Starting phenix.real_space_refine on Sun May 18 09:14:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuy_35733/05_2025/8iuy_35733.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuy_35733/05_2025/8iuy_35733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iuy_35733/05_2025/8iuy_35733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuy_35733/05_2025/8iuy_35733.map" model { file = "/net/cci-nas-00/data/ceres_data/8iuy_35733/05_2025/8iuy_35733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuy_35733/05_2025/8iuy_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.19, per 1000 atoms: 0.61 Number of scatterers: 16755 At special positions: 0 Unit cell: (152.792, 146.336, 147.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3309 8.00 N 2892 7.00 C 10470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 463 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.01 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 463 " distance=2.04 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 463 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 269 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 269 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 67 " distance=2.01 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 67 " distance=2.01 Simple disulfide: pdb=" SG CYS D 88 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 88 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 273 " - pdb=" SG CYS D 297 " distance=2.03 Simple disulfide: pdb=" SG CYS G 273 " - pdb=" SG CYS G 297 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 474 " distance=2.03 Simple disulfide: pdb=" SG CYS G 470 " - pdb=" SG CYS G 474 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 408 " " NAG A 502 " - " ASN A 29 " " NAG A 503 " - " ASN A 480 " " NAG D 501 " - " ASN D 408 " " NAG D 502 " - " ASN D 29 " " NAG D 503 " - " ASN D 480 " " NAG G 501 " - " ASN G 408 " " NAG G 502 " - " ASN G 29 " " NAG G 503 " - " ASN G 480 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.26 Conformation dependent library (CDL) restraints added in 2.6 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: 2.23 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: 7.70 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3524 1.32 - 1.46: 5200 1.46 - 1.59: 8262 1.59 - 1.72: 0 1.72 - 1.85: 120 Bond restraints: 17106 Sorted by residual: bond pdb=" CB TRP D 226 " pdb=" CG TRP D 226 " ideal model delta sigma weight residual 1.498 1.400 0.098 3.10e-02 1.04e+03 1.01e+01 bond pdb=" CB TRP G 226 " pdb=" CG TRP G 226 " ideal model delta sigma weight residual 1.498 1.400 0.098 3.10e-02 1.04e+03 1.00e+01 bond pdb=" CB TRP A 226 " pdb=" CG TRP A 226 " ideal model delta sigma weight residual 1.498 1.400 0.098 3.10e-02 1.04e+03 1.00e+01 bond pdb=" C GLY D 53 " pdb=" O GLY D 53 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.35e-02 5.49e+03 9.63e+00 bond pdb=" C GLY G 53 " pdb=" O GLY G 53 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.35e-02 5.49e+03 9.58e+00 ... (remaining 17101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 22229 3.10 - 6.20: 826 6.20 - 9.31: 87 9.31 - 12.41: 21 12.41 - 15.51: 9 Bond angle restraints: 23172 Sorted by residual: angle pdb=" N ASP E 32 " pdb=" CA ASP E 32 " pdb=" C ASP E 32 " ideal model delta sigma weight residual 108.52 117.91 -9.39 1.74e+00 3.30e-01 2.91e+01 angle pdb=" N ASP H 32 " pdb=" CA ASP H 32 " pdb=" C ASP H 32 " ideal model delta sigma weight residual 108.52 117.89 -9.37 1.74e+00 3.30e-01 2.90e+01 angle pdb=" N ASP B 32 " pdb=" CA ASP B 32 " pdb=" C ASP B 32 " ideal model delta sigma weight residual 108.52 117.89 -9.37 1.74e+00 3.30e-01 2.90e+01 angle pdb=" C CYS D 463 " pdb=" N PHE D 464 " pdb=" CA PHE D 464 " ideal model delta sigma weight residual 122.65 115.00 7.65 1.49e+00 4.50e-01 2.63e+01 angle pdb=" C CYS A 463 " pdb=" N PHE A 464 " pdb=" CA PHE A 464 " ideal model delta sigma weight residual 122.65 115.06 7.59 1.49e+00 4.50e-01 2.60e+01 ... (remaining 23167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.69: 8793 13.69 - 27.38: 1094 27.38 - 41.07: 310 41.07 - 54.76: 72 54.76 - 68.45: 21 