Starting phenix.real_space_refine on Sun Aug 24 03:50:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuy_35733/08_2025/8iuy_35733.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuy_35733/08_2025/8iuy_35733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iuy_35733/08_2025/8iuy_35733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuy_35733/08_2025/8iuy_35733.map" model { file = "/net/cci-nas-00/data/ceres_data/8iuy_35733/08_2025/8iuy_35733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuy_35733/08_2025/8iuy_35733.cif" } resolution = 2.9 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= -0.000 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10470 2.51 5 N 2892 2.21 5 O 3309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16755 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 940 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: D, G, E, H, F, I Time building chain proxies: 3.09, per 1000 atoms: 0.18 Number of scatterers: 16755 At special positions: 0 Unit cell: (152.792, 146.336, 147.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3309 8.00 N 2892 7.00 C 10470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 463 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.01 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 463 " distance=2.04 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 463 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 269 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 269 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 67 " distance=2.01 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 67 " distance=2.01 Simple disulfide: pdb=" SG CYS D 88 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 88 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 273 " - pdb=" SG CYS D 297 " distance=2.03 Simple disulfide: pdb=" SG CYS G 273 " - pdb=" SG CYS G 297 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 474 " distance=2.03 Simple disulfide: pdb=" SG CYS G 470 " - pdb=" SG CYS G 474 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 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=6, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 408 " " NAG A 502 " - " ASN A 29 " " NAG A 503 " - " ASN A 480 " " NAG D 501 " - " ASN D 408 " " NAG D 502 " - " ASN D 29 " " NAG D 503 " - " ASN D 480 " " NAG G 501 " - " ASN G 408 " " NAG G 502 " - " ASN G 29 " " NAG G 503 " - " ASN G 480 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 712.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 48 sheets defined 15.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 95 through 104 removed outlier: 3.869A pdb=" N ARG A 104 " --> pdb=" O ARG A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 363 through 367 removed outlier: 4.145A pdb=" N SER A 366 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 376 through 382 removed outlier: 4.414A pdb=" N ARG A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 423 removed outlier: 3.735A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 452 removed outlier: 3.564A pdb=" N ASN A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU A 436 " --> pdb=" O HIS A 432 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 removed outlier: 4.414A pdb=" N SER A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE A 478 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.503A pdb=" N ALA A 492 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 493' Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR B 91 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.105A pdb=" N ILE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 104 removed outlier: 3.869A pdb=" N ARG D 104 " --> pdb=" O ARG D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 363 through 367 removed outlier: 4.145A pdb=" N SER D 366 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 376 through 382 removed outlier: 4.414A pdb=" N ARG D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 423 removed outlier: 3.735A pdb=" N GLU D 423 " --> pdb=" O SER D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 452 removed outlier: 3.564A pdb=" N ASN D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 434 " --> pdb=" O ASN D 430 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP D 435 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU D 436 " --> pdb=" O HIS D 432 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 437 " --> pdb=" O THR D 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 449 " --> pdb=" O TYR D 445 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG D 450 " --> pdb=" O GLU D 446 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 451 " --> pdb=" O ARG D 447 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU D 452 " --> pdb=" O VAL D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 479 removed outlier: 4.414A pdb=" N SER D 477 " --> pdb=" O ASP D 473 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE D 478 " --> pdb=" O CYS D 474 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 493 removed outlier: 3.502A pdb=" N ALA D 492 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET D 493 " --> pdb=" O ARG D 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 488 through 493' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR E 91 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.105A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 104 removed outlier: 3.870A pdb=" N ARG G 104 " --> pdb=" O ARG G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 187 Processing helix chain 'G' and resid 363 through 367 removed outlier: 4.145A pdb=" N SER G 366 " --> pdb=" O ASP G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 372 Processing helix chain 'G' and resid 376 through 382 removed outlier: 4.414A pdb=" N ARG G 380 " --> pdb=" O GLY G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 423 removed outlier: 3.734A pdb=" N GLU G 423 " --> pdb=" O SER G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 452 removed outlier: 3.565A pdb=" N ASN G 430 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN G 431 " --> pdb=" O ALA G 427 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE G 434 " --> pdb=" O ASN G 430 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP G 435 " --> pdb=" O GLN G 431 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU G 436 " --> pdb=" O HIS G 432 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA G 437 " --> pdb=" O THR G 