Starting phenix.real_space_refine on Sat Sep 12 11:50:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e7z_9002/09_2026/6e7z_9002.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e7z_9002/09_2026/6e7z_9002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6e7z_9002/09_2026/6e7z_9002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e7z_9002/09_2026/6e7z_9002.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e7z_9002/09_2026/6e7z_9002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e7z_9002/09_2026/6e7z_9002.map" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.038 sd= 0.428 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 12 5.49 5 S 100 5.16 5 C 10192 2.51 5 N 2568 2.21 5 O 2744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15616 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "B" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "C" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "D" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'AQV': 1, 'HZ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'AQV': 1, 'HZ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'AQV': 1, 'HZ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'AQV': 1, 'HZ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.30, per 1000 atoms: 0.21 Number of scatterers: 15616 At special positions: 0 Unit cell: (123.05, 123.05, 113.42, 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 100 16.00 P 12 15.00 O 2744 8.00 N 2568 7.00 C 10192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.05 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.06 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.05 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.05 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.05 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.06 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.05 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 630.4 milliseconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 57.9% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.661A pdb=" N TYR A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.675A pdb=" N LYS A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 57 " --> pdb=" O CYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 106 removed outlier: 5.317A pdb=" N GLN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.578A pdb=" N TYR A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.742A pdb=" N VAL A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 327 removed outlier: 3.879A pdb=" N LEU A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.607A pdb=" N GLU A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 373 removed outlier: 3.724A pdb=" N LEU A 358 " --> pdb=" O TRP A 354 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 383 through 399 removed outlier: 4.170A pdb=" N THR A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 403 removed outlier: 3.600A pdb=" N ARG A 403 " --> pdb=" O GLY A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 403' Processing helix chain 'A' and resid 408 through 447 removed outlier: 3.629A pdb=" N ILE A 413 " --> pdb=" O HIS A 409 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 415 " --> pdb=" O TYR A 411 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 4.240A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N CYS A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 468 removed outlier: 4.228A pdb=" N VAL A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 Processing helix chain 'A' and resid 480 through 484 Processing helix chain 'A' and resid 487 through 506 removed outlier: 3.617A pdb=" N TRP A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 501 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 525 removed outlier: 3.955A pdb=" N LEU A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.661A pdb=" N TYR B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.675A pdb=" N LYS B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 57 " --> pdb=" O CYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 106 removed outlier: 5.317A pdb=" N GLN B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.578A pdb=" N TYR B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 removed outlier: 3.741A pdb=" N VAL B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 327 removed outlier: 3.878A pdb=" N LEU B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 351 removed outlier: 3.606A pdb=" N GLU B 349 " --> pdb=" O TRP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 373 removed outlier: 3.724A pdb=" N LEU B 358 " --> pdb=" O TRP B 354 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 383 through 399 removed outlier: 4.170A pdb=" N THR B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 403 removed outlier: 3.601A pdb=" N ARG B 403 " --> pdb=" O GLY B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 403' Processing helix chain 'B' and resid 408 through 447 removed outlier: 3.629A pdb=" N ILE B 413 " --> pdb=" O HIS B 409 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 415 " --> pdb=" O TYR B 411 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B 417 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 4.240A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 432 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 removed outlier: 4.228A pdb=" N VAL B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 Processing helix chain 'B' and resid 480 through 484 Processing helix chain 'B' and resid 487 through 506 removed outlier: 3.617A pdb=" N TRP B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 501 " --> pdb=" O TYR B 497 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 503 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 525 removed outlier: 3.954A pdb=" N LEU B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 47 removed outlier: 3.660A pdb=" N TYR C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.674A pdb=" N LYS C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C 57 " --> pdb=" O CYS C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 106 removed outlier: 5.318A pdb=" N GLN C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 138 removed outlier: 3.579A pdb=" N TYR C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 135 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.741A pdb=" N VAL C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 327 removed outlier: 3.879A pdb=" N LEU C 299 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 312 