Dihedral angle restraints: 10290 sinusoidal: 4221 harmonic: 6069 Sorted by residual: dihedral pdb=" CA TRP G 340 " pdb=" C TRP G 340 " pdb=" N GLU G 341 " pdb=" CA GLU G 341 " ideal model delta harmonic sigma weight residual 180.00 135.13 44.87 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA TRP D 340 " pdb=" C TRP D 340 " pdb=" N GLU D 341 " pdb=" CA GLU D 341 " ideal model delta harmonic sigma weight residual 180.00 135.14 44.86 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA TRP A 340 " pdb=" C TRP A 340 " pdb=" N GLU A 341 " pdb=" CA GLU A 341 " ideal model delta harmonic sigma weight residual 180.00 135.15 44.85 0 5.00e+00 4.00e-02 8.05e+01 ... (remaining 10287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1661 0.063 - 0.125: 684 0.125 - 0.188: 170 0.188 - 0.251: 14 0.251 - 0.313: 15 Chirality restraints: 2544 Sorted by residual: chirality pdb=" CB VAL A 301 " pdb=" CA VAL A 301 " pdb=" CG1 VAL A 301 " pdb=" CG2 VAL A 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL D 301 " pdb=" CA VAL D 301 " pdb=" CG1 VAL D 301 " pdb=" CG2 VAL D 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL G 301 " pdb=" CA VAL G 301 " pdb=" CG1 VAL G 301 " pdb=" CG2 VAL G 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 2541 not shown) Planarity restraints: 3021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " 0.035 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP A 143 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 143 " -0.035 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP D 143 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP D 143 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 143 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 143 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 143 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 143 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 143 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 143 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 143 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 143 " 0.035 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP G 143 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP G 143 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP G 143 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 143 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 143 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 143 " 0.004 2.00e-02 2.50e+03 ... (remaining 3018 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.56: 48 1.56 - 2.40: 150 2.40 - 3.23: 15260 3.23 - 4.07: 42288 4.07 - 4.90: 74645 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132391 Sorted by model distance: nonbonded pdb=" CE2 PHE A 329 " pdb=" CZ PHE G 329 " model vdw 0.727 3.640 nonbonded pdb=" CZ PHE A 329 " pdb=" CE2 PHE D 329 " model vdw 0.727 3.640 nonbonded pdb=" CZ PHE D 329 " pdb=" CE2 PHE G 329 " model vdw 0.728 3.640 nonbonded pdb=" NH1 ARG A 450 " pdb=" O ASP G 459 " model vdw 0.733 3.120 nonbonded pdb=" O ASP A 459 " pdb=" NH1 ARG D 450 " model vdw 0.734 3.120 ... (remaining 132386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 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: 5.410 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 42.030 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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:15.420 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5787 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.475 17145 Z= 0.984 Angle : 1.431 15.512 23247 Z= 0.789 Chirality : 0.073 0.313 2544 Planarity : 0.009 0.077 3012 Dihedral : 13.232 68.449 6348 Min Nonbonded Distance : 0.727 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 1.15 % Allowed : 7.85 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.62 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.01585 ( 9) link_NAG-ASN : angle 5.81541 ( 27) hydrogen bonds : bond 0.28380 ( 363) hydrogen bonds : angle 10.26250 ( 1017) SS BOND : bond 0.00771 ( 24) SS BOND : angle 2.03172 ( 48) covalent geometry : bond 0.01020 (17106) covalent geometry : angle 1.41635 (23172) Misc. bond : bond 0.46152 ( 6) *********************** 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 : 1.738 Fit side-chains revert: symmetry clash REVERT: A 17 VAL cc_start: 0.6192 (m) cc_final: 0.5969 (t) REVERT: A 433 THR cc_start: 0.5468 (p) cc_final: 0.4941 (m) REVERT: D 435 ASP cc_start: 0.5344 (p0) cc_final: 0.5130 (p0) REVERT: G 118 TYR cc_start: 0.7749 (m-80) cc_final: 0.7514 (m-80) outliers start: 21 outliers final: 0 residues processed: 277 average time/residue: 0.9936 time to fit residues: 315.8736 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 : 1.826 ------------------------------------------------------------------------------- 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: 0.4980 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 30.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 288 ASN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** B 40 GLN ** 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 G 147 ASN G 216 ASN G 368 GLN G 432 HIS ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS H 40 GLN H 77 ASN H 78 GLN I 90 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.248194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.202505 restraints weight = 23538.319| |-----------------------------------------------------------------------------| r_work (start): 0.4735 rms_B_bonded: 2.96 r_work: 0.4635 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17145 Z= 0.172 Angle : 0.772 9.838 23247 Z= 0.403 Chirality : 0.048 0.223 2544 Planarity : 0.012 0.312 3012 Dihedral : 9.367 141.665 2490 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.79 % Allowed : 13.34 % Favored : 82.87 % 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: -1.75 (0.22), residues: 435 loop : -2.44 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 143 HIS 0.006 0.002 HIS G 9 PHE 0.028 0.003 PHE A 137 TYR 0.013 0.001 TYR D 89 ARG 0.008 0.001 ARG G 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 9) link_NAG-ASN : angle 2.85393 ( 27) hydrogen bonds : bond 0.05069 ( 363) hydrogen bonds : angle 6.59602 ( 1017) SS BOND : bond 0.00283 ( 24) SS BOND : angle 0.75526 ( 48) covalent geometry : bond 0.00382 (17106) covalent geometry : angle 0.76629 (23172) Misc. bond : bond 0.00575 ( 6) *********************** 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: 69 poor density : 154 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4089 (tt0) cc_final: 0.3807 (tp30) REVERT: A 430 ASN cc_start: 0.4911 (OUTLIER) cc_final: 0.4271 (t0) REVERT: A 435 ASP cc_start: 0.6016 (p0) cc_final: 0.5462 (p0) REVERT: D 312 MET cc_start: 0.5278 (ttt) cc_final: 0.4896 (tmt) REVERT: D 430 ASN cc_start: 0.5149 (OUTLIER) cc_final: 0.4518 (t0) REVERT: D 435 ASP cc_start: 0.5739 (p0) cc_final: 0.5463 (p0) REVERT: E 4 LEU cc_start: 0.3631 (OUTLIER) cc_final: 0.3340 (pp) REVERT: G 264 GLN cc_start: 0.5193 (OUTLIER) cc_final: 0.4756 (pp30) REVERT: G 312 MET cc_start: 0.5636 (tmt) cc_final: 0.5191 (tmt) REVERT: G 430 ASN cc_start: 0.4848 (OUTLIER) cc_final: 0.4451 (t0) REVERT: G 435 ASP cc_start: 0.5872 (p0) cc_final: 0.5605 (p0) REVERT: H 4 LEU cc_start: 0.3025 (OUTLIER) cc_final: 0.2601 (pp) outliers start: 69 outliers final: 23 residues processed: 196 average time/residue: 0.9261 time to fit residues: 210.2891 Evaluate side-chains 131 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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 128 SER 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 128 SER Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 264 GLN Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 314 ASN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5205 r_free = 0.5205 target = 0.242498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.192337 restraints weight = 22679.000| |-----------------------------------------------------------------------------| r_work (start): 0.4702 rms_B_bonded: 3.13 r_work: 0.4589 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17145 Z= 0.157 Angle : 0.746 15.248 23247 Z= 0.386 Chirality : 0.047 0.212 2544 Planarity : 0.006 0.083 3012 Dihedral : 9.542 175.208 2490 