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS G 443 " --> pdb=" O SER G 439 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS G 449 " --> pdb=" O TYR G 445 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG G 450 " --> pdb=" O GLU G 446 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN G 451 " --> pdb=" O ARG G 447 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU G 452 " --> pdb=" O VAL G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 471 through 479 removed outlier: 4.415A pdb=" N SER G 477 " --> pdb=" O ASP G 473 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE G 478 " --> pdb=" O CYS G 474 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 493 removed outlier: 3.502A pdb=" N ALA G 492 " --> pdb=" O TYR G 488 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET G 493 " --> pdb=" O ARG G 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 488 through 493' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.105A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 3 through 4 removed outlier: 3.632A pdb=" N PHE A 464 " --> pdb=" O ILE A 4 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=3, first strand: chain 'A' and resid 41 through 43 removed outlier: 5.737A pdb=" N ILE A 42 " --> pdb=" O ASP A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'A' and resid 49 through 51 removed outlier: 6.444A pdb=" N ILE A 78 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 92 through 93 removed outlier: 7.200A pdb=" N LYS A 92 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N TRP A 226 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 227 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 170 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 171 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG A 248 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 92 through 93 removed outlier: 7.200A pdb=" N LYS A 92 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N TRP A 226 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 227 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 170 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N VAL A 171 " --> pdb=" O PRO A 246 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 127 through 131 removed outlier: 5.080A pdb=" N CYS A 130 " --> pdb=" O SER A 136 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 156 through 161 removed outlier: 3.656A pdb=" N MET A 156 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 239 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A 201 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=10, first strand: chain 'A' and resid 350 through 353 removed outlier: 3.783A pdb=" N HIS A 352 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 359 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 3 through 7 removed outlier: 4.733A pdb=" N GLN B 3 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 18 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS B 22 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.556A pdb=" N VAL B 12 " --> pdb=" O THR B 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=12 Processing sheet with id=13, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.739A pdb=" N SER B 59 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TRP B 37 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR B 51 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TRP B 35 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 94 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR B 112 " --> pdb=" O TYR B 94 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.890A pdb=" N HIS C 24 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 21 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 73 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER C 63 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.577A pdb=" N GLU C 105 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.912A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.632A pdb=" N PHE D 464 " --> pdb=" O ILE D 4 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=19, first strand: chain 'D' and resid 41 through 43 removed outlier: 5.737A pdb=" N ILE D 42 " --> pdb=" O ASP D 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=19 Processing sheet with id=20, first strand: chain 'D' and resid 49 through 51 removed outlier: 6.444A pdb=" N ILE D 78 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'D' and resid 92 through 93 removed outlier: 7.200A pdb=" N LYS D 92 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N TRP D 226 " --> pdb=" O LYS D 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 227 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 170 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL D 171 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG D 248 " --> pdb=" O VAL D 171 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'D' and resid 92 through 93 removed outlier: 7.200A pdb=" N LYS D 92 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N TRP D 226 " --> pdb=" O LYS D 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 227 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 170 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N VAL D 171 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'D' and resid 127 through 131 removed outlier: 5.080A pdb=" N CYS D 130 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'D' and resid 156 through 161 removed outlier: 3.655A pdb=" N MET D 156 " --> pdb=" O PHE D 239 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE D 239 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR D 201 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=26, first strand: chain 'D' and resid 350 through 353 removed outlier: 3.783A pdb=" N HIS D 352 " --> pdb=" O GLY D 359 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 359 " --> pdb=" O HIS D 352 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.732A pdb=" N GLN E 3 " --> pdb=" O THR E 25 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU E 18 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU E 83 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS E 22 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.556A pdb=" N VAL E 12 " --> pdb=" O THR E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=28 Processing sheet with id=29, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.738A pdb=" N SER E 59 