Starting phenix.real_space_refine on Tue Dec 31 21:50:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuy_35733/12_2024/8iuy_35733.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuy_35733/12_2024/8iuy_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_35733/12_2024/8iuy_35733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuy_35733/12_2024/8iuy_35733.map" model { file = "/net/cci-nas-00/data/ceres_data/8iuy_35733/12_2024/8iuy_35733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuy_35733/12_2024/8iuy_35733.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 10.58, per 1000 atoms: 0.63 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=8, 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 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: 4.19 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.28 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: 5.83 Time building geometry restraints manager: 4.58 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: 8777 13.69 - 27.38: 1078 27.38 - 41.07: 304 41.07 - 54.76: 64 54.76 - 68.45: 19 Dihedral angle restraints: 10242 sinusoidal: 4173 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 10239 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: 166 2.40 - 3.23: 15292 3.23 - 4.07: 42288 4.07 - 4.90: 74645 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132439 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 132434 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 3.420 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.060 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.600 ------------------------------------------------------------------------------- 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 : 0.010 0.098 17106 Z= 0.673 Angle : 1.416 15.512 23172 Z= 0.787 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (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 TRP 0.067 0.007 TRP A 143 HIS 0.015 0.004 HIS G 9 PHE 0.043 0.007 PHE A 464 TYR 0.034 0.004 TYR I 36 ARG 0.016 0.003 ARG D 380 *********************** 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 : 1.750 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: 1.0564 time to fit residues: 336.0675 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 : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 30.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN G 216 ASN G 368 GLN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS H 40 GLN H 77 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17106 Z= 0.248 Angle : 0.770 9.788 23172 Z= 0.403 Chirality : 0.048 0.241 2544 Planarity : 0.012 0.333 3012 Dihedral : 9.283 137.178 2490 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.68 % Allowed : 13.34 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.16), residues: 2103 helix: -0.51 (0.36), residues: 219 sheet: -1.77 (0.22), residues: 435 loop : -2.43 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 143 HIS 0.007 0.002 HIS G 9 PHE 0.027 0.003 PHE A 137 TYR 0.014 0.001 TYR D 89 ARG 0.012 0.001 ARG G 380 *********************** 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 223 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 156 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 ASN cc_start: 0.4762 (OUTLIER) cc_final: 0.4152 (t0) REVERT: A 435 ASP cc_start: 0.5857 (p0) cc_final: 0.5281 (p0) REVERT: D 430 ASN cc_start: 0.4697 (OUTLIER) cc_final: 0.4347 (t0) REVERT: E 4 LEU cc_start: 0.1977 (OUTLIER) cc_final: 0.1772 (pp) REVERT: G 141 MET cc_start: 0.7244 (mmt) cc_final: 0.7030 (mmm) REVERT: G 264 GLN cc_start: 0.5310 (OUTLIER) cc_final: 0.4848 (pp30) REVERT: G 312 MET cc_start: 0.5458 (tmt) cc_final: 0.5039 (tmt) REVERT: G 430 ASN cc_start: 0.4821 (OUTLIER) cc_final: 0.4491 (t0) REVERT: G 435 ASP cc_start: 0.5671 (p0) cc_final: 0.5457 (p0) outliers start: 67 outliers final: 20 residues processed: 197 average time/residue: 1.0269 time to fit residues: 233.3345 Evaluate side-chains 122 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 430 ASN 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 193 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 264 GLN Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 18 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.0020 chunk 58 optimal weight: 8.9990 chunk 156 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 188 optimal weight: 0.8980 chunk 203 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN D 373 GLN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN I 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17106 Z= 0.202 Angle : 0.721 14.805 23172 Z= 0.373 Chirality : 0.046 0.219 2544 Planarity : 0.006 0.079 3012 Dihedral : 9.465 173.652 2490 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.22 % Allowed : 16.31 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.16), residues: 2103 helix: -0.30 (0.37), residues: 219 sheet: -1.31 (0.21), residues: 483 loop : -2.22 (0.14), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 