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 removed outlier: 3.606A pdb=" N GLU C 349 " --> pdb=" O TRP C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 373 removed outlier: 3.724A pdb=" N LEU C 358 " --> pdb=" O TRP C 354 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 364 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 383 through 399 removed outlier: 4.171A pdb=" N THR C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP C 398 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 403 removed outlier: 3.600A pdb=" N ARG C 403 " --> pdb=" O GLY C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 400 through 403' Processing helix chain 'C' and resid 408 through 447 removed outlier: 3.629A pdb=" N ILE C 413 " --> pdb=" O HIS C 409 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE C 415 " --> pdb=" O TYR C 411 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 4.240A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 432 " --> pdb=" O PHE C 428 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY C 443 " --> pdb=" O TYR C 439 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 468 removed outlier: 4.228A pdb=" N VAL C 460 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 479 Processing helix chain 'C' and resid 480 through 484 Processing helix chain 'C' and resid 487 through 506 removed outlier: 3.617A pdb=" N TRP C 491 " --> pdb=" O SER C 487 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 501 " --> pdb=" O TYR C 497 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 502 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 503 " --> pdb=" O TYR C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 525 removed outlier: 3.956A pdb=" N LEU C 512 " --> pdb=" O MET C 508 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 519 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.661A pdb=" N TYR D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 51 through 59 removed outlier: 3.674A pdb=" N LYS D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG D 57 " --> pdb=" O CYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 106 removed outlier: 5.317A pdb=" N GLN D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 removed outlier: 3.579A pdb=" N TYR D 126 " --> pdb=" O ARG D 122 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D 135 " --> pdb=" O HIS D 131 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.742A pdb=" N VAL D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 327 removed outlier: 3.879A pdb=" N LEU D 299 " --> pdb=" O ASN D 295 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 311 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER D 312 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 351 removed outlier: 3.606A pdb=" N GLU D 349 " --> pdb=" O TRP D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 373 removed outlier: 3.724A pdb=" N LEU D 358 " --> pdb=" O TRP D 354 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 364 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR D 369 " --> pdb=" O THR D 365 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 376 No H-bonds generated for 'chain 'D' and resid 374 through 376' Processing helix chain 'D' and resid 383 through 399 removed outlier: 4.170A pdb=" N THR D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 395 " --> pdb=" O GLY D 391 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP D 398 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 403 removed outlier: 3.601A pdb=" N ARG D 403 " --> pdb=" O GLY D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 400 through 403' Processing helix chain 'D' and resid 408 through 447 removed outlier: 3.628A pdb=" N ILE D 413 " --> pdb=" O HIS D 409 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE D 415 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR D 417 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 4.240A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 432 " --> pdb=" O PHE D 428 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS D 442 " --> pdb=" O GLY D 438 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY D 443 " --> pdb=" O TYR D 439 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 468 removed outlier: 4.228A pdb=" N VAL D 460 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE D 465 " --> pdb=" O SER D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 479 Processing helix chain 'D' and resid 480 through 484 Processing helix chain 'D' and resid 487 through 506 removed outlier: 3.616A pdb=" N TRP D 491 " --> pdb=" O SER D 487 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 492 " --> pdb=" O SER D 488 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 501 " --> pdb=" O TYR D 497 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 502 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER D 503 " --> pdb=" O TYR D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 525 removed outlier: 3.955A pdb=" N LEU D 512 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE D 517 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 519 " --> pdb=" O ALA D 515 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 520 " --> pdb=" O LEU D 516 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.608A pdb=" N CYS A 253 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 237 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 231 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 165 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN A 167 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 191 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.608A pdb=" N CYS B 253 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 237 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 231 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 165 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN B 167 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 191 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.607A pdb=" N CYS C 253 " --> pdb=" O GLN C 282 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 237 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 231 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 165 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN C 167 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 191 " --> pdb=" O GLN C 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.607A pdb=" N CYS D 253 " --> pdb=" O GLN D 282 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 237 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 