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.49 % Allowed : 16.04 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.50 (0.16), residues: 2103 helix: -0.22 (0.37), residues: 219 sheet: -1.22 (0.23), residues: 435 loop : -2.18 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 143 HIS 0.006 0.002 HIS G 9 PHE 0.029 0.002 PHE D 137 TYR 0.012 0.001 TYR A 300 ARG 0.016 0.001 ARG G 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 9) link_NAG-ASN : angle 2.26530 ( 27) hydrogen bonds : bond 0.04485 ( 363) hydrogen bonds : angle 5.87311 ( 1017) SS BOND : bond 0.00269 ( 24) SS BOND : angle 0.84753 ( 48) covalent geometry : bond 0.00343 (17106) covalent geometry : angle 0.74220 (23172) Misc. bond : bond 0.00343 ( 6) *********************** 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 236 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 136 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6688 (pm20) REVERT: A 329 PHE cc_start: 0.5866 (OUTLIER) cc_final: 0.4616 (m-80) REVERT: A 340 TRP cc_start: 0.3558 (OUTLIER) cc_final: 0.2121 (m-10) REVERT: D 202 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6927 (pt0) REVERT: D 312 MET cc_start: 0.5621 (ttt) cc_final: 0.5022 (tmt) REVERT: D 314 ASN cc_start: 0.2596 (OUTLIER) cc_final: 0.2256 (t0) REVERT: D 329 PHE cc_start: 0.5367 (OUTLIER) cc_final: 0.4656 (m-80) REVERT: D 340 TRP cc_start: 0.3946 (OUTLIER) cc_final: 0.2523 (m-10) REVERT: D 430 ASN cc_start: 0.4918 (OUTLIER) cc_final: 0.4428 (t0) REVERT: D 446 GLU cc_start: 0.5298 (OUTLIER) cc_final: 0.4894 (mt-10) REVERT: E 4 LEU cc_start: 0.2853 (OUTLIER) cc_final: 0.2650 (pp) REVERT: G 110 ASP cc_start: 0.6799 (t0) cc_final: 0.6510 (t70) REVERT: G 114 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6697 (mtm) REVERT: G 121 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6422 (pt) REVERT: G 141 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.6934 (mmt) REVERT: G 302 LYS cc_start: 0.7620 (mmtt) cc_final: 0.7353 (mtmp) REVERT: G 312 MET cc_start: 0.5683 (tmt) cc_final: 0.5161 (tmt) REVERT: G 329 PHE cc_start: 0.5517 (OUTLIER) cc_final: 0.5076 (t80) REVERT: G 340 TRP cc_start: 0.3930 (OUTLIER) cc_final: 0.2255 (m-10) REVERT: G 435 ASP cc_start: 0.6412 (p0) cc_final: 0.6210 (p0) REVERT: G 446 GLU cc_start: 0.5090 (OUTLIER) cc_final: 0.4852 (mt-10) REVERT: G 493 MET cc_start: 0.0080 (OUTLIER) cc_final: -0.0169 (ppp) outliers start: 100 outliers final: 32 residues processed: 206 average time/residue: 0.8789 time to fit residues: 210.5599 Evaluate side-chains 162 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 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 B residue 57 THR 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 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 314 ASN 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 430 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 4 LEU 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 21 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 141 MET 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 329 PHE Chi-restraints excluded: chain G residue 340 TRP 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 G residue 446 GLU Chi-restraints excluded: chain G residue 493 MET Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 46 optimal weight: 0.4980 chunk 120 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 352 HIS ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.238968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.187405 restraints weight = 22802.980| |-----------------------------------------------------------------------------| r_work (start): 0.4652 rms_B_bonded: 3.21 r_work: 0.4542 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17145 Z= 0.168 Angle : 0.747 12.328 23247 Z= 0.381 Chirality : 0.047 0.214 2544 Planarity : 0.005 0.078 3012 Dihedral : 9.434 177.266 2490 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.77 % Allowed : 17.13 % Favored : 77.10 % 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: -2.33 (0.17), residues: 2103 helix: -0.35 (0.35), residues: 234 sheet: -1.06 (0.22), residues: 