143 HIS 0.005 0.002 HIS A 8 PHE 0.032 0.002 PHE D 137 TYR 0.010 0.001 TYR A 300 ARG 0.020 0.001 ARG G 380 *********************** 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 222 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 127 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6489 (pm20) REVERT: A 329 PHE cc_start: 0.5241 (OUTLIER) cc_final: 0.4041 (m-80) REVERT: A 340 TRP cc_start: 0.3237 (OUTLIER) cc_final: 0.1733 (m-10) REVERT: D 202 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6789 (pt0) REVERT: D 312 MET cc_start: 0.5478 (tmt) cc_final: 0.4906 (tmt) REVERT: D 329 PHE cc_start: 0.4637 (OUTLIER) cc_final: 0.4017 (m-80) REVERT: D 340 TRP cc_start: 0.3450 (OUTLIER) cc_final: 0.2259 (m-10) REVERT: D 446 GLU cc_start: 0.4708 (OUTLIER) cc_final: 0.4280 (mt-10) REVERT: G 110 ASP cc_start: 0.6345 (t0) cc_final: 0.6078 (t70) REVERT: G 121 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.6126 (pt) REVERT: G 312 MET cc_start: 0.5487 (OUTLIER) cc_final: 0.4979 (tmt) REVERT: G 329 PHE cc_start: 0.4887 (OUTLIER) cc_final: 0.4562 (t80) REVERT: G 340 TRP cc_start: 0.3375 (OUTLIER) cc_final: 0.1931 (m-10) outliers start: 95 outliers final: 28 residues processed: 195 average time/residue: 0.9155 time to fit residues: 208.6561 Evaluate side-chains 151 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 196 VAL 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 B residue 4 LEU 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 202 GLN 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 446 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 31 THR 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 196 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 312 MET Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 380 ARG Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 98 optimal weight: 0.0050 chunk 179 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.1200 ------------------------------------------------------------------------------- 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 288 ASN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 HIS ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 373 GLN D 387 GLN D 451 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** G 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN I 55 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17106 Z= 0.425 Angle : 0.944 12.193 23172 Z= 0.488 Chirality : 0.053 0.231 2544 Planarity : 0.010 0.396 3012 Dihedral : 9.703 178.646 2490 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 6.53 % Allowed : 17.96 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.17), residues: 2103 helix: -0.41 (0.34), residues: 216 sheet: -1.52 (0.21), residues: 501 loop : -2.23 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 102 HIS 0.013 0.003 HIS D 8 PHE 0.026 0.003 PHE D 329 TYR 0.022 0.002 TYR D 300 ARG 0.053 0.002 ARG A 380 *********************** 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 266 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 147 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7458 (mmtt) cc_final: 0.7238 (mtmp) REVERT: A 329 PHE cc_start: 0.6451 (OUTLIER) cc_final: 0.6117 (m-80) REVERT: A 340 TRP cc_start: 0.3075 (OUTLIER) cc_final: 0.2161 (m-10) REVERT: A 479 ARG cc_start: 0.3460 (mtm180) cc_final: 0.3008 (mpt180) REVERT: A 493 MET cc_start: -0.0734 (OUTLIER) cc_final: -0.0981 (ppp) REVERT: D 45 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7333 (tttt) REVERT: D 329 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6214 (m-80) REVERT: D 340 TRP cc_start: 0.3627 (OUTLIER) cc_final: 0.2114 (m-10) REVERT: G 329 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.5905 (m-80) REVERT: G 340 TRP cc_start: 0.3698 (OUTLIER) cc_final: 0.2187 (m-10) REVERT: G 429 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6808 (mp0) outliers start: 119 outliers final: 49 residues processed: 235 average time/residue: 1.0793 time to fit residues: 290.4596 Evaluate side-chains 177 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 120 time to evaluate : 1.911 ------------------------------------------------------------------------------- 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 21 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 430 ASN 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 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LYS 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 380 ARG Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 439 SER 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 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 17 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 45 LYS 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 257 MET Chi-restraints excluded: chain G residue 314 ASN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 179 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 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 