231 " --> pdb=" O PHE D 262 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 165 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN D 167 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP D 191 " --> pdb=" O GLN D 167 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1920 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: 2.21 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2340 1.30 - 1.44: 4673 1.44 - 1.57: 8827 1.57 - 1.71: 28 1.71 - 1.84: 140 Bond restraints: 16008 Sorted by residual: bond pdb=" C7 AQV D 802 " pdb=" O3 AQV D 802 " ideal model delta sigma weight residual 1.209 1.468 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C7 AQV C 802 " pdb=" O3 AQV C 802 " ideal model delta sigma weight residual 1.209 1.468 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C7 AQV B 802 " pdb=" O3 AQV B 802 " ideal model delta sigma weight residual 1.209 1.468 -0.259 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C7 AQV A 802 " pdb=" O3 AQV A 802 " ideal model delta sigma weight residual 1.209 1.467 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C8 AQV B 802 " pdb=" O2 AQV B 802 " ideal model delta sigma weight residual 1.213 1.450 -0.237 2.00e-02 2.50e+03 1.41e+02 ... (remaining 16003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 20901 2.73 - 5.47: 651 5.47 - 8.20: 146 8.20 - 10.93: 42 10.93 - 13.67: 8 Bond angle restraints: 21748 Sorted by residual: angle pdb=" C ASN C 247 " pdb=" N ASN C 248 " pdb=" CA ASN C 248 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C ASN D 247 " pdb=" N ASN D 248 " pdb=" CA ASN D 248 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C ASN B 247 " pdb=" N ASN B 248 " pdb=" CA ASN B 248 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C ASN A 247 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 angle pdb=" C21 AQV B 802 " pdb=" C11 AQV B 802 " pdb=" C22 AQV B 802 " ideal model delta sigma weight residual 110.45 96.78 13.67 3.00e+00 1.11e-01 2.08e+01 ... (remaining 21743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 9349 35.86 - 71.72: 107 71.72 - 107.57: 64 107.57 - 143.43: 20 143.43 - 179.29: 24 Dihedral angle restraints: 9564 sinusoidal: 4000 harmonic: 5564 Sorted by residual: dihedral pdb=" CA ASN B 179 " pdb=" C ASN B 179 " pdb=" N ASP B 180 " pdb=" CA ASP B 180 " ideal model delta harmonic sigma weight residual -180.00 -148.08 -31.92 0 5.00e+00 4.00e-02 4.07e+01 dihedral pdb=" CA ASN D 179 " pdb=" C ASN D 179 " pdb=" N ASP D 180 " pdb=" CA ASP D 180 " ideal model delta harmonic sigma weight residual -180.00 -148.09 -31.91 0 5.00e+00 4.00e-02 4.07e+01 dihedral pdb=" CA ASN A 179 " pdb=" C ASN A 179 " pdb=" N ASP A 180 " pdb=" CA ASP A 180 " ideal model delta harmonic sigma weight residual -180.00 -148.10 -31.90 0 5.00e+00 4.00e-02 4.07e+01 ... (remaining 9561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2179 0.084 - 0.168: 265 0.168 - 0.252: 20 0.252 - 0.337: 4 0.337 - 0.421: 4 Chirality restraints: 2472 Sorted by residual: chirality pdb=" C5 HZ7 C 801 " pdb=" C4 HZ7 C 801 " pdb=" C6 HZ7 C 801 " pdb=" O3 HZ7 C 801 " both_signs ideal model delta sigma weight residual False -2.05 -2.47 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C5 HZ7 B 801 " pdb=" C4 HZ7 B 801 " pdb=" C6 HZ7 B 801 " pdb=" O3 HZ7 B 801 " both_signs ideal model delta sigma weight residual False -2.05 -2.46 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" C5 HZ7 A 801 " pdb=" C4 HZ7 A 801 " pdb=" C6 HZ7 A 801 " pdb=" O3 HZ7 A 801 " both_signs ideal model delta sigma weight residual False -2.05 -2.46 0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 2469 not shown) Planarity restraints: 2660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 AQV C 802 " 0.039 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" C14 AQV C 802 " -0.033 2.00e-02 2.50e+03 pdb=" C15 AQV C 802 " -0.002 2.00e-02 2.50e+03 pdb=" C16 AQV C 802 " 0.039 2.00e-02 2.50e+03 pdb=" C17 AQV C 802 " 0.001 2.00e-02 2.50e+03 pdb=" C18 AQV C 802 " -0.010 2.00e-02 2.50e+03 pdb=" C19 AQV C 802 " -0.008 2.00e-02 2.50e+03 pdb=" N2 AQV C 802 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 AQV D 802 " 0.039 2.00e-02 2.50e+03 2.48e-02 1.23e+01 pdb=" C14 AQV D 802 " -0.033 2.00e-02 2.50e+03 pdb=" C15 AQV D 802 " -0.003 2.00e-02 2.50e+03 pdb=" C16 AQV D 802 " 0.038 2.00e-02 2.50e+03 pdb=" C17 AQV D 802 " 0.002 2.00e-02 2.50e+03 pdb=" C18 AQV D 802 " -0.010 2.00e-02 2.50e+03 pdb=" C19 AQV D 802 " -0.008 2.00e-02 2.50e+03 pdb=" N2 AQV D 802 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 AQV B 802 " 0.039 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" C14 AQV B 802 " -0.033 2.00e-02 2.50e+03 pdb=" C15 AQV B 802 " -0.003 2.00e-02 2.50e+03 pdb=" C16 AQV B 802 " 0.038 2.00e-02 2.50e+03 pdb=" C17 AQV B 802 " 0.002 2.00e-02 2.50e+03 pdb=" C18 AQV B 802 " -0.010 2.00e-02 2.50e+03 pdb=" C19 AQV B 802 " -0.007 2.00e-02 2.50e+03 pdb=" N2 AQV B 802 " -0.026 2.00e-02 2.50e+03 ... (remaining 2657 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3892 2.78 - 3.31: 14297 3.31 - 3.84: 24774 3.84 - 4.37: 28153 4.37 - 4.90: 46478 Nonbonded interactions: 117594 Sorted by model distance: nonbonded pdb=" CE2 TYR D 355 " pdb=" NH2 ARG D 403 " model vdw 2.249 3.420 nonbonded pdb=" OH TYR B 355 " pdb=" O11 HZ7 B 801 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR C 355 " pdb=" O11 HZ7 C 801 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR A 355 " pdb=" O11 HZ7 A 801 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR D 355 " pdb=" O11 HZ7 D 801 " model vdw 2.276 3.040 ... (remaining 117589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.270 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 : 0.013 0.371 16020 Z= 0.794 Angle : 1.266 13.668 21764 Z= 0.633 Chirality : 0.059 0.421 2472 Planarity : 0.008 0.072 2660 Dihedral : 19.866 179.288 5956 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.80 (0.13), residues: 1884 helix: -3.93 (0.09), residues: 988 sheet: -2.19 (0.39), residues: 160 loop : -3.91 (0.18), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 336 TYR 0.034 0.004 TYR A 436 PHE 0.026 0.003 PHE A 182 TRP 0.020 0.003 TRP C 491 HIS 0.010 0.003 HIS D 451 Details of bonding type rmsd/Z covalent geometry : bond 0.01112 / 0.54 (16008) covalent geometry : angle 1.26509 / 0.63 (21748) SS BOND : bond 0.02120 / 1.06 ( 8) SS BOND : angle 2.12518 / 1.06 ( 16) hydrogen bonds : bond 0.31769 / 20.61 ( 656) hydrogen bonds : angle 10.01158 / 6.93 ( 1920) Misc. bond : bond 0.37077 / 18.57 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 416 