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR E 51 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TRP E 35 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E 94 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR E 112 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.890A pdb=" N HIS F 24 " --> pdb=" O ASN F 5 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 21 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 73 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER F 63 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.576A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.912A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'G' and resid 3 through 4 removed outlier: 3.631A pdb=" N PHE G 464 " --> pdb=" O ILE G 4 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=35, first strand: chain 'G' and resid 41 through 43 removed outlier: 5.737A pdb=" N ILE G 42 " --> pdb=" O ASP G 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=35 Processing sheet with id=36, first strand: chain 'G' and resid 49 through 51 removed outlier: 6.444A pdb=" N ILE G 78 " --> pdb=" O ILE G 259 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'G' and resid 92 through 93 removed outlier: 7.200A pdb=" N LYS G 92 " --> pdb=" O PHE G 224 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N TRP G 226 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 227 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE G 170 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL G 171 " --> pdb=" O ARG G 248 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG G 248 " --> pdb=" O VAL G 171 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'G' and resid 92 through 93 removed outlier: 7.200A pdb=" N LYS G 92 " --> pdb=" O PHE G 224 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N TRP G 226 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 227 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE G 170 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N VAL G 171 " --> pdb=" O PRO G 246 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'G' and resid 127 through 131 removed outlier: 5.080A pdb=" N CYS G 130 " --> pdb=" O SER G 136 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'G' and resid 156 through 161 removed outlier: 3.656A pdb=" N MET G 156 " --> pdb=" O PHE G 239 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE G 239 " --> pdb=" O MET G 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR G 201 " --> pdb=" O SER G 198 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'G' and resid 273 through 274 Processing sheet with id=42, first strand: chain 'G' and resid 350 through 353 removed outlier: 3.783A pdb=" N HIS G 352 " --> pdb=" O GLY G 359 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY G 359 " --> pdb=" O HIS G 352 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.733A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS H 22 " --> pdb=" O PHE H 79 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.556A pdb=" N VAL H 12 " --> pdb=" O THR H 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=44 Processing sheet with id=45, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.739A pdb=" N SER H 59 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR H 94 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.890A pdb=" N HIS I 24 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE I 21 " --> pdb=" O LEU I 73 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU I 73 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER I 63 " --> pdb=" O THR I 74 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.577A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.912A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1017 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: 1.82 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3524 1.32 - 1.46: 5200 1.46 - 1.59: 8262 1.59 - 1.72: 0 1.72 - 1.85: 120 Bond restraints: 17106 Sorted by residual: bond pdb=" CB TRP D 226 " pdb=" CG TRP D 226 " ideal model delta sigma weight residual 1.498 1.400 0.098 3.10e-02 1.04e+03 1.01e+01 bond pdb=" CB TRP G 226 " pdb=" CG TRP G 226 " ideal model delta sigma weight residual 1.498 1.400 0.098 3.10e-02 1.04e+03 1.00e+01 bond pdb=" CB TRP A 226 " pdb=" CG TRP A 226 " ideal model delta sigma weight residual 1.498 1.400 0.098 3.10e-02 1.04e+03 1.00e+01 bond pdb=" C GLY D 53 " pdb=" O GLY D 53 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.35e-02 5.49e+03 9.63e+00 bond pdb=" C GLY G 53 " pdb=" O GLY G 53 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.35e-02 5.49e+03 9.58e+00 ... (remaining 17101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 22229 3.10 - 6.20: 826 6.20 - 9.31: 87 9.31 - 12.41: 21 12.41 - 15.51: 9 Bond angle restraints: 23172 Sorted by residual: angle pdb=" N ASP E 32 " pdb=" CA ASP E 32 " pdb=" C ASP E 32 " ideal model delta sigma weight residual 108.52 117.91 -9.39 1.74e+00 3.30e-01 2.91e+01 angle pdb=" N ASP H 32 " pdb=" CA ASP H 32 " pdb=" C ASP H 32 " ideal model delta sigma weight residual 108.52 117.89 -9.37 1.74e+00 3.30e-01 2.90e+01 angle pdb=" N ASP B 32 " pdb=" CA ASP B 32 " pdb=" C ASP B 32 " ideal model delta sigma weight residual 108.52 117.89 -9.37 1.74e+00 3.30e-01 2.90e+01 angle pdb=" C CYS D 463 " pdb=" N PHE D 464 " pdb=" CA PHE D 464 " ideal model delta sigma weight residual 122.65 115.00 7.65 1.49e+00 4.50e-01 2.63e+01 angle pdb=" C CYS A 463 " pdb=" N PHE A 464 " pdb=" CA PHE A 464 " ideal model delta sigma weight residual 122.65 115.06 7.59 1.49e+00 4.50e-01 2.60e+01 ... (remaining 23167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.69: 8793 13.69 - 27.38: 1094 27.38 - 41.07: 310 41.07 - 54.76: 72 54.76 - 68.45: 21 Dihedral angle restraints: 10290 sinusoidal: 4221 harmonic: 6069 Sorted by residual: dihedral pdb=" CA TRP G 340 " pdb=" C TRP G 340 " pdb=" N GLU G 341 " pdb=" CA GLU G 341 " ideal model delta harmonic sigma weight residual 180.00 135.13 44.87 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA TRP D 340 " pdb=" C TRP D 340 " pdb=" N GLU D 341 " pdb=" CA GLU D 341 " ideal model delta harmonic sigma weight residual 180.00 135.14 44.86 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA TRP A 340 " pdb=" C TRP A 340 " pdb=" N GLU A 341 " pdb=" CA GLU A 341 " ideal model delta harmonic sigma weight residual 180.00 135.15 44.85 0 5.00e+00 4.00e-02 8.05e+01 ... (remaining 10287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1661 