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17106 Z= 0.221 Angle : 0.778 19.835 23172 Z= 0.385 Chirality : 0.046 0.186 2544 Planarity : 0.008 0.327 3012 Dihedral : 9.146 175.606 2490 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.90 % Allowed : 22.08 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.17), residues: 2103 helix: 0.10 (0.35), residues: 222 sheet: -1.28 (0.21), residues: 561 loop : -1.99 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 35 HIS 0.005 0.002 HIS A 9 PHE 0.018 0.002 PHE G 116 TYR 0.016 0.001 TYR D 348 ARG 0.021 0.001 ARG G 23 *********************** 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 205 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 134 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7390 (mmtt) cc_final: 0.7172 (mtmp) REVERT: A 329 PHE cc_start: 0.6538 (OUTLIER) cc_final: 0.5966 (m-80) REVERT: A 340 TRP cc_start: 0.2692 (OUTLIER) cc_final: 0.1883 (m-10) REVERT: A 430 ASN cc_start: 0.4692 (OUTLIER) cc_final: 0.4420 (t0) REVERT: A 493 MET cc_start: -0.0258 (OUTLIER) cc_final: -0.0949 (tpp) REVERT: D 6 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6615 (mt) REVERT: D 329 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.5992 (m-80) REVERT: D 340 TRP cc_start: 0.3537 (OUTLIER) cc_final: 0.1772 (m-10) REVERT: D 493 MET cc_start: 0.0263 (tmt) cc_final: -0.1054 (tpt) REVERT: F 98 PHE cc_start: 0.4107 (OUTLIER) cc_final: 0.3217 (m-80) REVERT: G 203 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: G 329 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.6099 (m-80) REVERT: G 340 TRP cc_start: 0.3671 (OUTLIER) cc_final: 0.2203 (m-10) REVERT: G 493 MET cc_start: -0.0620 (tmt) cc_final: -0.1746 (tpp) REVERT: H 4 LEU cc_start: 0.1404 (OUTLIER) cc_final: 0.1203 (pp) outliers start: 71 outliers final: 22 residues processed: 190 average time/residue: 1.0149 time to fit residues: 222.4244 Evaluate side-chains 145 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 250 SER 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 430 ASN Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain D residue 6 LEU 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 433 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 203 GLN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 chunk 200 optimal weight: 6.9990 chunk 166 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17106 Z= 0.320 Angle : 0.831 18.365 23172 Z= 0.418 Chirality : 0.049 0.214 2544 Planarity : 0.012 0.431 3012 Dihedral : 9.403 158.859 2490 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.89 % Allowed : 22.41 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.17), residues: 2103 helix: 0.13 (0.35), residues: 222 sheet: -0.96 (0.21), residues: 597 loop : -2.09 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 35 HIS 0.008 0.002 HIS G 352 PHE 0.021 0.002 PHE D 329 TYR 0.025 0.002 TYR D 445 ARG 0.041 0.001 ARG D 23 *********************** 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 223 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 134 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7479 (mm) REVERT: A 302 LYS cc_start: 0.7364 (mmtt) cc_final: 0.7162 (mtmp) REVERT: A 329 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.6157 (m-80) REVERT: A 340 TRP cc_start: 0.2799 (OUTLIER) cc_final: 0.1899 (m-10) REVERT: A 378 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5512 (mt) REVERT: A 493 MET cc_start: -0.0306 (OUTLIER) cc_final: -0.0987 (tpp) REVERT: B 103 TYR cc_start: 0.2093 (OUTLIER) cc_final: 0.0418 (m-80) REVERT: C 98 PHE cc_start: 0.3918 (OUTLIER) cc_final: 0.3442 (m-80) REVERT: D 6 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6550 (mt) REVERT: D 131 ARG cc_start: 0.5020 (mtp85) cc_final: 0.3845 (pmt-80) REVERT: D 329 PHE cc_start: 0.6803 (OUTLIER) cc_final: 0.6050 (m-80) REVERT: D 340 TRP cc_start: 0.3650 (OUTLIER) cc_final: 0.1944 (m-10) REVERT: D 430 ASN cc_start: 0.5362 (OUTLIER) cc_final: 0.5030 (t0) REVERT: D 493 MET cc_start: -0.0306 (tmt) cc_final: -0.1701 (tpt) REVERT: E 103 TYR cc_start: 0.1697 (OUTLIER) cc_final: 0.0114 (m-80) REVERT: F 98 PHE cc_start: 0.4252 (OUTLIER) cc_final: 0.3342 (m-80) REVERT: G 203 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: G 329 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.6285 (m-80) REVERT: G 340 TRP cc_start: 0.3569 (OUTLIER) cc_final: 0.2203 (m-10) REVERT: G 493 MET cc_start: -0.0752 (tmt) cc_final: -0.1898 (tpp) REVERT: H 103 TYR cc_start: 0.1842 (OUTLIER) cc_final: 0.0293 (m-80) outliers start: 89 outliers final: 41 residues processed: 201 average time/residue: 0.9762 time to fit residues: 227.0577 Evaluate side-chains 178 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 120 time to evaluate : 1.808 ------------------------------------------------------------------------------- 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 174 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 360 THR 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 57 