480 loop : -2.06 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 143 HIS 0.008 0.002 HIS G 9 PHE 0.019 0.002 PHE A 116 TYR 0.018 0.001 TYR D 445 ARG 0.032 0.001 ARG A 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 9) link_NAG-ASN : angle 1.95003 ( 27) hydrogen bonds : bond 0.04252 ( 363) hydrogen bonds : angle 5.50796 ( 1017) SS BOND : bond 0.00283 ( 24) SS BOND : angle 0.93982 ( 48) covalent geometry : bond 0.00375 (17106) covalent geometry : angle 0.74408 (23172) Misc. bond : bond 0.00699 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 134 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.6450 (OUTLIER) cc_final: 0.4877 (m-80) REVERT: A 340 TRP cc_start: 0.3195 (OUTLIER) cc_final: 0.2192 (m-10) REVERT: A 430 ASN cc_start: 0.4956 (OUTLIER) cc_final: 0.4327 (t0) REVERT: A 465 GLU cc_start: 0.5621 (pp20) cc_final: 0.5289 (pp20) REVERT: A 493 MET cc_start: 0.0055 (OUTLIER) cc_final: -0.0291 (ppp) REVERT: B 40 GLN cc_start: 0.5414 (OUTLIER) cc_final: 0.5151 (tp-100) REVERT: D 312 MET cc_start: 0.5657 (ttt) cc_final: 0.5286 (tmt) REVERT: D 329 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.5283 (m-80) REVERT: D 340 TRP cc_start: 0.4001 (OUTLIER) cc_final: 0.2241 (m-10) REVERT: D 358 GLU cc_start: 0.3966 (OUTLIER) cc_final: 0.3617 (tm-30) REVERT: D 430 ASN cc_start: 0.5000 (OUTLIER) cc_final: 0.4740 (t0) REVERT: G 114 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6809 (mtm) REVERT: G 141 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7371 (mmm) REVERT: G 302 LYS cc_start: 0.7749 (mmtt) cc_final: 0.7487 (mtmp) REVERT: G 329 PHE cc_start: 0.6079 (OUTLIER) cc_final: 0.5686 (t80) REVERT: G 340 TRP cc_start: 0.4108 (OUTLIER) cc_final: 0.2172 (m-10) REVERT: G 358 GLU cc_start: 0.4418 (OUTLIER) cc_final: 0.4047 (tm-30) REVERT: G 430 ASN cc_start: 0.4935 (OUTLIER) cc_final: 0.4475 (t0) REVERT: G 493 MET cc_start: -0.0194 (OUTLIER) cc_final: -0.0427 (tmt) REVERT: H 4 LEU cc_start: 0.2515 (OUTLIER) cc_final: 0.2208 (pp) outliers start: 105 outliers final: 33 residues processed: 210 average time/residue: 0.9263 time to fit residues: 226.1093 Evaluate side-chains 154 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 104 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 127 THR 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 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 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 57 THR 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 45 LYS Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 141 MET 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 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 358 GLU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 493 MET 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 78 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 180 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 chunk 170 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 166 optimal weight: 0.3980 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 60 optimal weight: 20.0000 overall best weight: 0.8962 ------------------------------------------------------------------------------- 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 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 387 GLN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5166 r_free = 0.5166 target = 0.238265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.186538 restraints weight = 22412.722| |-----------------------------------------------------------------------------| r_work (start): 0.4666 rms_B_bonded: 3.45 r_work: 0.4528 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17145 Z= 0.156 Angle : 0.781 17.661 23247 Z= 0.387 Chirality : 0.046 0.221 2544 Planarity : 0.008 0.303 3012 Dihedral : 9.056 176.789 2490 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.83 % Allowed : 20.04 % Favored : 75.12 % 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: -2.16 (0.17), residues: 2103 helix: -0.28 (0.35), residues: 234 sheet: -1.04 (0.22), residues: 471 loop : -1.88 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 35 HIS 