 (pt0) cc_final: 0.8747 (pm20) REVERT: D 117 GLU cc_start: 0.9183 (tp30) cc_final: 0.8910 (tp30) REVERT: D 298 ILE cc_start: 0.6372 (tt) cc_final: 0.6091 (mp) REVERT: D 299 ASP cc_start: 0.8728 (m-30) cc_final: 0.8144 (t0) REVERT: D 309 PHE cc_start: 0.6431 (m-80) cc_final: 0.6099 (m-10) REVERT: D 311 PHE cc_start: 0.9380 (t80) cc_final: 0.8743 (t80) REVERT: D 320 MET cc_start: 0.4358 (mtt) cc_final: 0.3161 (ptt) REVERT: D 326 MET cc_start: 0.6874 (mmp) cc_final: 0.6574 (mmp) REVERT: D 336 ARG cc_start: 0.7585 (mmm160) cc_final: 0.6512 (mtt-85) REVERT: D 351 LEU cc_start: 0.7637 (mt) cc_final: 0.7275 (mt) REVERT: D 414 ARG cc_start: 0.9351 (mtp-110) cc_final: 0.9062 (ttp80) REVERT: D 446 TYR cc_start: 0.8710 (t80) cc_final: 0.8384 (m-80) REVERT: E 62 MET cc_start: 0.7647 (tpp) cc_final: 0.7019 (tpp) REVERT: E 90 MET cc_start: 0.8897 (mmm) cc_final: 0.8380 (mmm) REVERT: E 299 ASP cc_start: 0.7952 (t0) cc_final: 0.7594 (t0) REVERT: E 324 LEU cc_start: 0.8473 (tp) cc_final: 0.8142 (tp) REVERT: E 404 GLN cc_start: 0.8523 (tt0) cc_final: 0.8098 (tm-30) REVERT: F 62 MET cc_start: 0.9112 (mtp) cc_final: 0.8777 (mtp) REVERT: F 73 VAL cc_start: 0.9319 (t) cc_final: 0.9119 (t) REVERT: F 74 LEU cc_start: 0.8909 (tp) cc_final: 0.8640 (tp) REVERT: F 90 MET cc_start: 0.9086 (ttt) cc_final: 0.8814 (tpp) REVERT: F 119 LEU cc_start: 0.9243 (mt) cc_final: 0.8931 (mt) REVERT: F 317 GLU cc_start: 0.8805 (tp30) cc_final: 0.8583 (tp30) REVERT: F 326 MET cc_start: 0.9309 (ptp) cc_final: 0.8529 (mtm) outliers start: 2 outliers final: 0 residues processed: 297 average time/residue: 0.2625 time to fit residues: 113.0284 Evaluate side-chains 217 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 46 optimal weight: 0.2980 chunk 168 optimal weight: 0.1980 chunk 181 optimal weight: 0.0270 chunk 149 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 135 optimal weight: 10.0000 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 HIS C 247 ASN C 305 HIS ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 GLN F 25 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14740 Z= 0.148 Angle : 0.623 8.457 19910 Z= 0.303 Chirality : 0.044 0.320 2362 Planarity : 0.004 0.045 2538 Dihedral : 8.464 109.840 2070 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.18), residues: 1847 helix: -1.88 (0.16), residues: 807 sheet: -0.97 (0.38), residues: 189 loop : -1.87 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 283 HIS 0.002 0.001 HIS C 305 PHE 0.017 0.001 PHE D 309 TYR 0.018 0.001 TYR B 405 ARG 0.005 0.000 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.648 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: A 64 ARG cc_start: 0.7556 (mtt180) cc_final: 0.6724 (mmm-85) REVERT: A 286 TYR cc_start: 0.8436 (m-10) cc_final: 0.7991 (m-80) REVERT: A 300 PHE cc_start: 0.8513 (t80) cc_final: 0.8190 (t80) REVERT: A 301 VAL cc_start: 0.8781 (t) cc_final: 0.8470 (t) REVERT: A 369 GLN cc_start: 0.9328 (tt0) cc_final: 0.8495 (tm-30) REVERT: A 373 GLN cc_start: 0.9582 (mp10) cc_final: 0.9150 (mp10) REVERT: A 435 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8360 (pt0) REVERT: B 44 ASN cc_start: 0.9007 (t0) cc_final: 0.8309 (t0) REVERT: B 420 ASN cc_start: 0.8926 (m-40) cc_final: 0.8513 (t0) REVERT: C 86 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8455 (mp0) REVERT: C 96 MET cc_start: 0.9342 (ppp) cc_final: 0.8805 (ppp) REVERT: C 113 MET cc_start: 0.9093 (tpt) cc_final: 0.8701 (ttm) REVERT: C 371 MET cc_start: 0.9025 (ttm) cc_final: 0.8789 (tmm) REVERT: C 384 ILE cc_start: 0.9495 (mt) cc_final: 0.9279 (mm) REVERT: C 410 LEU cc_start: 0.9355 (mt) cc_final: 0.9006 (tt) REVERT: C 428 GLU cc_start: 0.8857 (pt0) cc_final: 0.8587 (pm20) REVERT: D 68 ILE cc_start: 0.7306 (tp) cc_final: 0.7049 (tp) REVERT: D 113 MET cc_start: 0.6539 (ptt) cc_final: 0.6189 (ppp) REVERT: D 117 GLU cc_start: 0.9224 (tp30) cc_final: 0.8257 (mt-10) REVERT: D 298 ILE cc_start: 0.6482 (tt) cc_final: 0.5957 (mp) REVERT: D 299 ASP cc_start: 0.8530 (m-30) cc_final: 0.8012 (t0) REVERT: D 301 VAL cc_start: 0.7119 (t) cc_final: 0.6864 (m) REVERT: D 311 PHE cc_start: 0.9362 (t80) cc_final: 0.8752 (t80) REVERT: D 320 MET cc_start: 0.4277 (mtt) cc_final: 0.3053 (ptt) REVERT: D 326 MET cc_start: 0.6587 (mmp) cc_final: 0.5257 (mmp) REVERT: D 351 LEU cc_start: 0.7755 (mt) cc_final: 0.7461 (mt) REVERT: D 363 SER cc_start: 0.7765 (t) cc_final: 0.7522 (p) REVERT: D 414 ARG cc_start: 0.9307 (mtp-110) cc_final: 0.8943 (ttp80) REVERT: D 415 LYS cc_start: 0.8608 (tppp) cc_final: 0.7983 (tppt) REVERT: D 446 TYR cc_start: 0.8676 (t80) cc_final: 0.8367 (m-80) REVERT: E 61 GLU cc_start: 0.8589 (pt0) cc_final: 0.7685 (tt0) REVERT: E 62 MET cc_start: 0.7666 (tpp) cc_final: 0.6531 (tpp) REVERT: E 68 ILE cc_start: 0.9253 (tp) cc_final: 0.8974 (tp) REVERT: E 113 MET cc_start: 0.9057 (ttp) cc_final: 0.8780 (ppp) REVERT: E 297 PHE cc_start: 0.9198 (t80) cc_final: 0.8787 (t80) REVERT: E 324 LEU cc_start: 0.8517 (tp) cc_final: 0.8189 (tp) REVERT: E 325 ILE cc_start: 0.8187 (mt) cc_final: 0.7920 (mt) REVERT: E 374 ARG cc_start: 0.8984 (mmm160) cc_final: 0.8423 (mmm160) REVERT: E 404 GLN cc_start: 0.8581 (tt0) cc_final: 0.8093 (tm-30) REVERT: E 427 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8469 (mmmm) REVERT: E 443 MET cc_start: 0.8896 (mmt) cc_final: 0.8459 (mmm) REVERT: E 452 PHE cc_start: 0.7248 (m-80) cc_final: 0.6773 (m-80) REVERT: F 62 MET cc_start: 0.9107 (mtp) cc_final: 0.8858 (mtp) REVERT: F 73 VAL cc_start: 0.9359 (t) cc_final: 0.9123 (t) REVERT: F 90 MET cc_start: 0.9137 (ttt) cc_final: 0.8820 (tpp) REVERT: F 113 MET cc_start: 0.7230 (ptp) cc_final: 0.6602 (ptp) REVERT: F 303 MET cc_start: 0.9160 (mmm) cc_final: 0.8847 (mpp) REVERT: F 305 ASP cc_start: 0.9127 (p0) cc_final: 0.8787 (p0) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.2674 time to fit residues: 119.2518 Evaluate side-chains 223 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.0670 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 HIS B 393 HIS C 247 ASN C 305 HIS ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14740 Z= 0.145 Angle : 0.615 9.275 19910 Z= 0.295 Chirality : 0.043 0.200 2362 Planarity : 0.004 0.054 2538 Dihedral : 8.140 109.214 2070 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.19), residues: 1847 helix: -1.37 (0.17), residues: 792 sheet: -0.93 (0.37), residues: 197 loop : -1.59 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 283 HIS 0.003 0.001 HIS B 305 PHE 0.010 0.001 PHE D 309 TYR 0.018 0.001 TYR E 442 ARG 0.011 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.754 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: A 64 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6678 (mmm-85) REVERT: A 275 LEU cc_start: 0.8564 (mt) cc_final: 0.8078 (tp) REVERT: A 286 TYR cc_start: 0.8415 (m-10) cc_final: 0.7825 (m-80) REVERT: A 300 PHE cc_start: 0.8557 (t80) cc_final: 0.8254 (t80) REVERT: A 301 VAL cc_start: 0.8762 (t) cc_final: 0.8417 (t) REVERT: A 369 GLN cc_start: 0.9316 (tt0) cc_final: 0.8821 (tm-30) REVERT: A 435 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8341 (pt0) REVERT: B 44 ASN cc_start: 0.8953 (t0) cc_final: 0.8222 (t0) REVERT: B 61 MET cc_start: 0.8464 (tpp) cc_final: 0.8215 (tpp) REVERT: B 306 MET cc_start: 0.8725 (mtm) cc_final: 0.8234 (mpp) REVERT: B 364 MET cc_start: 0.7824 (mmp) cc_final: 0.7549 (mmp) REVERT: B 420 ASN cc_start: 0.8974 (m-40) cc_final: 0.8584 (t0) REVERT: B 431 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8891 (mt-10) REVERT: C 86 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8521 (tp30) REVERT: C 96 MET cc_start: 0.9400 (ppp) cc_final: 0.8841 (ppp) REVERT: C 113 MET cc_start: 0.9087 (tpt) cc_final: 0.8740 (ttm) REVERT: C 306 MET cc_start: 0.8824 (mpp) cc_final: 0.8569 (mpp) REVERT: C 339 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7657 (ttm110) REVERT: C 371 MET cc_start: 0.9021 (ttm) cc_final: 0.8548 (mtp) REVERT: C 409 LEU cc_start: 0.9029 (mt) cc_final: 0.8732 (mp) REVERT: C 410 LEU cc_start: 0.9345 (mt) cc_final: 0.9007 (tt) REVERT: D 68 ILE cc_start: 0.7237 (tp) cc_final: 0.6995 (tp) REVERT: D 113 MET cc_start: 0.6505 (ptt) cc_final: 0.6178 (ppp) REVERT: D 117 GLU cc_start: 0.9213 (tp30) cc_final: 0.8261 (mt-10) REVERT: D 277 ASN cc_start: 0.7582 (p0) cc_final: 0.7326 (p0) REVERT: D 299 ASP cc_start: 0.8503 (m-30) cc_final: 0.8058 (t0) REVERT: D 311 PHE cc_start: 0.9397 (t80) cc_final: 0.8799 (t80) REVERT: D 320 MET cc_start: 0.4215 (mtt) cc_final: 0.2871 (ptt) REVERT: D 326 MET cc_start: 0.6537 (mmp) cc_final: 0.4647 (mmp) REVERT: D 414 ARG cc_start: 0.9296 (mtp-110) cc_final: 0.8953 (ttp80) REVERT: D 415 LYS cc_start: 0.8517 (tppp) cc_final: 0.7889 (tppt) REVERT: D 446 TYR cc_start: 0.8703 (t80) cc_final: 0.8346 (m-80) REVERT: E 61 GLU cc_start: 0.8560 (pt0) cc_final: 0.7705 (tt0) REVERT: E 62 MET cc_start: 0.7651 (tpp) cc_final: 0.6570 (tpp) REVERT: E 68 ILE cc_start: 0.9208 (tp) cc_final: 0.8997 (tp) REVERT: E 90 MET cc_start: 0.8993 (mmm) cc_final: 0.8696 (mmm) REVERT: E 297 PHE cc_start: 0.9115 (t80) cc_final: 0.8706 (t80) REVERT: E 324 LEU cc_start: 0.8549 (tp) cc_final: 0.8221 (tp) REVERT: E 326 MET cc_start: 0.8679 (mpp) cc_final: 0.8420 (mpp) REVERT: E 354 LEU cc_start: 0.8845 (mm) cc_final: 0.8627 (mm) REVERT: E 374 ARG cc_start: 0.8949 (mmm160) cc_final: 0.8355 (mmm160) REVERT: E 404 GLN cc_start: 0.8439 (tt0) cc_final: 0.8019 (tm-30) REVERT: E 427 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8514 (mmmm) REVERT: E 443 MET cc_start: 0.8961 (mmt) cc_final: 0.8560 (mmm) REVERT: E 452 PHE cc_start: 0.7258 (m-80) cc_final: 0.6776 (m-80) REVERT: F 62 MET cc_start: 0.9133 (mtp) cc_final: 0.8796 (mtp) REVERT: F 90 MET cc_start: 0.9138 (ttt) cc_final: 0.8860 (tpp) REVERT: F 113 MET cc_start: 0.7180 (ptp) cc_final: 0.6654 (ptp) REVERT: F 317 GLU cc_start: 0.8815 (tp30) cc_final: 0.8559 (tp30) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2730 time to fit residues: 119.7072 Evaluate side-chains 231 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 133 optimal weight: 0.0070 chunk 73 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 289 GLN B 393 HIS C 247 ASN C 332 ASN C 380 GLN ** D 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14740 Z= 0.218 Angle : 0.662 10.468 19910 Z= 0.325 Chirality : 0.045 0.209 2362 Planarity : 0.004 0.078 2538 Dihedral : 9.041 175.527 2070 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.19), residues: 1847 helix: -1.17 (0.17), residues: 807 sheet: -0.84 (0.38), residues: 195 loop : -1.46 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 283 HIS 0.004 0.001 HIS A 18 PHE 0.023 0.002 PHE A 93 TYR 0.016 0.001 TYR E 442 ARG 0.011 0.001 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 280 time to evaluate : 1.711 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: A 64 ARG cc_start: 0.7732 (mtt180) cc_final: 0.6768 (mmm-85) REVERT: A 286 TYR cc_start: 0.8357 (m-10) cc_final: 0.7724 (m-80) REVERT: A 300 PHE cc_start: 0.8683 (t80) cc_final: 0.8279 (t80) REVERT: A 301 VAL cc_start: 0.8842 (t) cc_final: 0.8449 (t) REVERT: A 369 GLN cc_start: 0.9326 (tt0) cc_final: 0.8742 (tm-30) REVERT: A 373 GLN cc_start: 0.9583 (mp10) cc_final: 0.9194 (mp10) REVERT: A 435 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8353 (pt0) REVERT: B 44 ASN cc_start: 0.9008 (t0) cc_final: 0.8335 (t0) REVERT: B 61 MET cc_start: 0.8877 (tpp) cc_final: 0.8557 (tpp) REVERT: B 364 MET cc_start: 0.7765 (mmp) cc_final: 0.7395 (mmp) REVERT: B 420 ASN cc_start: 0.8992 (m-40) cc_final: 0.8572 (t0) REVERT: C 86 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8506 (mp0) REVERT: C 96 MET cc_start: 0.9453 (ppp) cc_final: 0.8813 (ppp) REVERT: C 113 MET cc_start: 0.9081 (tpt) cc_final: 0.8617 (tpt) REVERT: C 371 MET cc_start: 0.9091 (ttm) cc_final: 0.8623 (mtp) REVERT: D 68 ILE cc_start: 0.7283 (tp) cc_final: 0.7079 (tp) REVERT: D 113 MET cc_start: 0.6473 (ptt) cc_final: 0.6079 (ppp) REVERT: D 117 GLU cc_start: 0.9234 (tp30) cc_final: 0.8347 (mt-10) REVERT: D 277 ASN cc_start: 0.7529 (p0) cc_final: 0.7302 (p0) REVERT: D 299 ASP cc_start: 0.8480 (m-30) cc_final: 0.8052 (t0) REVERT: D 311 PHE cc_start: 0.9368 (t80) cc_final: 0.8736 (t80) REVERT: D 320 MET cc_start: 0.4293 (mtt) cc_final: 0.2975 (ptt) REVERT: D 326 MET cc_start: 0.6618 (mmp) cc_final: 0.4798 (ppp) REVERT: D 415 LYS cc_start: 0.8580 (tppp) cc_final: 0.8356 (tppt) REVERT: D 446 TYR cc_start: 0.8704 (t80) cc_final: 0.8342 (m-80) REVERT: E 61 GLU cc_start: 0.8602 (pt0) cc_final: 0.7715 (tt0) REVERT: E 62 MET cc_start: 0.7792 (tpp) cc_final: 0.6764 (tpp) REVERT: E 68 ILE cc_start: 0.9235 (tp) cc_final: 0.8996 (tp) REVERT: E 90 MET cc_start: 0.8968 (mmm) cc_final: 0.8522 (mmm) REVERT: E 297 PHE cc_start: 0.9178 (t80) cc_final: 0.8692 (t80) REVERT: E 354 LEU cc_start: 0.8962 (mm) cc_final: 0.8540 (mm) REVERT: E 374 ARG cc_start: 0.8997 (mmm160) cc_final: 0.8382 (mmm160) REVERT: E 404 GLN cc_start: 0.8383 (tt0) cc_final: 0.8028 (tm-30) REVERT: E 427 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8561 (mmmm) REVERT: E 443 MET cc_start: 0.9045 (mmt) cc_final: 0.8631 (mmm) REVERT: E 452 PHE cc_start: 0.7341 (m-80) cc_final: 0.6915 (m-80) REVERT: F 62 MET cc_start: 0.9114 (mtp) cc_final: 0.8771 (mtp) REVERT: F 74 LEU cc_start: 0.8811 (tp) cc_final: 0.8225 (mm) REVERT: F 90 MET cc_start: 0.9140 (ttt) cc_final: 0.8916 (tpp) REVERT: F 305 ASP cc_start: 0.8990 (p0) cc_final: 0.8731 (p0) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.2534 time to fit residues: 104.3906 Evaluate side-chains 204 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 93 optimal weight: 0.0370 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** D 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14740 Z= 0.193 Angle : 0.644 7.327 19910 Z= 0.313 Chirality : 0.044 0.182 2362 Planarity : 0.004 0.058 2538 Dihedral : 8.937 173.412 2070 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.19), residues: 1847 helix: -0.97 (0.17), residues: 805 sheet: -0.73 (0.38), residues: 190 loop : -1.46 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 283 HIS 0.005 0.001 HIS B 305 PHE 0.018 0.001 PHE A 93 TYR 0.017 0.001 TYR E 442 ARG 0.006 0.000 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.435 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: A 64 ARG cc_start: 0.7614 (mtt180) cc_final: 0.6563 (mmm-85) REVERT: A 67 LEU cc_start: 0.7510 (pp) cc_final: 0.7199 (pp) REVERT: A 286 TYR cc_start: 0.8247 (m-10) cc_final: 0.7716 (m-80) REVERT: A 300 PHE cc_start: 0.8739 (t80) cc_final: 0.8302 (t80) REVERT: A 369 GLN cc_start: 0.9339 (tt0) cc_final: 0.8953 (tm-30) REVERT: A 435 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8421 (pt0) REVERT: B 44 ASN cc_start: 0.9080 (t0) cc_final: 0.8487 (t0) REVERT: B 61 MET cc_start: 0.8962 (tpp) cc_final: 0.8695 (tpp) REVERT: B 276 ARG cc_start: 0.8645 (mpt-90) cc_final: 0.8292 (mtm-85) REVERT: B 420 ASN cc_start: 0.9047 (m-40) cc_final: 0.8626 (t0) REVERT: C 86 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8588 (mp0) REVERT: C 96 MET cc_start: 0.9453 (ppp) cc_final: 0.8860 (ppp) REVERT: C 113 MET cc_start: 0.9116 (tpt) cc_final: 0.8684 (tpt) REVERT: C 371 MET cc_start: 0.9067 (ttm) cc_final: 0.8584 (mtp) REVERT: D 68 ILE cc_start: 0.7111 (tp) cc_final: 0.6909 (tp) REVERT: D 113 MET cc_start: 0.6417 (ptt) cc_final: 0.4760 (mmm) REVERT: D 277 ASN cc_start: 0.7630 (p0) cc_final: 0.7394 (p0) REVERT: D 299 ASP cc_start: 0.8483 (m-30) cc_final: 0.8077 (t0) REVERT: D 311 PHE cc_start: 0.9359 (t80) cc_final: 0.8777 (t80) REVERT: D 320 MET cc_start: 0.4331 (mtt) cc_final: 0.2957 (ptt) REVERT: D 326 MET cc_start: 0.6715 (mmp) cc_final: 0.4759 (ppp) REVERT: D 415 LYS cc_start: 0.8578 (tppp) cc_final: 0.8352 (tppt) REVERT: D 446 TYR cc_start: 0.8721 (t80) cc_final: 0.8289 (m-80) REVERT: E 61 GLU cc_start: 0.8530 (pt0) cc_final: 0.7613 (tt0) REVERT: E 62 MET cc_start: 0.7800 (tpp) cc_final: 0.6673 (tpp) REVERT: E 68 ILE cc_start: 0.9217 (tp) cc_final: 0.8965 (tp) REVERT: E 113 MET cc_start: 0.8817 (ppp) cc_final: 0.8362 (ppp) REVERT: E 257 PHE cc_start: 0.4289 (t80) cc_final: 0.3300 (t80) REVERT: E 297 PHE cc_start: 0.9160 (t80) cc_final: 0.8664 (t80) REVERT: E 324 LEU cc_start: 0.8466 (tp) cc_final: 0.8086 (tp) REVERT: E 354 LEU cc_start: 0.8879 (mm) cc_final: 0.8437 (mm) REVERT: E 374 ARG cc_start: 0.9007 (mmm160) cc_final: 0.8385 (mmm160) REVERT: E 404 GLN cc_start: 0.8425 (tt0) cc_final: 0.8044 (tm-30) REVERT: E 427 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8525 (mmmm) REVERT: E 443 MET cc_start: 0.9086 (mmt) cc_final: 0.8722 (mmm) REVERT: E 452 PHE cc_start: 0.7307 (m-80) cc_final: 0.6871 (m-80) REVERT: F 62 MET cc_start: 0.9091 (mtp) cc_final: 0.8821 (mtp) REVERT: F 64 ARG cc_start: 0.8194 (mpp80) cc_final: 0.7814 (mtm-85) REVERT: F 90 MET cc_start: 0.9148 (ttt) cc_final: 0.8907 (tpp) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2521 time to fit residues: 102.0927 Evaluate side-chains 210 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.9980 chunk 20 optimal weight: 0.0000 chunk 101 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 178 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 82 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN C 247 ASN ** D 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS F 25 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14740 Z= 0.144 Angle : 0.630 7.079 19910 Z= 0.302 Chirality : 0.044 0.320 2362 Planarity : 0.005 0.181 2538 Dihedral : 8.777 173.657 2070 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.19), residues: 1847 helix: -0.75 (0.18), residues: 807 sheet: -0.64 (0.39), residues: 193 loop : -1.49 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 283 HIS 0.007 0.001 HIS B 305 PHE 0.018 0.001 PHE D 309 TYR 0.014 0.001 TYR C 286 ARG 0.010 0.000 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.677 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: A 64 ARG cc_start: 0.7479 (mtt180) cc_final: 0.6463 (mmm-85) REVERT: A 286 TYR cc_start: 0.8255 (m-10) cc_final: 0.7717 (m-80) REVERT: A 300 PHE cc_start: 0.8725 (t80) cc_final: 0.8344 (t80) REVERT: A 369 GLN cc_start: 0.9325 (tt0) cc_final: 0.8944 (tm-30) REVERT: A 435 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8403 (pt0) REVERT: B 44 ASN cc_start: 0.9022 (t0) cc_final: 0.8399 (t0) REVERT: B 52 ILE cc_start: 0.9353 (mm) cc_final: 0.9102 (tp) REVERT: B 306 MET cc_start: 0.8270 (mpp) cc_final: 0.7795 (mpp) REVERT: B 420 ASN cc_start: 0.9027 (m-40) cc_final: 0.8569 (t0) REVERT: C 86 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8573 (tp30) REVERT: C 96 MET cc_start: 0.9481 (ppp) cc_final: 0.8800 (ppp) REVERT: C 113 MET cc_start: 0.9093 (tpt) cc_final: 0.8608 (tpt) REVERT: C 371 MET cc_start: 0.8998 (ttm) cc_final: 0.8539 (mtp) REVERT: C 409 LEU cc_start: 0.8795 (mp) cc_final: 0.8551 (mp) REVERT: C 410 LEU cc_start: 0.9308 (mt) cc_final: 0.8997 (tt) REVERT: D 68 ILE cc_start: 0.6971 (tp) cc_final: 0.6756 (tp) REVERT: D 74 LEU cc_start: 0.8743 (mm) cc_final: 0.8467 (mm) REVERT: D 113 MET cc_start: 0.6371 (ptt) cc_final: 0.4672 (mmm) REVERT: D 299 ASP cc_start: 0.8411 (m-30) cc_final: 0.8025 (t0) REVERT: D 311 PHE cc_start: 0.9319 (t80) cc_final: 0.8784 (t80) REVERT: D 320 MET cc_start: 0.4115 (mtt) cc_final: 0.2736 (ptt) REVERT: D 326 MET cc_start: 0.6583 (mmp) cc_final: 0.6331 (mpp) REVERT: D 415 LYS cc_start: 0.8487 (tppp) cc_final: 0.8257 (tppt) REVERT: D 446 TYR cc_start: 0.8679 (t80) cc_final: 0.8237 (m-80) REVERT: E 61 GLU cc_start: 0.8446 (pt0) cc_final: 0.7496 (tt0) REVERT: E 62 MET cc_start: 0.7825 (tpp) cc_final: 0.6744 (tpp) REVERT: E 68 ILE cc_start: 0.9148 (tp) cc_final: 0.8940 (tp) REVERT: E 90 MET cc_start: 0.9035 (mmm) cc_final: 0.8754 (mmt) REVERT: E 113 MET cc_start: 0.8988 (ppp) cc_final: 0.8438 (ppp) REVERT: E 297 PHE cc_start: 0.9098 (t80) cc_final: 0.8642 (t80) REVERT: E 299 ASP cc_start: 0.7574 (t0) cc_final: 0.7284 (t0) REVERT: E 324 LEU cc_start: 0.8412 (tp) cc_final: 0.8076 (tp) REVERT: E 354 LEU cc_start: 0.8845 (mm) cc_final: 0.8618 (mm) REVERT: E 374 ARG cc_start: 0.8989 (mmm160) cc_final: 0.8335 (mmm160) REVERT: E 404 GLN cc_start: 0.8523 (tt0) cc_final: 0.8000 (tm-30) REVERT: E 427 LYS cc_start: 0.8801 (mmtt) cc_final: 0.7638 (pttm) REVERT: E 443 MET cc_start: 0.9145 (mmt) cc_final: 0.8756 (mmm) REVERT: E 452 PHE cc_start: 0.7319 (m-80) cc_final: 0.6876 (m-80) REVERT: F 62 MET cc_start: 0.9194 (mtp) cc_final: 0.8908 (mtp) REVERT: F 64 ARG cc_start: 0.8315 (mpp80) cc_final: 0.7952 (ptp-170) REVERT: F 65 GLU cc_start: 0.8983 (mp0) cc_final: 0.8503 (mp0) REVERT: F 73 VAL cc_start: 0.9281 (t) cc_final: 0.8718 (t) REVERT: F 74 LEU cc_start: 0.8833 (tp) cc_final: 0.8233 (mm) REVERT: F 78 GLN cc_start: 0.8846 (mm110) cc_final: 0.8626 (mp10) REVERT: F 90 MET cc_start: 0.9171 (ttt) cc_final: 0.8675 (tpt) REVERT: F 305 ASP cc_start: 0.8870 (p0) cc_final: 0.8654 (p0) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.2526 time to fit residues: 109.4616 Evaluate side-chains 218 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN C 414 ASN D 245 HIS ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14740 Z= 0.147 Angle : 0.629 7.317 19910 Z= 0.303 Chirality : 0.044 0.167 2362 Planarity : 0.004 0.105 2538 Dihedral : 8.630 175.890 2070 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.19), residues: 1847 helix: -0.59 (0.18), residues: 803 sheet: -0.54 (0.40), residues: 190 loop : -1.38 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 283 HIS 0.007 0.001 HIS B 305 PHE 0.015 0.001 PHE C 329 TYR 0.014 0.001 TYR C 286 ARG 0.008 0.000 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.752 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: A 64 ARG cc_start: 0.7613 (mtt180) cc_final: 0.6468 (mmm-85) REVERT: A 68 LEU cc_start: 0.7907 (tp) cc_final: 0.7491 (mm) REVERT: A 286 TYR cc_start: 0.8244 (m-10) cc_final: 0.7705 (m-80) REVERT: A 300 PHE cc_start: 0.8735 (t80) cc_final: 0.8381 (t80) REVERT: A 301 VAL cc_start: 0.8799 (t) cc_final: 0.8526 (t) REVERT: A 369 GLN cc_start: 0.9310 (tt0) cc_final: 0.8896 (tm-30) REVERT: A 392 ASN cc_start: 0.9015 (t0) cc_final: 0.8767 (m-40) REVERT: A 435 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8382 (pt0) REVERT: B 44 ASN cc_start: 0.9027 (t0) cc_final: 0.8409 (t0) REVERT: B 420 ASN cc_start: 0.9049 (m-40) cc_final: 0.8585 (t0) REVERT: C 86 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8509 (tp30) REVERT: C 96 MET cc_start: 0.9467 (ppp) cc_final: 0.8813 (ppp) REVERT: C 113 MET cc_start: 0.9105 (tpt) cc_final: 0.8626 (tpt) REVERT: C 306 MET cc_start: 0.8721 (mpp) cc_final: 0.8489 (mpp) REVERT: C 309 ILE cc_start: 0.8801 (tp) cc_final: 0.8582 (mm) REVERT: C 371 MET cc_start: 0.8967 (ttm) cc_final: 0.8516 (mtp) REVERT: C 409 LEU cc_start: 0.8889 (mp) cc_final: 0.8634 (mp) REVERT: C 410 LEU cc_start: 0.9290 (mt) cc_final: 0.8957 (tt) REVERT: D 68 ILE cc_start: 0.7048 (tp) cc_final: 0.6809 (tp) REVERT: D 74 LEU cc_start: 0.8774 (mm) cc_final: 0.8523 (mm) REVERT: D 113 MET cc_start: 0.6772 (ptt) cc_final: 0.5346 (mmm) REVERT: D 277 ASN cc_start: 0.7728 (p0) cc_final: 0.7492 (p0) REVERT: D 298 ILE cc_start: 0.6467 (tt) cc_final: 0.5864 (mp) REVERT: D 299 ASP cc_start: 0.8403 (m-30) cc_final: 0.7882 (t0) REVERT: D 311 PHE cc_start: 0.9264 (t80) cc_final: 0.8750 (t80) REVERT: D 320 MET cc_start: 0.4200 (mtt) cc_final: 0.2793 (ptt) REVERT: D 414 ARG cc_start: 0.9154 (mtp-110) cc_final: 0.8809 (ttp80) REVERT: D 415 LYS cc_start: 0.8418 (tppp) cc_final: 0.7943 (tppt) REVERT: D 446 TYR cc_start: 0.8736 (t80) cc_final: 0.8334 (m-80) REVERT: E 61 GLU cc_start: 0.8462 (pt0) cc_final: 0.7460 (tt0) REVERT: E 62 MET cc_start: 0.7803 (tpp) cc_final: 0.6792 (tpp) REVERT: E 68 ILE cc_start: 0.9116 (tp) cc_final: 0.8890 (tp) REVERT: E 90 MET cc_start: 0.9052 (mmm) cc_final: 0.8753 (mmt) REVERT: E 113 MET cc_start: 0.8996 (ppp) cc_final: 0.8434 (ppp) REVERT: E 297 PHE cc_start: 0.9077 (t80) cc_final: 0.8657 (t80) REVERT: E 299 ASP cc_start: 0.7608 (t0) cc_final: 0.7195 (t0) REVERT: E 324 LEU cc_start: 0.8261 (tp) cc_final: 0.7905 (tp) REVERT: E 354 LEU cc_start: 0.8840 (mm) cc_final: 0.8605 (mm) REVERT: E 374 ARG cc_start: 0.9023 (mmm160) cc_final: 0.8345 (mmm160) REVERT: E 404 GLN cc_start: 0.8463 (tt0) cc_final: 0.7971 (tm-30) REVERT: E 427 LYS cc_start: 0.8779 (mmtt) cc_final: 0.7578 (pttm) REVERT: E 443 MET cc_start: 0.9175 (mmt) cc_final: 0.8797 (mmm) REVERT: E 452 PHE cc_start: 0.7323 (m-80) cc_final: 0.6859 (m-80) REVERT: F 62 MET cc_start: 0.9190 (mtp) cc_final: 0.8880 (mtp) REVERT: F 64 ARG cc_start: 0.8320 (mpp80) cc_final: 0.7937 (ptp-170) REVERT: F 65 GLU cc_start: 0.8954 (mp0) cc_final: 0.8391 (mp0) REVERT: F 90 MET cc_start: 0.9177 (ttt) cc_final: 0.8725 (tpt) REVERT: F 300 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7078 (tp30) REVERT: F 303 MET cc_start: 0.8805 (mmt) cc_final: 0.8400 (mpp) REVERT: F 305 ASP cc_start: 0.8839 (p0) cc_final: 0.8580 (p0) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2576 time to fit residues: 110.6848 Evaluate side-chains 218 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 ASN D 245 HIS D 313 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14740 Z= 0.243 Angle : 0.698 8.078 19910 Z= 0.342 Chirality : 0.045 0.176 2362 Planarity : 0.005 0.083 2538 Dihedral : 8.952 176.581 2070 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.19), residues: 1847 helix: -0.70 (0.18), residues: 807 sheet: -0.72 (0.38), residues: 195 loop : -1.35 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 283 HIS 0.008 0.002 HIS B 305 PHE 0.031 0.002 PHE D 309 TYR 0.018 0.002 TYR E 442 ARG 0.010 0.001 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.002 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: A 64 ARG cc_start: 0.7667 (mtt180) cc_final: 0.6586 (mmm-85) REVERT: A 286 TYR cc_start: 0.8155 (m-10) cc_final: 0.7610 (m-80) REVERT: A 300 PHE cc_start: 0.8816 (t80) cc_final: 0.8394 (t80) REVERT: A 369 GLN cc_start: 0.9379 (tt0) cc_final: 0.8744 (tm-30) REVERT: A 372 LYS cc_start: 0.9231 (mtmt) cc_final: 0.8944 (mtpp) REVERT: A 373 GLN cc_start: 0.9606 (mp10) cc_final: 0.9187 (mp10) REVERT: A 435 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8490 (pt0) REVERT: B 44 ASN cc_start: 0.9093 (t0) cc_final: 0.8469 (t0) REVERT: B 364 MET cc_start: 0.7578 (mmp) cc_final: 0.7070 (mmp) REVERT: B 420 ASN cc_start: 0.9066 (m-40) cc_final: 0.8577 (t0) REVERT: C 86 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8740 (tp30) REVERT: C 96 MET cc_start: 0.9459 (ppp) cc_final: 0.8854 (ppp) REVERT: C 113 MET cc_start: 0.9159 (tpt) cc_final: 0.8735 (tpt) REVERT: C 306 MET cc_start: 0.8724 (mpp) cc_final: 0.8499 (mpp) REVERT: C 371 MET cc_start: 0.9055 (ttm) cc_final: 0.8277 (mtt) REVERT: D 68 ILE cc_start: 0.7207 (tp) cc_final: 0.7000 (tp) REVERT: D 74 LEU cc_start: 0.8824 (mm) cc_final: 0.8490 (mm) REVERT: D 90 MET cc_start: 0.8666 (tmm) cc_final: 0.8341 (ppp) REVERT: D 113 MET cc_start: 0.6473 (ptt) cc_final: 0.5013 (mmm) REVERT: D 277 ASN cc_start: 0.7650 (p0) cc_final: 0.7443 (p0) REVERT: D 298 ILE cc_start: 0.6772 (tt) cc_final: 0.6298 (pt) REVERT: D 299 ASP cc_start: 0.8406 (m-30) cc_final: 0.8038 (m-30) REVERT: D 311 PHE cc_start: 0.9362 (t80) cc_final: 0.8771 (t80) REVERT: D 320 MET cc_start: 0.4363 (mtt) cc_final: 0.2980 (ptt) REVERT: D 415 LYS cc_start: 0.8418 (tppp) cc_final: 0.8209 (tppt) REVERT: D 446 TYR cc_start: 0.8814 (t80) cc_final: 0.8345 (m-80) REVERT: E 61 GLU cc_start: 0.8549 (pt0) cc_final: 0.7594 (tt0) REVERT: E 62 MET cc_start: 0.7815 (tpp) cc_final: 0.6774 (tpp) REVERT: E 68 ILE cc_start: 0.9144 (tp) cc_final: 0.8797 (tp) REVERT: E 73 VAL cc_start: 0.9525 (t) cc_final: 0.9037 (t) REVERT: E 90 MET cc_start: 0.9011 (mmm) cc_final: 0.8679 (mmm) REVERT: E 113 MET cc_start: 0.8964 (ppp) cc_final: 0.8733 (ppp) REVERT: E 297 PHE cc_start: 0.9153 (t80) cc_final: 0.8578 (t80) REVERT: E 350 LEU cc_start: 0.8931 (tp) cc_final: 0.8605 (tt) REVERT: E 354 LEU cc_start: 0.8929 (mm) cc_final: 0.8558 (mm) REVERT: E 374 ARG cc_start: 0.9030 (mmm160) cc_final: 0.8521 (mmm-85) REVERT: E 404 GLN cc_start: 0.8413 (tt0) cc_final: 0.8051 (tm-30) REVERT: E 427 LYS cc_start: 0.8807 (mmtt) cc_final: 0.7647 (pttm) REVERT: E 443 MET cc_start: 0.9174 (mmt) cc_final: 0.8808 (mmm) REVERT: F 62 MET cc_start: 0.9137 (mtp) cc_final: 0.8865 (mtp) REVERT: F 74 LEU cc_start: 0.8997 (tp) cc_final: 0.8548 (mm) REVERT: F 90 MET cc_start: 0.9189 (ttt) cc_final: 0.8783 (tpt) REVERT: F 305 ASP cc_start: 0.9220 (p0) cc_final: 0.8982 (p0) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2497 time to fit residues: 97.5373 Evaluate side-chains 204 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.0470 chunk 89 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 ASN D 245 HIS ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14740 Z= 0.156 Angle : 0.654 7.795 19910 Z= 0.315 Chirality : 0.044 0.179 2362 Planarity : 0.004 0.078 2538 Dihedral : 8.668 171.608 2070 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 1847 helix: -0.52 (0.18), residues: 786 sheet: -0.48 (0.40), residues: 183 loop : -1.38 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 283 HIS 0.007 0.001 HIS B 305 PHE 0.024 0.001 PHE E 450 TYR 0.018 0.001 TYR E 442 ARG 0.016 0.000 ARG B 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.758 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: A 64 ARG cc_start: 0.7562 (mtt180) cc_final: 0.6616 (mmm-85) REVERT: A 68 LEU cc_start: 0.7960 (tp) cc_final: 0.7537 (mm) REVERT: A 286 TYR cc_start: 0.8233 (m-10) cc_final: 0.7713 (m-80) REVERT: A 300 PHE cc_start: 0.8492 (t80) cc_final: 0.8157 (t80) REVERT: A 369 GLN cc_start: 0.9350 (tt0) cc_final: 0.8985 (tm-30) REVERT: A 435 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8447 (pt0) REVERT: B 44 ASN cc_start: 0.9038 (t0) cc_final: 0.8463 (t0) REVERT: B 364 MET cc_start: 0.7431 (mmp) cc_final: 0.6969 (mmp) REVERT: B 420 ASN cc_start: 0.9014 (m-40) cc_final: 0.8521 (t0) REVERT: C 86 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8642 (tp30) REVERT: C 96 MET cc_start: 0.9469 (ppp) cc_final: 0.8906 (ppp) REVERT: C 113 MET cc_start: 0.9118 (tpt) cc_final: 0.8666 (tpt) REVERT: C 305 HIS cc_start: 0.8528 (p90) cc_final: 0.8327 (p90) REVERT: C 371 MET cc_start: 0.8903 (ttm) cc_final: 0.8576 (mtp) REVERT: C 409 LEU cc_start: 0.8883 (mp) cc_final: 0.8639 (mp) REVERT: C 410 LEU cc_start: 0.9261 (mt) cc_final: 0.8971 (tt) REVERT: D 68 ILE cc_start: 0.7145 (tp) cc_final: 0.6899 (tp) REVERT: D 74 LEU cc_start: 0.8877 (mm) cc_final: 0.8582 (mm) REVERT: D 90 MET cc_start: 0.8588 (tmm) cc_final: 0.8281 (ppp) REVERT: D 113 MET cc_start: 0.6606 (ptt) cc_final: 0.5300 (mmm) REVERT: D 298 ILE cc_start: 0.6796 (tt) cc_final: 0.6457 (mp) REVERT: D 299 ASP cc_start: 0.8374 (m-30) cc_final: 0.8125 (m-30) REVERT: D 311 PHE cc_start: 0.9325 (t80) cc_final: 0.8852 (t80) REVERT: D 320 MET cc_start: 0.4396 (mtt) cc_final: 0.3043 (ptt) REVERT: D 414 ARG cc_start: 0.9083 (mtp-110) cc_final: 0.8782 (ttp80) REVERT: D 415 LYS cc_start: 0.8479 (tppp) cc_final: 0.8274 (ttmm) REVERT: D 446 TYR cc_start: 0.8778 (t80) cc_final: 0.8350 (m-80) REVERT: E 61 GLU cc_start: 0.8471 (pt0) cc_final: 0.7483 (tt0) REVERT: E 62 MET cc_start: 0.7799 (tpp) cc_final: 0.6725 (tpp) REVERT: E 68 ILE cc_start: 0.9115 (tp) cc_final: 0.8785 (tp) REVERT: E 73 VAL cc_start: 0.9521 (t) cc_final: 0.9058 (t) REVERT: E 90 MET cc_start: 0.8991 (mmm) cc_final: 0.8600 (mmt) REVERT: E 297 PHE cc_start: 0.9045 (t80) cc_final: 0.8541 (t80) REVERT: E 299 ASP cc_start: 0.7714 (t0) cc_final: 0.7167 (t0) REVERT: E 350 LEU cc_start: 0.8847 (tp) cc_final: 0.8517 (tt) REVERT: E 354 LEU cc_start: 0.8860 (mm) cc_final: 0.8568 (mm) REVERT: E 374 ARG cc_start: 0.9005 (mmm160) cc_final: 0.8180 (mmm160) REVERT: E 404 GLN cc_start: 0.8453 (tt0) cc_final: 0.8009 (tm-30) REVERT: E 427 LYS cc_start: 0.8787 (mmtt) cc_final: 0.7685 (pttm) REVERT: E 443 MET cc_start: 0.9187 (mmt) cc_final: 0.8848 (mmm) REVERT: E 452 PHE cc_start: 0.7313 (m-80) cc_final: 0.6845 (m-80) REVERT: F 62 MET cc_start: 0.9085 (mtp) cc_final: 0.8692 (mtp) REVERT: F 64 ARG cc_start: 0.8260 (mpp80) cc_final: 0.7935 (ptp-170) REVERT: F 65 GLU cc_start: 0.8931 (mp0) cc_final: 0.8551 (mp0) REVERT: F 90 MET cc_start: 0.9204 (ttt) cc_final: 0.8715 (tpt) REVERT: F 108 ILE cc_start: 0.8448 (tp) cc_final: 0.8234 (tp) REVERT: F 443 MET cc_start: 0.7739 (tpp) cc_final: 0.7357 (tpp) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2434 time to fit residues: 100.3745 Evaluate side-chains 219 residues out of total 1579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.0030 chunk 129 optimal weight: 3.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN D 245 HIS E 422 GLN F 25 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.102309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079562 restraints weight = 50731.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081984 restraints weight = 33695.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.083597 restraints weight = 24991.154| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14740 Z= 0.167 Angle : 0.647 8.806 19910 Z= 0.312 Chirality : 0.044 0.192 2362 Planarity : 0.004 0.072 2538 Dihedral : 8.576 172.091 2070 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.19), residues: 1847 helix: -0.51 (0.18), residues: 788 sheet: -0.60 (0.40), residues: 183 loop : -1.30 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 283 HIS 0.007 0.001 HIS B 305 PHE 0.028 0.001 PHE F 109 TYR 0.024 0.001 TYR D 430 ARG 0.010 0.000 ARG B 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2960.89 seconds wall clock time: 54 minutes 41.18 seconds (3281.18 seconds total)