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 74 SER 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 430 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 103 TYR 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 25 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 314 ASN Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 103 TYR 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 193 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 199 optimal weight: 9.9990 chunk 124 optimal weight: 0.0170 chunk 121 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7822 ------------------------------------------------------------------------------- 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** D 191 ASN D 373 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17106 Z= 0.218 Angle : 0.744 16.208 23172 Z= 0.368 Chirality : 0.045 0.197 2544 Planarity : 0.008 0.252 3012 Dihedral : 8.866 165.948 2490 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.90 % Allowed : 23.78 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.18), residues: 2103 helix: -0.01 (0.35), residues: 243 sheet: -0.80 (0.22), residues: 561 loop : -1.87 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 35 HIS 0.005 0.001 HIS G 9 PHE 0.018 0.002 PHE D 329 TYR 0.019 0.001 TYR G 445 ARG 0.032 0.001 ARG D 23 *********************** 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 206 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 135 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7449 (mm) REVERT: A 203 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7159 (mt0) REVERT: A 302 LYS cc_start: 0.7356 (mmtt) cc_final: 0.7155 (mtmp) REVERT: A 329 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: A 340 TRP cc_start: 0.2784 (OUTLIER) cc_final: 0.1844 (m-10) REVERT: A 378 LEU cc_start: 0.5725 (OUTLIER) cc_final: 0.5503 (mt) REVERT: A 493 MET cc_start: -0.0285 (OUTLIER) cc_final: -0.1026 (tpt) REVERT: B 103 TYR cc_start: 0.1899 (OUTLIER) cc_final: 0.0178 (m-80) REVERT: C 98 PHE cc_start: 0.3697 (OUTLIER) cc_final: 0.3226 (m-80) REVERT: D 74 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8226 (m) REVERT: D 131 ARG cc_start: 0.4941 (mtp85) cc_final: 0.3866 (pmt-80) REVERT: D 329 PHE cc_start: 0.6613 (OUTLIER) cc_final: 0.5903 (m-80) REVERT: D 340 TRP cc_start: 0.3652 (OUTLIER) cc_final: 0.1779 (m-10) REVERT: E 103 TYR cc_start: 0.1718 (OUTLIER) cc_final: 0.0102 (m-80) REVERT: F 98 PHE cc_start: 0.4232 (OUTLIER) cc_final: 0.3282 (m-80) REVERT: G 203 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: G 329 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6189 (m-80) REVERT: G 340 TRP cc_start: 0.3344 (OUTLIER) cc_final: 0.1907 (m-10) REVERT: G 493 MET cc_start: -0.0855 (tmt) cc_final: -0.1621 (tpt) REVERT: H 103 TYR cc_start: 0.1386 (OUTLIER) cc_final: -0.0113 (m-80) outliers start: 71 outliers final: 36 residues processed: 190 average time/residue: 0.9915 time to fit residues: 218.3445 Evaluate side-chains 172 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 119 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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 127 THR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 GLN 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 378 LEU Chi-restraints excluded: chain A residue 380 ARG 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 B residue 103 TYR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 74 SER 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 257 MET Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP 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 E residue 72 ARG Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 296 LYS Chi-restraints excluded: chain G residue 314 ASN Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 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 103 TYR Chi-restraints excluded: chain I residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.0170 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 18 optimal weight: 0.0010 chunk 156 optimal weight: 3.9990 overall best weight: 0.9226 ------------------------------------------------------------------------------- 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** D 468 HIS ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 451 GLN G 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.7172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17106 Z= 0.240 Angle : 0.762 19.281 23172 Z= 0.378 Chirality : 0.046 0.221 2544 Planarity : 0.010 0.437 3012 Dihedral : 9.212 176.650 2490 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.73 % Allowed : 24.44 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.18), residues: 2103 helix: 0.02 (0.35), residues: 243 sheet: -0.86 (0.21), residues: 591 loop : -1.89 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 35 HIS 0.006 0.002 HIS A 9 PHE 0.017 0.002 PHE D 329 TYR 0.020 0.001 TYR G 445 ARG 0.034 0.001 ARG A 23 *********************** 