0.063 - 0.125: 684 0.125 - 0.188: 170 0.188 - 0.251: 14 0.251 - 0.313: 15 Chirality restraints: 2544 Sorted by residual: chirality pdb=" CB VAL A 301 " pdb=" CA VAL A 301 " pdb=" CG1 VAL A 301 " pdb=" CG2 VAL A 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL D 301 " pdb=" CA VAL D 301 " pdb=" CG1 VAL D 301 " pdb=" CG2 VAL D 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL G 301 " pdb=" CA VAL G 301 " pdb=" CG1 VAL G 301 " pdb=" CG2 VAL G 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 2541 not shown) Planarity restraints: 3021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " 0.035 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP A 143 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 143 " -0.035 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP D 143 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP D 143 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 143 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 143 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 143 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 143 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 143 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 143 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 143 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 143 " 0.035 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP G 143 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP G 143 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP G 143 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 143 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 143 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 143 " 0.004 2.00e-02 2.50e+03 ... (remaining 3018 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.56: 48 1.56 - 2.40: 150 2.40 - 3.23: 15260 3.23 - 4.07: 42288 4.07 - 4.90: 74645 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132391 Sorted by model distance: nonbonded pdb=" CE2 PHE A 329 " pdb=" CZ PHE G 329 " model vdw 0.727 3.640 nonbonded pdb=" CZ PHE A 329 " pdb=" CE2 PHE D 329 " model vdw 0.727 3.640 nonbonded pdb=" CZ PHE D 329 " pdb=" CE2 PHE G 329 " model vdw 0.728 3.640 nonbonded pdb=" NH1 ARG A 450 " pdb=" O ASP G 459 " model vdw 0.733 3.120 nonbonded pdb=" O ASP A 459 " pdb=" NH1 ARG D 450 " model vdw 0.734 3.120 ... (remaining 132386 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 13.090 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:5.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5787 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 0.475 17145 Z= 0.984 Angle : 1.431 15.512 23247 Z= 0.789 Chirality : 0.073 0.313 2544 Planarity : 0.009 0.077 3012 Dihedral : 13.232 68.449 6348 Min Nonbonded Distance : 0.727 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 1.15 % Allowed : 7.85 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.62 % 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 aren not related in a simple way. whole: -3.89 (0.15), residues: 2103 helix: -2.36 (0.28), residues: 225 sheet: -1.90 (0.24), residues: 393 loop : -3.04 (0.13), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.003 ARG D 380 TYR 0.034 0.004 TYR I 36 PHE 0.043 0.007 PHE A 464 TRP 0.067 0.007 TRP A 143 HIS 0.015 0.004 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.01020 (17106) covalent geometry : angle 1.41635 (23172) SS BOND : bond 0.00771 ( 24) SS BOND : angle 2.03172 ( 48) hydrogen bonds : bond 0.28380 ( 363) hydrogen bonds : angle 10.26250 ( 1017) Misc. bond : bond 0.46152 ( 6) link_NAG-ASN : bond 0.01585 ( 9) link_NAG-ASN : angle 5.81541 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 262 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 17 VAL cc_start: 0.6192 (m) cc_final: 0.5969 (t) REVERT: A 433 THR cc_start: 0.5468 (p) cc_final: 0.4941 (m) REVERT: D 435 ASP cc_start: 0.5344 (p0) cc_final: 0.5130 (p0) REVERT: G 118 TYR cc_start: 0.7749 (m-80) cc_final: 0.7514 (m-80) outliers start: 21 outliers final: 0 residues processed: 277 average time/residue: 0.4224 time to fit residues: 133.3199 Evaluate side-chains 148 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 0.0570 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.0040 chunk 122 optimal weight: 1.9990 overall best weight: 0.3710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 288 ASN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS B 40 GLN B 77 ASN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN D 54 GLN D 147 ASN D 216 ASN D 314 ASN D 368 GLN D 432 HIS ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS E 40 GLN E 77 ASN ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN G 147 ASN G 216 ASN ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN G 432 HIS ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS H 40 GLN H 77 ASN H 78 GLN I 90 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5263 r_free = 0.5263 target = 0.252035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.206858 restraints weight = 23673.562| |-----------------------------------------------------------------------------| r_work (start): 0.4787 rms_B_bonded: 3.03 r_work: 0.4689 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17145 Z= 0.145 Angle : 0.747 9.146 23247 Z= 0.391 Chirality : 0.047 0.211 2544 Planarity : 0.012 0.310 3012 Dihedral : 9.347 141.818 2490 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.35 % Allowed : 13.84 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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 aren not related in a simple way. whole: -2.95 (0.16), residues: 2103 helix: -0.99 (0.34), residues: 237 sheet: -1.40 (0.23), residues: 387 loop : -2.46 (0.13), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 23 TYR 0.012 0.001 TYR D 445 PHE 0.029 0.003 PHE A 137 TRP 0.021 0.002 TRP G 143 HIS 0.005 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00310 (17106) covalent geometry : angle 0.74121 (23172) SS BOND : bond 0.00289 ( 24) SS BOND : angle 0.62980 ( 48) hydrogen bonds : bond 0.05325 ( 363) hydrogen bonds : angle 6.71827 ( 1017) Misc. bond : bond 0.00510 ( 6) link_NAG-ASN : bond 0.00427 ( 9) link_NAG-ASN : angle 2.88528 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 166 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ASN cc_start: 0.4960 (OUTLIER) cc_final: 0.4133 (t0) REVERT: A 435 ASP cc_start: 0.5718 (p0) cc_final: 0.5194 (p0) REVERT: D 312 MET cc_start: 0.5077 (ttt) cc_final: 0.4850 (tmt) REVERT: D 435 ASP cc_start: 0.5728 (p0) cc_final: 0.5439 (p0) REVERT: E 4 LEU cc_start: 0.3454 (OUTLIER) cc_final: 0.3158 (pp) REVERT: G 118 TYR cc_start: 0.8000 (m-80) cc_final: 0.7770 (m-80) REVERT: G 264 GLN cc_start: 0.5088 (OUTLIER) cc_final: 0.4650 (pp30) REVERT: G 312 MET cc_start: 0.5343 (OUTLIER) cc_final: 0.5014 (tmt) REVERT: G 435 ASP cc_start: 0.5751 (p0) cc_final: 0.5482 (p0) REVERT: H 4 LEU cc_start: 0.3075 (OUTLIER) cc_final: 0.2641 (pp) outliers start: 61 outliers final: 23 residues processed: 203 average time/residue: 0.4092 time to fit residues: 96.7874 Evaluate side-chains 136 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 264 GLN Chi-restraints excluded: chain G residue 312 MET Chi-restraints excluded: chain G residue 379 ASN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 35 optimal weight: 0.0570 chunk 75 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 373 GLN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 373 GLN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5195 r_free = 0.5195 target = 0.241486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.190716 restraints weight = 22944.451| |-----------------------------------------------------------------------------| r_work (start): 0.4688 rms_B_bonded: 3.24 r_work: 0.4574 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17145 Z= 0.195 Angle : 0.798 16.957 23247 Z= 0.415 Chirality : 0.048 0.291 2544 Planarity : 0.007 0.170 3012 Dihedral : 9.472 166.451 2490 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 5.44 % Allowed : 16.04 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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 aren not related in a simple way. whole: -2.59 (0.16), residues: 2103 helix: -0.43 (0.36), residues: 219 sheet: -1.26 (0.23), residues: 435 loop : -2.22 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 380 TYR 0.016 0.002 TYR D 445 PHE 0.029 0.003 PHE D 137 TRP 0.020 0.002 TRP D 143 HIS 0.008 0.002 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00420 (17106) covalent geometry : angle 0.79339 (23172) SS BOND : bond 0.00277 ( 24) SS BOND : angle 0.96098 ( 48) hydrogen bonds : bond 0.04665 ( 363) hydrogen bonds : angle 5.93027 ( 1017) Misc. bond : bond 0.00701 ( 6) link_NAG-ASN : bond 0.00385 ( 9) link_NAG-ASN : angle 2.43913 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 132 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6842 (pm20) REVERT: A 329 PHE cc_start: 0.6024 (OUTLIER) cc_final: 0.5044 (m-80) REVERT: A 340 TRP cc_start: 0.3500 (OUTLIER) cc_final: 0.2092 (m-10) REVERT: D 202 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.6883 (pt0) REVERT: D 312 MET cc_start: 0.5741 (ttt) cc_final: 0.5292 (tmt) REVERT: D 340 TRP cc_start: 0.3987 (OUTLIER) cc_final: 0.2533 (m-10) REVERT: D 430 ASN cc_start: 0.4735 (OUTLIER) cc_final: 0.4380 (t0) REVERT: D 446 GLU cc_start: 0.5513 (OUTLIER) cc_final: 0.5061 (mt-10) REVERT: G 110 ASP cc_start: 0.6883 (t0) cc_final: 0.6622 (t70) REVERT: G 121 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6598 (pt) REVERT: G 202 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7268 (pt0) REVERT: G 329 PHE cc_start: 0.5787 (OUTLIER) cc_final: 0.5031 (m-80) REVERT: G 340 TRP cc_start: 0.4012 (OUTLIER) cc_final: 0.2293 (m-10) REVERT: G 446 GLU cc_start: 0.5375 (OUTLIER) cc_final: 0.5115 (mt-10) REVERT: G 493 MET cc_start: -0.0048 (OUTLIER) cc_final: -0.0470 (ppp) outliers start: 99 outliers final: 36 residues processed: 207 average time/residue: 0.3944 time to fit residues: 94.7709 Evaluate side-chains 158 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 109 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain G residue 493 MET Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 186 optimal weight: 0.2980 chunk 128 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN D 155 GLN D 191 ASN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5181 r_free = 0.5181 target = 0.240076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.188663 restraints weight = 22899.119| |-----------------------------------------------------------------------------| r_work (start): 0.4663 rms_B_bonded: 3.15 r_work: 0.4554 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17145 Z= 0.155 Angle : 0.737 16.551 23247 Z= 0.372 Chirality : 0.046 0.229 2544 Planarity : 0.005 0.063 3012 Dihedral : 9.408 178.285 2490 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.66 % Allowed : 17.63 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 aren not related in a simple way. whole: -2.38 (0.16), residues: 2103 helix: 0.20 (0.37), residues: 204 sheet: -1.26 (0.21), residues: 522 loop : -2.10 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 380 TYR 0.019 0.001 TYR D 445 PHE 0.017 0.002 PHE A 335 TRP 0.015 0.002 TRP F 35 HIS 0.007 0.002 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00342 (17106) covalent geometry : angle 0.73430 (23172) SS BOND : bond 0.00253 ( 24) SS BOND : angle 0.86603 ( 48) hydrogen bonds : bond 0.04176 ( 363) hydrogen bonds : angle 5.55281 ( 1017) Misc. bond : bond 0.00654 ( 6) link_NAG-ASN : bond 0.00479 ( 9) link_NAG-ASN : angle 1.88277 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 136 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.6310 (OUTLIER) cc_final: 0.4757 (m-80) REVERT: A 340 TRP cc_start: 0.3072 (OUTLIER) cc_final: 0.2016 (m-10) REVERT: A 430 ASN cc_start: 0.4804 (OUTLIER) cc_final: 0.4170 (t0) REVERT: A 465 GLU cc_start: 0.5819 (pp20) cc_final: 0.5290 (pp20) REVERT: A 493 MET cc_start: 0.0132 (OUTLIER) cc_final: -0.0212 (ppp) REVERT: B 40 GLN cc_start: 0.5442 (OUTLIER) cc_final: 0.5229 (tp-100) REVERT: D 329 PHE cc_start: 0.5960 (OUTLIER) cc_final: 0.5027 (m-80) REVERT: D 340 TRP cc_start: 0.3915 (OUTLIER) cc_final: 0.2182 (m-10) REVERT: D 358 GLU cc_start: 0.3947 (OUTLIER) cc_final: 0.3643 (tm-30) REVERT: D 446 GLU cc_start: 0.5433 (OUTLIER) cc_final: 0.5180 (mt-10) REVERT: E 4 LEU cc_start: 0.2074 (OUTLIER) cc_final: 0.1858 (pp) REVERT: G 329 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.5045 (m-80) REVERT: G 340 TRP cc_start: 0.4079 (OUTLIER) cc_final: 0.2172 (m-10) REVERT: G 358 GLU cc_start: 0.4294 (OUTLIER) cc_final: 0.3970 (tm-30) REVERT: G 429 GLU cc_start: 0.6945 (tm-30) cc_final: 0.6719 (mp0) REVERT: H 4 LEU cc_start: 0.2580 (OUTLIER) cc_final: 0.2262 (pp) outliers start: 103 outliers final: 35 residues processed: 213 average time/residue: 0.3929 time to fit residues: 96.7329 Evaluate side-chains 156 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 107 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 358 GLU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 56 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 192 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 28 optimal weight: 0.0670 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 172 optimal weight: 0.0670 chunk 57 optimal weight: 9.