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7800 (t80) cc_final: 0.7471 (t80) REVERT: A 495 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8367 (tp40) REVERT: A 511 SER cc_start: 0.9283 (m) cc_final: 0.8736 (p) REVERT: B 93 PHE cc_start: 0.7838 (t80) cc_final: 0.7563 (t80) REVERT: B 495 GLN cc_start: 0.8751 (tp-100) cc_final: 0.8395 (tp40) REVERT: B 511 SER cc_start: 0.9253 (m) cc_final: 0.8696 (p) REVERT: C 47 TYR cc_start: 0.7491 (m-80) cc_final: 0.7267 (m-80) REVERT: C 495 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8336 (tp40) REVERT: C 511 SER cc_start: 0.9158 (m) cc_final: 0.8580 (p) REVERT: D 335 TRP cc_start: 0.7082 (m-10) cc_final: 0.6829 (m-90) REVERT: D 495 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8358 (tp40) REVERT: D 511 SER cc_start: 0.9268 (m) cc_final: 0.8714 (p) outliers start: 1 outliers final: 0 residues processed: 416 average time/residue: 0.1121 time to fit residues: 71.5379 Evaluate side-chains 200 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN A 234 HIS A 469 ASN B 69 GLN B 234 HIS B 469 ASN C 69 GLN C 103 HIS C 234 HIS C 469 ASN ** C 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 234 HIS D 469 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.106158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.091677 restraints weight = 48759.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.093857 restraints weight = 26928.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.095077 restraints weight = 17512.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.096211 restraints weight = 13323.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.096849 restraints weight = 10510.370| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16020 Z= 0.163 Angle : 0.825 11.012 21764 Z= 0.399 Chirality : 0.046 0.238 2472 Planarity : 0.006 0.053 2660 Dihedral : 24.049 170.416 2452 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.72 % Allowed : 10.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.17), residues: 1884 helix: -2.16 (0.14), residues: 1020 sheet: 0.01 (0.44), residues: 176 loop : -3.51 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 322 TYR 0.020 0.002 TYR B 436 PHE 0.025 0.002 PHE C 474 TRP 0.016 0.001 TRP A 157 HIS 0.014 0.001 HIS B 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (16008) covalent geometry : angle 0.81828 / 0.40 (21748) SS BOND : bond 0.01221 / 0.64 ( 8) SS BOND : angle 3.85027 / 2.24 ( 16) hydrogen bonds : bond 0.06130 / 3.92 ( 656) hydrogen bonds : angle 5.72249 / 3.99 ( 1920) Misc. bond : bond 0.00908 / 0.45 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 292 time to evaluate : 0.601 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 46 LYS cc_start: 0.9125 (tptt) cc_final: 0.8823 (tppt) REVERT: A 499 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: A 511 SER cc_start: 0.9210 (m) cc_final: 0.8753 (p) REVERT: B 46 LYS cc_start: 0.9120 (tptt) cc_final: 0.8810 (tppt) REVERT: B 499 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: B 511 SER cc_start: 0.9210 (m) cc_final: 0.8729 (p) REVERT: C 46 LYS cc_start: 0.9110 (tptt) cc_final: 0.8806 (tppt) REVERT: C 47 TYR cc_start: 0.7364 (m-80) cc_final: 0.7064 (m-80) REVERT: C 499 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7486 (m-80) REVERT: C 508 MET cc_start: 0.7621 (mtt) cc_final: 0.7395 (tmm) REVERT: C 511 SER cc_start: 0.9204 (m) cc_final: 0.8764 (p) REVERT: D 46 LYS cc_start: 0.9090 (tptt) cc_final: 0.8802 (tppt) REVERT: D 242 LEU cc_start: 0.9106 (mt) cc_final: 0.8617 (tp) REVERT: D 499 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: D 511 SER cc_start: 0.9236 (m) cc_final: 0.8777 (p) outliers start: 63 outliers final: 26 residues processed: 346 average time/residue: 0.1041 time to fit residues: 56.7552 Evaluate side-chains 233 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 386 CYS Chi-restraints excluded: chain D residue 499 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 114 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 GLN B 481 GLN D 481 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.106428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092042 restraints weight = 48431.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094049 restraints weight = 27139.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.095531 restraints weight = 17837.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.096598 restraints weight = 13494.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.097344 restraints weight = 10683.681| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16020 Z= 0.133 Angle : 0.725 9.218 21764 Z= 0.342 Chirality : 0.042 0.241 2472 Planarity : 0.005 0.051 2660 Dihedral : 21.610 172.035 2452 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.26 % Allowed : 13.12 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.18), residues: 1884 helix: -1.40 (0.15), residues: 1008 sheet: -0.19 (0.44), residues: 200 loop : -3.28 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 151 TYR 0.014 0.001 TYR B 436 PHE 0.021 0.001 PHE C 474 TRP 0.012 0.001 TRP A 157 HIS 0.012 0.001 HIS B 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16008) covalent geometry : angle 0.72333 / 0.34 (21748) SS BOND : bond 0.00762 / 0.39 ( 8) SS BOND : angle 1.84168 / 1.03 ( 16) hydrogen bonds : bond 0.04847 / 3.10 ( 656) hydrogen bonds : angle 4.94415 / 3.45 ( 1920) Misc. bond : bond 0.00659 / 0.33 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 232 time to evaluate : 0.550 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 46 LYS cc_start: 0.9115 (tptt) cc_final: 0.8819 (tppt) REVERT: A 334 MET cc_start: 0.5946 (mtp) cc_final: 0.5497 (mmp) REVERT: A 499 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: A 511 SER cc_start: 0.9139 (m) cc_final: 0.8740 (p) REVERT: B 46 LYS cc_start: 0.9137 (tptt) cc_final: 0.8871 (tppp) REVERT: B 334 MET cc_start: 0.6022 (mtp) cc_final: 0.5550 (mmp) REVERT: B 499 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: B 511 SER cc_start: 0.9147 (m) cc_final: 0.8746 (p) REVERT: B 516 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8846 (mp) REVERT: C 46 LYS cc_start: 0.9146 (tptt) cc_final: 0.8826 (tppt) REVERT: C 297 PHE cc_start: 0.6598 (m-80) cc_final: 0.6169 (t80) REVERT: C 311 LEU cc_start: 0.8711 (pt) cc_final: 0.8004 (mt) REVERT: C 434 VAL cc_start: 0.9289 (t) cc_final: 0.9064 (p) REVERT: C 499 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: C 508 MET cc_start: 0.7636 (mtt) cc_final: 0.7386 (tmm) REVERT: C 511 SER cc_start: 0.9158 (m) cc_final: 0.8699 (p) REVERT: D 46 LYS cc_start: 0.9075 (tptt) cc_final: 0.8767 (tppt) REVERT: D 334 MET cc_start: 0.5978 (mtp) cc_final: 0.5704 (mmp) REVERT: D 459 MET cc_start: 0.8284 (tmm) cc_final: 0.7751 (tmm) REVERT: D 499 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: D 511 SER cc_start: 0.9144 (m) cc_final: 0.8747 (p) outliers start: 72 outliers final: 45 residues processed: 292 average time/residue: 0.0905 time to fit residues: 43.5039 Evaluate side-chains 242 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 86 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.106436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.091901 restraints weight = 48822.