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 201 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 133 time to evaluate : 1.868 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 174 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7562 (mm) REVERT: A 329 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.6376 (m-80) REVERT: A 340 TRP cc_start: 0.2607 (OUTLIER) cc_final: 0.1636 (m-10) REVERT: A 378 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.5386 (mt) REVERT: A 436 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.6019 (mm) REVERT: A 493 MET cc_start: -0.0058 (OUTLIER) cc_final: -0.1059 (tpt) REVERT: B 103 TYR cc_start: 0.1814 (OUTLIER) cc_final: 0.0149 (m-80) REVERT: C 98 PHE cc_start: 0.3692 (OUTLIER) cc_final: 0.3219 (m-80) REVERT: D 74 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.8076 (m) REVERT: D 131 ARG cc_start: 0.5045 (mtp85) cc_final: 0.3932 (pmt-80) REVERT: D 329 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.5938 (m-80) REVERT: D 340 TRP cc_start: 0.3663 (OUTLIER) cc_final: 0.1734 (m-10) REVERT: D 453 ARG cc_start: 0.3784 (OUTLIER) cc_final: 0.3382 (tpm-80) REVERT: D 493 MET cc_start: -0.0299 (tmt) cc_final: -0.1270 (tpp) REVERT: E 103 TYR cc_start: 0.1586 (OUTLIER) cc_final: 0.0007 (m-80) REVERT: F 98 PHE cc_start: 0.4187 (OUTLIER) cc_final: 0.3214 (m-80) REVERT: G 329 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: G 340 TRP cc_start: 0.3237 (OUTLIER) cc_final: 0.1811 (m-10) REVERT: G 493 MET cc_start: -0.0858 (tmt) cc_final: -0.1605 (tpt) REVERT: H 103 TYR cc_start: 0.1347 (OUTLIER) cc_final: -0.0141 (m-80) outliers start: 68 outliers final: 34 residues processed: 187 average time/residue: 0.9714 time to fit residues: 210.9641 Evaluate side-chains 174 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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 127 THR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 193 LEU 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 436 LEU Chi-restraints excluded: chain A residue 493 MET 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 C residue 98 PHE Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 74 SER 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 257 MET 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 D residue 453 ARG Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 189 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 360 THR Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 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 103 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 368 GLN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.7478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17106 Z= 0.255 Angle : 0.771 15.277 23172 Z= 0.382 Chirality : 0.047 0.217 2544 Planarity : 0.007 0.205 3012 Dihedral : 9.669 178.307 2490 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.68 % Allowed : 24.71 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.18), residues: 2103 helix: -0.36 (0.34), residues: 261 sheet: -0.88 (0.21), residues: 591 loop : -1.82 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 35 HIS 0.006 0.002 HIS D 275 PHE 0.017 0.002 PHE G 116 TYR 0.022 0.001 TYR G 445 ARG 0.023 0.001 ARG A 23 *********************** 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 196 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 129 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7538 (mm) REVERT: A 329 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: A 340 TRP cc_start: 0.2636 (OUTLIER) cc_final: 0.1644 (m-10) REVERT: A 378 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5850 (mt) REVERT: A 436 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6109 (mm) REVERT: A 493 MET cc_start: 0.0041 (OUTLIER) cc_final: -0.0707 (tpt) REVERT: B 103 TYR cc_start: 0.1740 (OUTLIER) cc_final: -0.0099 (m-80) REVERT: C 98 PHE cc_start: 0.3557 (OUTLIER) cc_final: 0.3152 (m-80) REVERT: D 131 ARG cc_start: 0.5037 (mtp85) cc_final: 0.3943 (pmt-80) REVERT: D 329 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6019 (m-80) REVERT: D 340 TRP cc_start: 0.3663 (OUTLIER) cc_final: 0.1686 (m-10) REVERT: D 493 MET cc_start: -0.0441 (tmt) cc_final: -0.0995 (tpt) REVERT: E 103 TYR cc_start: 0.1724 (OUTLIER) cc_final: 0.0044 (m-80) REVERT: F 98 PHE cc_start: 0.4367 (OUTLIER) cc_final: 0.3484 (m-80) REVERT: G 296 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7308 (mptp) REVERT: G 329 PHE cc_start: 0.6777 (OUTLIER) cc_final: 0.6368 (m-80) REVERT: G 340 TRP cc_start: 0.3158 (OUTLIER) cc_final: 0.1802 (m-10) REVERT: G 493 MET cc_start: -0.1304 (tmt) cc_final: -0.2009 (tpt) REVERT: H 103 TYR cc_start: 0.1365 (OUTLIER) cc_final: -0.0244 (m-80) REVERT: I 4 MET cc_start: 0.0842 (pmm) cc_final: 0.0295 (mtm) outliers start: 67 outliers final: 38 residues processed: 182 average time/residue: 0.9511 time to fit residues: 201.0917 Evaluate side-chains 171 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 117 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 