0.006 0.002 HIS G 9 PHE 0.017 0.002 PHE A 116 TYR 0.011 0.001 TYR G 187 ARG 0.012 0.001 ARG G 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 9) link_NAG-ASN : angle 2.04487 ( 27) hydrogen bonds : bond 0.03988 ( 363) hydrogen bonds : angle 5.36170 ( 1017) SS BOND : bond 0.00248 ( 24) SS BOND : angle 0.88189 ( 48) covalent geometry : bond 0.00348 (17106) covalent geometry : angle 0.77797 (23172) Misc. bond : bond 0.00799 ( 6) *********************** 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 209 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 121 time to evaluate : 1.841 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 329 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.5122 (m-80) REVERT: A 340 TRP cc_start: 0.2923 (OUTLIER) cc_final: 0.1982 (m-10) REVERT: A 358 GLU cc_start: 0.4008 (OUTLIER) cc_final: 0.3753 (tm-30) REVERT: A 465 GLU cc_start: 0.5576 (pp20) cc_final: 0.5195 (pp20) REVERT: A 493 MET cc_start: 0.0056 (OUTLIER) cc_final: -0.0352 (ppp) REVERT: B 40 GLN cc_start: 0.5360 (OUTLIER) cc_final: 0.5119 (tp-100) REVERT: D 329 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.5346 (m-80) REVERT: D 340 TRP cc_start: 0.3820 (OUTLIER) cc_final: 0.2029 (m-10) REVERT: D 358 GLU cc_start: 0.4003 (OUTLIER) cc_final: 0.3658 (tm-30) REVERT: D 430 ASN cc_start: 0.5268 (OUTLIER) cc_final: 0.4817 (t0) REVERT: G 302 LYS cc_start: 0.7757 (mmtt) cc_final: 0.7508 (mtmp) REVERT: G 329 PHE cc_start: 0.6066 (OUTLIER) cc_final: 0.5851 (t80) REVERT: G 340 TRP cc_start: 0.4070 (OUTLIER) cc_final: 0.2312 (m-10) REVERT: G 493 MET cc_start: 0.0154 (OUTLIER) cc_final: -0.0116 (tmt) REVERT: H 4 LEU cc_start: 0.2492 (OUTLIER) cc_final: 0.2210 (pp) REVERT: I 33 LEU cc_start: 0.4927 (OUTLIER) cc_final: 0.4711 (mp) outliers start: 88 outliers final: 40 residues processed: 181 average time/residue: 0.9721 time to fit residues: 202.2250 Evaluate side-chains 162 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 108 time to evaluate : 1.628 ------------------------------------------------------------------------------- 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 196 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 358 GLU 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 E residue 23 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 17 VAL 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 206 VAL Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 493 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain I residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 156 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 206 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 8 optimal weight: 0.0770 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5151 r_free = 0.5151 target = 0.236517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.182476 restraints weight = 21838.047| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 3.71 r_work: 0.4503 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17145 Z= 0.167 Angle : 0.778 16.335 23247 Z= 0.388 Chirality : 0.047 0.314 2544 Planarity : 0.011 0.421 3012 Dihedral : 8.682 171.459 2490 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.50 % Allowed : 21.20 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.05 (0.17), residues: 2103 helix: -0.13 (0.35), residues: 240 sheet: -0.87 (0.22), residues: 525 loop : -1.89 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 35 HIS 0.006 0.002 HIS G 352 PHE 0.017 0.002 PHE D 329 TYR 0.016 0.001 TYR G 445 ARG 0.035 0.001 ARG G 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 9) link_NAG-ASN : angle 2.13125 ( 27) hydrogen bonds : bond 0.03958 ( 363) hydrogen bonds : angle 5.34874 ( 1017) SS BOND : bond 0.00250 ( 24) SS BOND : angle 0.91680 ( 48) covalent geometry : bond 0.00374 (17106) covalent geometry : angle 0.77428 (23172) Misc. bond : bond 0.00830 ( 6) *********************** 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 215 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 133 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.6449 (OUTLIER) cc_final: 0.5707 (m-80) REVERT: A 340 