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.094012 restraints weight = 28105.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095338 restraints weight = 18826.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.096329 restraints weight = 14268.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.096994 restraints weight = 11556.388| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16020 Z= 0.137 Angle : 0.725 9.339 21764 Z= 0.343 Chirality : 0.043 0.221 2472 Planarity : 0.005 0.049 2660 Dihedral : 20.419 175.525 2452 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 5.26 % Allowed : 13.83 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.18), residues: 1884 helix: -1.07 (0.15), residues: 1008 sheet: -0.97 (0.39), residues: 244 loop : -3.12 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 322 TYR 0.014 0.001 TYR D 436 PHE 0.018 0.001 PHE B 474 TRP 0.009 0.001 TRP C 157 HIS 0.009 0.001 HIS B 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (16008) covalent geometry : angle 0.71678 / 0.34 (21748) SS BOND : bond 0.00608 / 0.31 ( 8) SS BOND : angle 4.05391 / 2.36 ( 16) hydrogen bonds : bond 0.04364 / 2.79 ( 656) hydrogen bonds : angle 4.88769 / 3.40 ( 1920) Misc. bond : bond 0.00611 / 0.31 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 223 time to evaluate : 0.635 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: A 46 LYS cc_start: 0.9128 (tptt) cc_final: 0.8796 (tppt) REVERT: A 50 MET cc_start: 0.7519 (ttt) cc_final: 0.7063 (tmm) REVERT: A 62 LYS cc_start: 0.6190 (mttm) cc_final: 0.5924 (mmtp) REVERT: A 334 MET cc_start: 0.5821 (mtp) cc_final: 0.5420 (mmp) REVERT: A 499 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: A 511 SER cc_start: 0.9158 (m) cc_final: 0.8757 (p) REVERT: B 46 LYS cc_start: 0.9149 (tptt) cc_final: 0.8918 (tppp) REVERT: B 334 MET cc_start: 0.5772 (mtp) cc_final: 0.5386 (mmp) REVERT: B 499 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: B 511 SER cc_start: 0.9151 (m) cc_final: 0.8745 (p) REVERT: B 516 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8893 (mp) REVERT: C 46 LYS cc_start: 0.9185 (tptt) cc_final: 0.8859 (tppt) REVERT: C 297 PHE cc_start: 0.6708 (m-80) cc_final: 0.6282 (t80) REVERT: C 467 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9063 (tt) REVERT: C 499 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: C 508 MET cc_start: 0.7704 (mtt) cc_final: 0.7387 (tmm) REVERT: C 511 SER cc_start: 0.9169 (m) cc_final: 0.8700 (p) REVERT: D 46 LYS cc_start: 0.9101 (tptt) cc_final: 0.8785 (tppt) REVERT: D 291 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.4740 (pt0) REVERT: D 418 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8691 (tm) REVERT: D 459 MET cc_start: 0.7931 (tmm) cc_final: 0.7651 (tmm) REVERT: D 499 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: D 511 SER cc_start: 0.9151 (m) cc_final: 0.8749 (p) outliers start: 89 outliers final: 59 residues processed: 288 average time/residue: 0.0925 time to fit residues: 44.1528 Evaluate side-chains 257 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 190 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 177 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 0.1980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS B 103 HIS D 103 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.104914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.090104 restraints weight = 49389.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.092169 restraints weight = 28630.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.093611 restraints weight = 19290.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.094615 restraints weight = 14525.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095301 restraints weight = 11629.705| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16020 Z= 0.162 Angle : 0.720 11.159 21764 Z= 0.342 Chirality : 0.043 0.244 2472 Planarity : 0.005 0.046 2660 Dihedral : 19.714 179.276 2452 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 5.79 % Allowed : 13.95 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.19), residues: 1884 helix: -0.89 (0.15), residues: 1008 sheet: 0.04 (0.43), residues: 200 loop : -3.23 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 322 TYR 0.014 0.002 TYR D 436 PHE 0.020 0.002 PHE D 474 TRP 0.008 0.001 TRP D 335 HIS 0.007 0.001 HIS B 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (16008) covalent geometry : angle 0.71878 / 0.34 (21748) SS BOND : bond 0.00733 / 0.34 ( 8) SS BOND : angle 1.70030 / 0.93 ( 16) hydrogen bonds : bond 0.04230 / 2.71 ( 656) hydrogen bonds : angle 4.73716 / 3.31 ( 1920) Misc. bond : bond 0.00609 / 0.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 208 time to evaluate : 0.646 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: A 46 LYS cc_start: 0.9156 (tptt) cc_final: 0.8797 (tppt) REVERT: A 62 LYS cc_start: 0.6352 (mttm) cc_final: 0.6057 (mmtp) REVERT: A 334 MET cc_start: 0.5717 (mtp) cc_final: 0.5515 (mmp) REVERT: A 499 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: A 511 SER cc_start: 0.9152 (m) cc_final: 0.8779 (p) REVERT: B 46 LYS cc_start: 0.9181 (tptt) cc_final: 0.8906 (tppp) REVERT: B 499 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: B 511 SER cc_start: 0.9173 (m) cc_final: 0.8802 (p) REVERT: B 516 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8879 (mp) REVERT: C 46 LYS cc_start: 0.9180 (tptt) cc_final: 0.8832 (tppt) REVERT: C 297 PHE cc_start: 0.6672 (m-80) cc_final: 0.6287 (t80) REVERT: C 334 MET cc_start: 0.5773 (mtp) cc_final: 0.5531 (mmp) REVERT: C 467 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9028 (tt) REVERT: C 499 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: C 508 MET cc_start: 0.7696 (mtt) cc_final: 0.7465 (tmm) REVERT: C 511 SER cc_start: 0.9256 (m) cc_final: 0.8836 (p) REVERT: D 46 LYS cc_start: 0.9168 (tptt) cc_final: 