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN D 387 GLN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN F 90 GLN G 314 ASN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5202 r_free = 0.5202 target = 0.242040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.190174 restraints weight = 22318.749| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 3.57 r_work: 0.4569 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17145 Z= 0.130 Angle : 0.754 19.314 23247 Z= 0.371 Chirality : 0.046 0.226 2544 Planarity : 0.007 0.265 3012 Dihedral : 8.934 174.488 2490 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.50 % Allowed : 20.15 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 aren not related in a simple way. whole: -2.13 (0.17), residues: 2103 helix: -0.03 (0.37), residues: 222 sheet: -0.92 (0.21), residues: 522 loop : -1.95 (0.15), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 23 TYR 0.022 0.001 TYR D 445 PHE 0.038 0.002 PHE D 137 TRP 0.015 0.001 TRP I 35 HIS 0.004 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00289 (17106) covalent geometry : angle 0.75244 (23172) SS BOND : bond 0.00234 ( 24) SS BOND : angle 0.78288 ( 48) hydrogen bonds : bond 0.03873 ( 363) hydrogen bonds : angle 5.27875 ( 1017) Misc. bond : bond 0.00753 ( 6) link_NAG-ASN : bond 0.00454 ( 9) link_NAG-ASN : angle 1.70853 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 120 time to evaluate : 0.718 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 329 PHE cc_start: 0.6192 (OUTLIER) cc_final: 0.4942 (m-80) REVERT: A 340 TRP cc_start: 0.3333 (OUTLIER) cc_final: 0.1723 (m-10) REVERT: A 465 GLU cc_start: 0.5386 (pp20) cc_final: 0.5038 (pp20) REVERT: A 493 MET cc_start: 0.0009 (OUTLIER) cc_final: -0.0385 (ppp) REVERT: D 114 MET cc_start: 0.7521 (mmm) cc_final: 0.6959 (mtm) REVERT: D 329 PHE cc_start: 0.6012 (OUTLIER) cc_final: 0.5467 (m-80) REVERT: D 336 ILE cc_start: 0.4334 (mt) cc_final: 0.3830 (pp) REVERT: D 340 TRP cc_start: 0.3767 (OUTLIER) cc_final: 0.2226 (m-10) REVERT: D 429 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6653 (mp0) REVERT: F 4 MET cc_start: 0.1394 (pmm) cc_final: 0.0980 (ptp) REVERT: G 155 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: G 329 PHE cc_start: 0.5977 (OUTLIER) cc_final: 0.5773 (t80) REVERT: G 340 TRP cc_start: 0.3824 (OUTLIER) cc_final: 0.1981 (m-10) REVERT: G 429 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6733 (mp0) REVERT: H 4 LEU cc_start: 0.2573 (OUTLIER) cc_final: 0.2279 (pp) outliers start: 82 outliers final: 32 residues processed: 180 average time/residue: 0.4328 time to fit residues: 89.4549 Evaluate side-chains 156 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 155 GLN Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 153 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 144 optimal weight: 0.3980 chunk 2 optimal weight: 0.0570 chunk 120 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 HIS D 191 ASN D 373 GLN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN G 373 GLN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5097 r_free = 0.5097 target = 0.230725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.177765 restraints weight = 21925.858| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 3.26 r_work: 0.4447 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 17145 Z= 0.276 Angle : 0.961 20.249 23247 Z= 0.484 Chirality : 0.052 0.218 2544 Planarity : 0.009 0.312 3012 Dihedral : 9.444 174.536 2490 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 4.72 % Allowed : 21.69 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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 aren not related in a simple way. whole: -2.30 (0.17), residues: 2103 helix: -0.52 (0.33), residues: 240 sheet: -0.98 (0.22), residues: 537 loop : -2.06 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG G 380 TYR 0.022 0.002 TYR D 445 PHE 0.028 0.003 PHE D 137 TRP 0.025 0.003 TRP I 35 HIS 0.012 0.003 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00631 (17106) covalent geometry : angle 0.95530 (23172) SS BOND : bond 0.00400 ( 24) SS BOND : angle 1.28284 ( 48) hydrogen bonds : bond 0.04876 ( 363) hydrogen bonds : angle 5.91626 ( 1017) Misc. bond : bond 0.00941 ( 6) link_NAG-ASN : bond 0.00575 ( 9) link_NAG-ASN : angle 3.01909 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 151 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.5899 (m-80) REVERT: A 340 TRP cc_start: 0.3267 (OUTLIER) cc_final: 0.2168 (m-10) REVERT: A 353 GLN cc_start: 0.3558 (tt0) cc_final: 0.3339 (mt0) REVERT: A 378 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5805 (mt) REVERT: A 493 MET cc_start: 0.0170 (OUTLIER) cc_final: -0.0226 (ppp) REVERT: B 40 GLN cc_start: 0.5097 (OUTLIER) cc_final: 0.4820 (tp-100) REVERT: D 329 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: D 340 TRP cc_start: 0.3973 (OUTLIER) cc_final: 0.2413 (m-10) REVERT: D 358 GLU cc_start: 0.4296 (OUTLIER) cc_final: 0.3882 (tm-30) REVERT: D 378 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5610 (mt) REVERT: D 436 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5853 (mm) REVERT: D 493 MET cc_start: 0.0177 (OUTLIER) cc_final: -0.0686 (tpt) REVERT: F 98 PHE cc_start: 0.5343 (OUTLIER) cc_final: 0.3951 (m-80) REVERT: G 145 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8762 (mm) REVERT: G 203 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7662 (tp40) REVERT: G 329 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: G 340 TRP cc_start: 0.3676 (OUTLIER) cc_final: 0.2326 (m-10) REVERT: G 438 ASP cc_start: 0.6102 (t0) cc_final: 0.5857 (t0) REVERT: I 33 LEU cc_start: 0.5138 (OUTLIER) cc_final: 0.4938 (tt) outliers start: 86 outliers final: 36 residues processed: 214 average time/residue: 0.4099 time to fit residues: 100.4654 Evaluate side-chains 186 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain I residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 68 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 