127 THR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 360 THR 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 436 LEU Chi-restraints excluded: chain A residue 493 MET 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 C residue 98 PHE Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 74 SER 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 257 MET Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 8 HIS 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 360 THR Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 380 ARG Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 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 103 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 206 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.7973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 17106 Z= 0.481 Angle : 0.977 16.754 23172 Z= 0.497 Chirality : 0.055 0.245 2544 Planarity : 0.010 0.350 3012 Dihedral : 9.803 177.990 2490 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 3.79 % Allowed : 25.04 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.17), residues: 2103 helix: -1.18 (0.31), residues: 270 sheet: -1.02 (0.22), residues: 570 loop : -2.06 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP I 35 HIS 0.013 0.003 HIS A 9 PHE 0.018 0.003 PHE E 80 TYR 0.028 0.002 TYR G 445 ARG 0.060 0.002 ARG A 23 ********************** 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 188 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 119 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7395 (mm) REVERT: A 329 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: A 340 TRP cc_start: 0.3069 (OUTLIER) cc_final: 0.2037 (m-10) REVERT: A 378 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5943 (mt) REVERT: A 436 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.6066 (mm) REVERT: A 493 MET cc_start: 0.0245 (OUTLIER) cc_final: -0.0371 (tpp) REVERT: B 103 TYR cc_start: 0.1973 (OUTLIER) cc_final: 0.0349 (m-80) REVERT: C 98 PHE cc_start: 0.3356 (OUTLIER) cc_final: 0.3039 (m-80) REVERT: D 131 ARG cc_start: 0.4953 (mtp85) cc_final: 0.3867 (pmt-80) REVERT: D 165 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6796 (tm-30) REVERT: D 340 TRP cc_start: 0.3724 (OUTLIER) cc_final: 0.2393 (m-10) REVERT: D 436 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5731 (mm) REVERT: D 493 MET cc_start: -0.1011 (tmt) cc_final: -0.1617 (tpt) REVERT: E 103 TYR cc_start: 0.1826 (OUTLIER) cc_final: -0.0174 (m-80) REVERT: F 98 PHE cc_start: 0.4223 (OUTLIER) cc_final: 0.3619 (m-80) REVERT: G 329 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6531 (m-80) REVERT: G 340 TRP cc_start: 0.3280 (OUTLIER) cc_final: 0.2078 (m-10) REVERT: G 493 MET cc_start: -0.1448 (tmt) cc_final: -0.1950 (tpt) REVERT: H 103 TYR cc_start: 0.1883 (OUTLIER) cc_final: -0.0062 (m-80) REVERT: I 4 MET cc_start: 0.1157 (pmm) cc_final: 0.0710 (mmm) outliers start: 69 outliers final: 40 residues processed: 175 average time/residue: 1.0361 time to fit residues: 210.4519 Evaluate side-chains 165 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 110 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 174 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 360 THR 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 436 LEU Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 74 SER 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 257 MET Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 373 GLN Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 6 LEU 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 360 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 72 ARG 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 174 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 151 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 168 optimal weight: 0.4980 chunk 20 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 368 GLN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.234230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.184250 restraints weight = 23005.624| |-----------------------------------------------------------------------------| r_work (start): 0.4571 rms_B_bonded: 2.98 r_work: 0.4455 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.8067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 17106 Z= 0.237 Angle : 0.816 26.514 23172 Z= 0.402 Chirality : 0.047 0.274 2544 Planarity : 0.010 0.369 3012 Dihedral : 9.364 168.306 2490 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.13 % Allowed : 25.86 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.18), residues: 2103 helix: -0.07 (0.35), residues: 243 sheet: -1.00 (0.21), residues: 585 loop : -1.77 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 35 HIS 0.006 0.001 HIS A 9 PHE 0.016 0.002 PHE A 467 TYR 0.023 0.001 TYR G 445 ARG 0.046 0.001 ARG D 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5250.04 seconds wall clock time: 95 minutes 43.89 seconds (5743.89 seconds total)