0.8809 (tppt) REVERT: D 62 LYS cc_start: 0.6173 (mttm) cc_final: 0.5828 (mmtp) REVERT: D 291 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.4887 (pt0) REVERT: D 297 PHE cc_start: 0.6930 (m-80) cc_final: 0.6448 (t80) REVERT: D 373 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8325 (mm) REVERT: D 418 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8733 (tm) REVERT: D 459 MET cc_start: 0.7928 (tmm) cc_final: 0.7699 (tmm) REVERT: D 499 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: D 511 SER cc_start: 0.9161 (m) cc_final: 0.8797 (p) outliers start: 98 outliers final: 67 residues processed: 285 average time/residue: 0.0905 time to fit residues: 41.7482 Evaluate side-chains 260 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 184 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 121 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 chunk 17 optimal weight: 0.0070 chunk 42 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN B 69 GLN C 69 GLN D 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.107642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.093128 restraints weight = 48961.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.095180 restraints weight = 28174.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.096667 restraints weight = 19012.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097422 restraints weight = 14156.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.098199 restraints weight = 11729.301| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16020 Z= 0.123 Angle : 0.724 9.891 21764 Z= 0.333 Chirality : 0.042 0.226 2472 Planarity : 0.004 0.043 2660 Dihedral : 19.032 178.431 2452 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 5.08 % Allowed : 15.66 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.19), residues: 1884 helix: -0.69 (0.16), residues: 1032 sheet: 0.97 (0.44), residues: 176 loop : -3.15 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 322 TYR 0.013 0.001 TYR D 436 PHE 0.016 0.001 PHE A 313 TRP 0.016 0.001 TRP B 398 HIS 0.008 0.001 HIS B 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (16008) covalent geometry : angle 0.71148 / 0.33 (21748) SS BOND : bond 0.00847 / 0.44 ( 8) SS BOND : angle 4.89939 / 2.88 ( 16) hydrogen bonds : bond 0.04013 / 2.57 ( 656) hydrogen bonds : angle 4.63982 / 3.24 ( 1920) Misc. bond : bond 0.00555 / 0.28 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 222 time to evaluate : 0.537 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 46 LYS cc_start: 0.9117 (tptt) cc_final: 0.8756 (tppt) REVERT: A 62 LYS cc_start: 0.6218 (mttm) cc_final: 0.5978 (mmtp) REVERT: A 334 MET cc_start: 0.5716 (mtp) cc_final: 0.5497 (mmp) REVERT: A 408 PHE cc_start: 0.5212 (OUTLIER) cc_final: 0.4868 (m-80) REVERT: A 499 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: A 511 SER cc_start: 0.9170 (m) cc_final: 0.8750 (p) REVERT: B 46 LYS cc_start: 0.9138 (tptt) cc_final: 0.8861 (tppp) REVERT: B 499 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: B 511 SER cc_start: 0.9163 (m) cc_final: 0.8759 (p) REVERT: B 516 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8885 (mp) REVERT: C 46 LYS cc_start: 0.9150 (tptt) cc_final: 0.8811 (tppt) REVERT: C 297 PHE cc_start: 0.6607 (m-80) cc_final: 0.6229 (t80) REVERT: C 334 MET cc_start: 0.5738 (mtp) cc_final: 0.5501 (mmp) REVERT: C 373 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8236 (mm) REVERT: C 499 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: C 508 MET cc_start: 0.7618 (mtt) cc_final: 0.7272 (tmm) REVERT: C 510 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8078 (mm) REVERT: C 511 SER cc_start: 0.9245 (m) cc_final: 0.8807 (p) REVERT: D 46 LYS cc_start: 0.9130 (tptt) cc_final: 0.8785 (tppt) REVERT: D 62 LYS cc_start: 0.5997 (mttm) cc_final: 0.5793 (mmtp) REVERT: D 291 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.4945 (mt0) REVERT: D 297 PHE cc_start: 0.6912 (m-80) cc_final: 0.6402 (t80) REVERT: D 298 ARG cc_start: 0.8235 (ttp-170) cc_final: 0.7898 (ttm110) REVERT: D 373 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8239 (mm) REVERT: D 418 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8765 (tm) REVERT: D 499 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: D 511 SER cc_start: 0.9158 (m) cc_final: 0.8758 (p) outliers start: 86 outliers final: 53 residues processed: 287 average time/residue: 0.0997 time to fit residues: 45.2965 Evaluate side-chains 265 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 42 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.104593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089755 restraints weight = 49586.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.091827 restraints weight = 28723.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.093215 restraints weight = 19361.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094040 restraints weight = 14576.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094815 restraints weight = 12015.939| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 16020 Z= 0.174 Angle : 0.790 17.126 21764 Z= 0.371 Chirality : 0.046 0.382 2472 Planarity : 0.005 0.044 2660 Dihedral : 18.881 177.048 2452 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.85 % Allowed : 16.90 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.19), residues: 1884 helix: -0.54 (0.16), residues: 1008 sheet: 0.32 (0.42), residues: 200 loop : -2.97 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 322 TYR 0.013 0.001 TYR A 436 PHE 0.019 0.002 PHE D 474 TRP 0.010 0.001 TRP B 398 HIS 0.007 0.001 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (16008) covalent geometry : angle 0.77845 / 0.37 (21748) SS BOND : bond 0.01143 / 0.56 ( 8) SS BOND : angle 5.03423 / 2.90 ( 16) hydrogen bonds : bond 0.04099 / 2.62 ( 656) hydrogen bonds : angle 4.64957 / 3.25 ( 1920) Misc. bond : bond 0.00571 / 0.29 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 200 time to evaluate : 0.784 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: A 499 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7518 (m-80) REVERT: A 511 SER cc_start: 0.9169 (m) cc_final: 0.8772 (p) REVERT: B 46 LYS cc_start: 0.9187 (tptt) cc_final: 0.8807 (tppt) REVERT: B 334 MET cc_start: 0.5978 (mtp) cc_final: 0.5613 (mmp) REVERT: B 499 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: B 511 SER cc_start: 0.9187 (m) cc_final: 0.8822 (p) REVERT: B 516 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8892 (mp) REVERT: C 46 LYS cc_start: 0.9188 (tptt) cc_final: 0.8817 (tppt) REVERT: C 297 PHE cc_start: 0.6666 (m-80) cc_final: 0.6396 (t80) REVERT: C 334 MET cc_start: 0.5738 (mtp) cc_final: 0.5534 (mmp) REVERT: C 373 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8258 (mm) REVERT: C 499 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: C 502 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8472 (mp) REVERT: C 511 SER cc_start: 0.9251 (m) cc_final: 0.8840 (p) REVERT: D 46 LYS cc_start: 0.9163 (tptt) cc_final: 0.8804 (tppt) REVERT: D 291 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.4851 (mt0) REVERT: D 297 PHE cc_start: 0.7047 (m-80) cc_final: 0.6364 (t80) REVERT: D 373 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8248 (mm) REVERT: D 418 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8583 (tm) REVERT: D 467 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9042 (tt) REVERT: D 499 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: D 511 SER cc_start: 0.9227 (m) cc_final: 0.8870 (p) outliers start: 99 outliers final: 70 residues processed: 275 average time/residue: 0.0933 time to fit residues: 42.6288 Evaluate side-chains 273 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 192 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 180 optimal weight: 0.5980 chunk 170 optimal weight: 6.9990 chunk 169 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.105359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.090462 restraints weight = 49339.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.092510 restraints weight = 28556.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.093970 restraints weight = 19258.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.094809 restraints weight = 14311.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.095663 restraints weight = 11834.510| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16020 Z= 0.148 Angle : 0.776 13.217 21764 Z= 0.361 Chirality : 0.043 0.292 2472 Planarity : 0.004 0.041 2660 Dihedral : 18.699 179.644 2452 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 5.97 % Allowed : 16.84 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.19), residues: 1884 helix: -0.38 (0.16), residues: 1000 sheet: 0.30 (0.42), residues: 200 loop : -2.91 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 322 TYR 0.014 0.001 TYR D 254 PHE 0.021 0.001 PHE A 313 TRP 0.015 0.001 TRP B 398 HIS 0.007 0.001 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (16008) covalent geometry : angle 0.76205 / 0.35 (21748) SS BOND : bond 0.01185 / 0.59 ( 8) SS BOND : angle 5.50488 / 3.26 ( 16) hydrogen bonds : bond 0.04072 / 2.61 ( 656) hydrogen bonds : angle 4.61540 / 3.23 ( 1920) Misc. bond : bond 0.00548 / 0.27 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 209 time to evaluate : 0.605 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: A 46 LYS cc_start: 0.9199 (tptt) cc_final: 0.8791 (tppt) REVERT: A 499 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: A 511 SER cc_start: 0.9234 (m) cc_final: 0.8849 (p) REVERT: B 334 MET cc_start: 0.5984 (mtp) cc_final: 0.5597 (mmp) REVERT: B 408 PHE cc_start: 0.5102 (OUTLIER) cc_final: 0.4863 (m-80) REVERT: B 499 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: B 502 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8417 (mp) REVERT: B 511 SER cc_start: 0.9227 (m) cc_final: 0.8870 (p) REVERT: B 516 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8847 (mp) REVERT: C 46 LYS cc_start: 0.9202 (tptt) cc_final: 0.8823 (tppt) REVERT: C 297 PHE cc_start: 0.6652 (m-80) cc_final: 0.6382 (t80) REVERT: C 334 MET cc_start: 0.5764 (mtp) cc_final: 0.5522 (mmp) REVERT: C 373 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8197 (mm) REVERT: C 499 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: C 502 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8446 (mp) REVERT: C 511 SER cc_start: 0.9230 (m) cc_final: 0.8806 (p) REVERT: D 46 LYS cc_start: 0.9184 (tptt) cc_final: 0.8798 (tppt) REVERT: D 291 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.5080 (mt0) REVERT: D 297 PHE cc_start: 0.7036 (m-80) cc_final: 0.6348 (t80) REVERT: D 373 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8184 (mm) REVERT: D 459 MET cc_start: 0.8542 (tmm) cc_final: 0.7958 (tmm) REVERT: D 499 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: D 502 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8394 (mp) REVERT: D 511 SER cc_start: 0.9234 (m) cc_final: 0.8880 (p) outliers start: 101 outliers final: 74 residues processed: 288 average time/residue: 0.0882 time to fit residues: 41.9341 Evaluate side-chains 274 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 188 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 159 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 469 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.106375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.091246 restraints weight = 48432.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.093348 restraints weight = 27980.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.094688 restraints weight = 18756.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.095696 restraints weight = 14258.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.096557 restraints weight = 11487.934| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16020 Z= 0.124 Angle : 0.738 14.241 21764 Z= 0.335 Chirality : 0.042 0.315 2472 Planarity : 0.004 0.040 2660 Dihedral : 18.322 173.989 2452 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.96 % Allowed : 18.38 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.19), residues: 1884 helix: -0.20 (0.16), residues: 1000 sheet: -0.53 (0.39), residues: 240 loop : -2.60 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 168 TYR 0.012 0.001 TYR D 436 PHE 0.024 0.001 PHE D 313 TRP 0.017 0.001 TRP B 398 HIS 0.007 0.001 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (16008) covalent geometry : angle 0.73387 / 0.33 (21748) SS BOND : bond 0.00829 / 0.43 ( 8) SS BOND : angle 2.90372 / 1.33 ( 16) hydrogen bonds : bond 0.03773 / 2.42 ( 656) hydrogen bonds : angle 4.43982 / 3.11 ( 1920) Misc. bond : bond 0.00511 / 0.26 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 204 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9172 (tptt) cc_final: 0.8787 (tppt) REVERT: A 50 MET cc_start: 0.7085 (ttt) cc_final: 0.6595 (ttt) REVERT: A 334 MET cc_start: 0.5861 (mtm) cc_final: 0.5618 (mmp) REVERT: A 499 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: A 511 SER cc_start: 0.9242 (m) cc_final: 0.8860 (p) REVERT: B 50 MET cc_start: 