49 optimal weight: 30.0000 chunk 158 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5160 r_free = 0.5160 target = 0.237277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.183949 restraints weight = 21657.059| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 3.59 r_work: 0.4515 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17145 Z= 0.138 Angle : 0.761 18.424 23247 Z= 0.377 Chirality : 0.045 0.186 2544 Planarity : 0.010 0.438 3012 Dihedral : 8.588 170.164 2490 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.51 % Allowed : 24.60 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 aren not related in a simple way. whole: -1.90 (0.17), residues: 2103 helix: -0.05 (0.35), residues: 240 sheet: -0.73 (0.22), residues: 561 loop : -1.82 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG G 380 TYR 0.022 0.001 TYR D 445 PHE 0.025 0.002 PHE D 137 TRP 0.039 0.002 TRP C 35 HIS 0.006 0.002 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00305 (17106) covalent geometry : angle 0.75751 (23172) SS BOND : bond 0.00351 ( 24) SS BOND : angle 0.84112 ( 48) hydrogen bonds : bond 0.03549 ( 363) hydrogen bonds : angle 5.32802 ( 1017) Misc. bond : bond 0.00852 ( 6) link_NAG-ASN : bond 0.00492 ( 9) link_NAG-ASN : angle 2.08572 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 140 time to evaluate : 0.615 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 329 PHE cc_start: 0.6562 (OUTLIER) cc_final: 0.6056 (m-80) REVERT: A 340 TRP cc_start: 0.2970 (OUTLIER) cc_final: 0.1949 (m-10) REVERT: A 493 MET cc_start: 0.0489 (OUTLIER) cc_final: -0.0210 (tpp) REVERT: B 40 GLN cc_start: 0.5224 (OUTLIER) cc_final: 0.4942 (tp-100) REVERT: D 329 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.6296 (t80) REVERT: D 340 TRP cc_start: 0.3947 (OUTLIER) cc_final: 0.2237 (m-10) REVERT: D 358 GLU cc_start: 0.3764 (OUTLIER) cc_final: 0.3467 (tm-30) REVERT: D 380 ARG cc_start: 0.4988 (OUTLIER) cc_final: 0.4607 (tmt-80) REVERT: D 430 ASN cc_start: 0.5314 (m110) cc_final: 0.4839 (t0) REVERT: D 493 MET cc_start: -0.0054 (OUTLIER) cc_final: -0.0946 (tpt) REVERT: F 4 MET cc_start: 0.1195 (pmm) cc_final: 0.0795 (ptp) REVERT: G 114 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6976 (mtp) REVERT: G 296 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7389 (mptp) REVERT: G 329 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.6041 (m-80) REVERT: G 340 TRP cc_start: 0.3770 (OUTLIER) cc_final: 0.2139 (m-10) REVERT: G 493 MET cc_start: -0.0214 (tmt) cc_final: -0.1390 (tpp) REVERT: H 4 LEU cc_start: 0.2213 (OUTLIER) cc_final: 0.1944 (pp) outliers start: 64 outliers final: 27 residues processed: 188 average time/residue: 0.3816 time to fit residues: 83.6465 Evaluate side-chains 163 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 296 LYS Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 14 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.236804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.183748 restraints weight = 21807.303| |-----------------------------------------------------------------------------| r_work (start): 0.4640 rms_B_bonded: 3.36 r_work: 0.4507 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17145 Z= 0.153 Angle : 0.802 19.615 23247 Z= 0.396 Chirality : 0.046 0.214 2544 Planarity : 0.010 0.419 3012 Dihedral : 8.596 171.686 2490 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.35 % Allowed : 24.27 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 aren not related in a simple way. whole: -1.76 (0.18), residues: 2103 helix: 0.08 (0.35), residues: 240 sheet: -0.56 (0.22), residues: 561 loop : -1.76 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.001 ARG G 380 TYR 0.016 0.001 TYR G 348 PHE 0.017 0.002 PHE D 137 TRP 0.043 0.002 TRP I 35 HIS 0.006 0.002 HIS G 8 Details of bonding type rmsd covalent geometry : bond 0.00346 (17106) covalent geometry : angle 0.79833 (23172) SS BOND : bond 0.00264 ( 24) SS BOND : angle 1.19955 ( 48) hydrogen bonds : bond 0.03615 ( 363) hydrogen bonds : angle 5.16195 ( 1017) Misc. bond : bond 0.00915 ( 6) link_NAG-ASN : bond 0.00446 ( 9) link_NAG-ASN : angle 2.14058 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 129 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASN cc_start: 0.4945 (OUTLIER) cc_final: 0.4615 (t160) REVERT: A 329 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5838 (m-80) REVERT: A 340 TRP cc_start: 0.3038 (OUTLIER) cc_final: 0.1984 (m-10) REVERT: A 493 MET cc_start: 0.0431 (OUTLIER) cc_final: -0.0268 (tpp) REVERT: B 40 GLN cc_start: 0.5234 (OUTLIER) cc_final: 0.4893 (tp-100) REVERT: B 103 TYR cc_start: 0.2909 (OUTLIER) cc_final: -0.0026 (m-80) REVERT: D 312 MET cc_start: 0.6110 (tmt) cc_final: 0.5703 (tmt) REVERT: D 329 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6372 (m-80) REVERT: D 340 TRP cc_start: 0.4138 (OUTLIER) cc_final: 0.2241 (m-10) REVERT: D 358 GLU cc_start: 0.4046 (OUTLIER) cc_final: 0.3731 (tm-30) REVERT: D 493 MET cc_start: 0.0247 (OUTLIER) cc_final: -0.0988 (tpt) REVERT: G 105 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7125 (mm-30) REVERT: G 114 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7150 (mtp) REVERT: G 296 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7398 (mptp) REVERT: G 329 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.6109 (m-80) REVERT: G 340 TRP cc_start: 0.3776 (OUTLIER) cc_final: 0.2046 (m-10) REVERT: G 430 ASN cc_start: 0.5458 (OUTLIER) cc_final: 0.4791 (t0) REVERT: G 493 MET cc_start: -0.0326 (tmt) cc_final: -0.1835 (tpp) REVERT: H 4 LEU cc_start: 0.2403 (OUTLIER) cc_final: 0.2138 (pp) outliers start: 61 outliers final: 28 residues processed: 173 average time/residue: 0.3609 time to fit residues: 73.2505 Evaluate side-chains 163 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 296 LYS Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 15 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 195 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 173 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5150 r_free = 0.5150 target = 0.236782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.184208 restraints weight = 22050.580| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 3.32 r_work: 0.4503 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.7042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17145 Z= 0.151 Angle : 0.753 14.413 23247 Z= 0.373 Chirality : 0.046 0.210 2544 Planarity : 0.007 0.239 3012 Dihedral : 8.837 171.728 2490 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.97 % Allowed : 25.21 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 aren not related in a simple way. whole: -1.68 (0.18), residues: 2103 helix: 0.11 (0.35), residues: 240 sheet: -0.54 (0.22), residues: 561 loop : -1.69 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 23 TYR 0.017 0.001 TYR G 348 PHE 0.018 0.002 PHE D 137 TRP 0.040 0.002 TRP I 35 HIS 0.005 0.002 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00343 (17106) covalent geometry : angle 0.74949 (23172) SS BOND : bond 0.00264 ( 24) SS BOND : angle 1.09429 ( 48) hydrogen bonds : bond 0.03550 ( 363) hydrogen bonds : angle 5.15775 ( 1017) Misc. bond : bond 0.00770 ( 6) link_NAG-ASN : bond 0.00441 ( 9) link_NAG-ASN : angle 2.13041 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 128 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.6364 (OUTLIER) cc_final: 0.5938 (m-80) REVERT: A 340 TRP cc_start: 0.3026 (OUTLIER) cc_final: 0.1879 (m-10) REVERT: A 493 MET cc_start: 0.0616 (OUTLIER) cc_final: -0.0183 (tpp) REVERT: B 40 GLN cc_start: 0.5197 (OUTLIER) cc_final: 0.4863 (tp-100) REVERT: B 103 TYR cc_start: 0.2797 (OUTLIER) cc_final: -0.0216 (m-80) REVERT: D 329 PHE cc_start: 0.6844 (OUTLIER) cc_final: 0.6335 (m-80) REVERT: D 340 TRP cc_start: 0.4201 (OUTLIER) cc_final: 0.2150 (m-10) REVERT: D 493 MET cc_start: 0.0620 (OUTLIER) cc_final: -0.0922 (tpt) REVERT: G 296 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7287 (mptp) REVERT: G 329 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6129 (m-80) REVERT: G 340 TRP cc_start: 0.3689 (OUTLIER) cc_final: 0.2014 (m-10) REVERT: G 430 ASN cc_start: 0.5098 (OUTLIER) cc_final: 0.4890 (t0) REVERT: G 493 MET cc_start: -0.0460 (tmt) cc_final: -0.1301 (tpt) REVERT: H 4 LEU cc_start: 0.2306 (OUTLIER) cc_final: 0.2061 (pp) REVERT: H 103 TYR cc_start: 0.2578 (OUTLIER) cc_final: -0.0473 (m-80) outliers start: 54 outliers final: 30 residues processed: 172 average time/residue: 0.3891 time to fit residues: 78.7580 Evaluate side-chains 169 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 296 LYS Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 103 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 4 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 176 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.233083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.179957 restraints weight = 22228.087| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 3.31 r_work: 0.4459 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.7362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17145 Z= 0.204 Angle : 0.844 14.412 23247 Z= 0.421 Chirality : 0.049 0.221 2544 Planarity : 0.009 0.353 3012 Dihedral : 8.987 172.162 2490 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.69 % Allowed : 25.81 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 aren not related in a simple way. whole: -1.94 (0.18), residues: 2103 helix: -0.40 (0.33), residues: 258 sheet: -0.83 (0.21), residues: 588 loop : -1.76 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG D 23 TYR 0.015 0.002 TYR D 348 PHE 0.020 0.003 PHE D 329 TRP 0.035 0.002 TRP I 35 HIS 0.009 0.002 HIS D 352 Details of bonding type rmsd covalent geometry : bond 0.00470 (17106) covalent geometry : angle 0.83937 (23172) SS BOND : bond 0.00313 ( 24) SS BOND : angle 1.16979 ( 48) hydrogen bonds : bond 0.04052 ( 363) hydrogen bonds : angle 5.37293 ( 1017) Misc. bond : bond 0.00860 ( 6) link_NAG-ASN : bond 0.00397 ( 9) link_NAG-ASN : angle 2.51282 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6295 (m-80) REVERT: A 340 TRP cc_start: 0.3099 (OUTLIER) cc_final: 0.1975 (m-10) REVERT: A 353 GLN cc_start: 0.3654 (tt0) cc_final: 0.3420 (mp10) REVERT: A 493 MET cc_start: 0.0589 (OUTLIER) cc_final: -0.0382 (tpt) REVERT: B 40 GLN cc_start: 0.5091 (OUTLIER) cc_final: 0.4732 (tp-100) REVERT: B 103 TYR cc_start: 0.3178 (OUTLIER) cc_final: -0.0327 (m-80) REVERT: D 329 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6683 (m-80) REVERT: D 340 TRP cc_start: 0.4467 (OUTLIER) cc_final: 0.2411 (m-10) REVERT: D 493 MET cc_start: 0.0491 (OUTLIER) cc_final: -0.1113 (tpt) REVERT: E 103 TYR cc_start: 0.3024 (OUTLIER) cc_final: -0.0264 (m-80) REVERT: G 329 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6319 (m-80) REVERT: G 340 TRP cc_start: 0.3678 (OUTLIER) cc_final: 0.2348 (m-10) REVERT: G 430 ASN cc_start: 0.5224 (OUTLIER) cc_final: 0.4856 (t0) REVERT: G 493 MET cc_start: -0.0159 (tmt) cc_final: -0.1034 (tpt) REVERT: H 4 LEU cc_start: 0.2346 (OUTLIER) cc_final: 0.2088 (pp) REVERT: H 103 TYR cc_start: 0.2632 (OUTLIER) cc_final: -0.0523 (m-80) outliers start: 49 outliers final: 28 residues processed: 167 average time/residue: 0.3627 time to fit residues: 71.0875 Evaluate side-chains 164 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 296 LYS Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 103 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 24 optimal weight: 0.0670 chunk 166 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5106 r_free = 0.5106 target = 0.234633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.185148 restraints weight = 22344.389| |-----------------------------------------------------------------------------| r_work (start): 0.4615 rms_B_bonded: 3.26 r_work: 0.4466 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17145 Z= 0.179 Angle : 0.810 15.676 23247 Z= 0.401 Chirality : 0.047 0.212 2544 Planarity : 0.008 0.277 3012 Dihedral : 9.427 172.562 2490 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.58 % Allowed : 25.97 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 aren not related in a simple way. whole: -1.86 (0.18), residues: 2103 helix: -0.04 (0.35), residues: 240 sheet: -0.83 (0.22), residues: 588 loop : -1.72 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 380 TYR 0.018 0.001 TYR D 348 PHE 0.021 0.002 PHE G 116 TRP 0.032 0.002 TRP I 35 HIS 0.007 0.002 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00411 (17106) covalent geometry : angle 0.80613 (23172) SS BOND : bond 0.00367 ( 24) SS BOND : angle 1.10827 ( 48) hydrogen bonds : bond 0.03694 ( 363) hydrogen bonds : angle 5.23823 ( 1017) Misc. bond : bond 0.00822 ( 6) link_NAG-ASN : bond 0.00459 ( 9) link_NAG-ASN : angle 2.32715 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5959.50 seconds wall clock time: 102 minutes 10.54 seconds (6130.54 seconds total)