0.7344 (tmm) cc_final: 0.6996 (tmm) REVERT: B 334 MET cc_start: 0.5923 (mtp) cc_final: 0.5570 (mmp) REVERT: B 499 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7475 (m-80) REVERT: B 502 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8423 (mp) REVERT: B 511 SER cc_start: 0.9233 (m) cc_final: 0.8872 (p) REVERT: C 297 PHE cc_start: 0.6621 (m-80) cc_final: 0.6355 (t80) REVERT: C 334 MET cc_start: 0.5752 (mtp) cc_final: 0.5517 (mmp) REVERT: C 373 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8053 (mt) REVERT: C 499 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: C 511 SER cc_start: 0.9222 (m) cc_final: 0.8792 (p) REVERT: D 46 LYS cc_start: 0.9160 (tptt) cc_final: 0.8792 (tppt) REVERT: D 291 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.5256 (mt0) REVERT: D 297 PHE cc_start: 0.6927 (m-80) cc_final: 0.6295 (t80) REVERT: D 373 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8066 (mt) REVERT: D 459 MET cc_start: 0.8508 (tmm) cc_final: 0.7713 (tmm) REVERT: D 499 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: D 502 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8454 (mp) REVERT: D 511 SER cc_start: 0.9229 (m) cc_final: 0.8877 (p) outliers start: 84 outliers final: 68 residues processed: 271 average time/residue: 0.0909 time to fit residues: 40.6510 Evaluate side-chains 268 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 191 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 44 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 79 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 469 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.107292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.092204 restraints weight = 48165.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094219 restraints weight = 27593.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.095742 restraints weight = 18587.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.096646 restraints weight = 13807.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.097439 restraints weight = 11359.265| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16020 Z= 0.131 Angle : 0.802 19.145 21764 Z= 0.365 Chirality : 0.043 0.279 2472 Planarity : 0.004 0.039 2660 Dihedral : 18.238 177.899 2452 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.96 % Allowed : 18.97 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.20), residues: 1884 helix: -0.05 (0.16), residues: 1000 sheet: 0.60 (0.42), residues: 200 loop : -2.78 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 403 TYR 0.012 0.001 TYR C 47 PHE 0.024 0.001 PHE D 313 TRP 0.018 0.001 TRP B 398 HIS 0.008 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (16008) covalent geometry : angle 0.78829 / 0.36 (21748) SS BOND : bond 0.01391 / 0.77 ( 8) SS BOND : angle 5.48717 / 3.28 ( 16) hydrogen bonds : bond 0.03908 / 2.50 ( 656) hydrogen bonds : angle 4.48951 / 3.14 ( 1920) Misc. bond : bond 0.00495 / 0.25 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 203 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9150 (tptt) cc_final: 0.8771 (tppt) REVERT: A 50 MET cc_start: 0.6811 (ttt) cc_final: 0.6420 (ttt) REVERT: A 437 LEU cc_start: 0.8755 (tm) cc_final: 0.8442 (tm) REVERT: A 499 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: A 511 SER cc_start: 0.9228 (m) cc_final: 0.8839 (p) REVERT: B 46 LYS cc_start: 0.9159 (tptt) cc_final: 0.8775 (tppt) REVERT: B 298 ARG cc_start: 0.8377 (ttp-170) cc_final: 0.8012 (ttm110) REVERT: B 334 MET cc_start: 0.5977 (mtp) cc_final: 0.5576 (mmp) REVERT: B 499 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7372 (m-80) REVERT: B 502 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8441 (mp) REVERT: B 511 SER cc_start: 0.9204 (m) cc_final: 0.8852 (p) REVERT: C 46 LYS cc_start: 0.9220 (tptt) cc_final: 0.8829 (tppt) REVERT: C 297 PHE cc_start: 0.6556 (m-80) cc_final: 0.6298 (t80) REVERT: C 334 MET cc_start: 0.5691 (mtp) cc_final: 0.5464 (mmp) REVERT: C 373 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8049 (mt) REVERT: C 499 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: C 511 SER cc_start: 0.9258 (m) cc_final: 0.8820 (p) REVERT: D 46 LYS cc_start: 0.9175 (tptt) cc_final: 0.8811 (tppt) REVERT: D 291 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.5230 (mt0) REVERT: D 297 PHE cc_start: 0.6901 (m-80) cc_final: 0.6248 (t80) REVERT: D 298 ARG cc_start: 0.8324 (ttp-170) cc_final: 0.8027 (ttm110) REVERT: D 373 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8055 (mt) REVERT: D 459 MET cc_start: 0.8485 (tmm) cc_final: 0.7718 (tmm) REVERT: D 499 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: D 511 SER cc_start: 0.9217 (m) cc_final: 0.8862 (p) outliers start: 84 outliers final: 71 residues processed: 266 average time/residue: 0.0962 time to fit residues: 41.2987 Evaluate side-chains 268 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 189 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 142 optimal weight: 0.4980 chunk 114 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 469 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.107269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.092228 restraints weight = 47962.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094354 restraints weight = 27569.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.095826 restraints weight = 18345.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.096767 restraints weight = 13544.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.097603 restraints weight = 10992.291| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16020 Z= 0.136 Angle : 0.812 17.143 21764 Z= 0.370 Chirality : 0.043 0.294 2472 Planarity : 0.004 0.039 2660 Dihedral : 18.208 176.147 2452 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 5.08 % Allowed : 19.21 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.20), residues: 1884 helix: 0.00 (0.16), residues: 1000 sheet: 0.87 (0.42), residues: 196 loop : -2.79 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 403 TYR 0.014 0.001 TYR D 254 PHE 0.023 0.001 PHE D 313 TRP 0.017 0.001 TRP C 398 HIS 0.009 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (16008) covalent geometry : angle 0.79916 / 0.36 (21748) SS BOND : bond 0.01137 / 0.62 ( 8) SS BOND : angle 5.42400 / 3.22 ( 16) hydrogen bonds : bond 0.03754 / 2.39 ( 656) hydrogen bonds : angle 4.45209 / 3.12 ( 1920) Misc. bond : bond 0.00501 / 0.25 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.15 seconds wall clock time: 38 minutes 20.85 seconds (2300.85 seconds total)