TRP cc_start: 0.2973 (OUTLIER) cc_final: 0.1945 (m-10) REVERT: A 358 GLU cc_start: 0.4090 (OUTLIER) cc_final: 0.3817 (tm-30) REVERT: A 378 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5702 (mt) REVERT: A 465 GLU cc_start: 0.5735 (pp20) cc_final: 0.5327 (pp20) REVERT: A 493 MET cc_start: -0.0018 (OUTLIER) cc_final: -0.0398 (ppp) REVERT: B 40 GLN cc_start: 0.5330 (OUTLIER) cc_final: 0.5108 (tp-100) REVERT: D 329 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.5844 (m-80) REVERT: D 340 TRP cc_start: 0.3755 (OUTLIER) cc_final: 0.2047 (m-10) REVERT: D 358 GLU cc_start: 0.3975 (OUTLIER) cc_final: 0.3583 (tm-30) REVERT: D 430 ASN cc_start: 0.5358 (OUTLIER) cc_final: 0.4843 (t0) REVERT: D 493 MET cc_start: 0.0138 (OUTLIER) cc_final: -0.0670 (tpt) REVERT: G 141 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7131 (mmt) REVERT: G 302 LYS cc_start: 0.7746 (mmtt) cc_final: 0.7480 (mtmp) REVERT: G 329 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5821 (m-80) REVERT: G 340 TRP cc_start: 0.3893 (OUTLIER) cc_final: 0.2227 (m-10) REVERT: G 493 MET cc_start: 0.0050 (OUTLIER) cc_final: -0.0203 (tmt) REVERT: H 4 LEU cc_start: 0.2254 (OUTLIER) cc_final: 0.2012 (pp) outliers start: 82 outliers final: 40 residues processed: 190 average time/residue: 0.9664 time to fit residues: 211.3601 Evaluate side-chains 170 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 114 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS 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 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 358 GLU 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 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 23 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 31 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 141 MET Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 206 VAL 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 403 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 493 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 109 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 373 GLN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5144 r_free = 0.5144 target = 0.235724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.183014 restraints weight = 21668.501| |-----------------------------------------------------------------------------| r_work (start): 0.4636 rms_B_bonded: 3.45 r_work: 0.4500 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17145 Z= 0.171 Angle : 0.774 14.399 23247 Z= 0.388 Chirality : 0.046 0.186 2544 Planarity : 0.010 0.432 3012 Dihedral : 8.784 177.917 2490 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.61 % Allowed : 21.97 % Favored : 73.42 % 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: -1.92 (0.17), residues: 2103 helix: -0.09 (0.35), residues: 243 sheet: -0.72 (0.23), residues: 519 loop : -1.81 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 35 HIS 0.006 0.002 HIS G 9 PHE 0.018 0.002 PHE D 329 TYR 0.013 0.001 TYR D 348 ARG 0.036 0.001 ARG G 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 9) link_NAG-ASN : angle 2.15068 ( 27) hydrogen bonds : bond 0.03848 ( 363) hydrogen bonds : angle 5.26283 ( 1017) SS BOND : bond 0.00259 ( 24) SS BOND : angle 1.11715 ( 48) covalent geometry : bond 0.00389 (17106) covalent geometry : angle 0.77026 (23172) Misc. bond : bond 0.00784 ( 6) *********************** 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 215 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 131 time to evaluate : 1.804 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 329 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.5908 (m-80) REVERT: A 340 TRP cc_start: 0.3062 (OUTLIER) cc_final: 0.1904 (m-10) REVERT: A 358 GLU cc_start: 0.4274 (OUTLIER) cc_final: 0.3997 (tm-30) REVERT: A 493 MET cc_start: 0.0220 (OUTLIER) cc_final: -0.0165 (ppp) REVERT: B 40 GLN cc_start: 0.5321 (OUTLIER) cc_final: 0.5014 (tp-100) REVERT: C 98 PHE cc_start: 0.4994 (OUTLIER) cc_final: 0.3854 (m-80) REVERT: D 329 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.6101 (m-80) REVERT: D 340 TRP cc_start: 0.3893 (OUTLIER) cc_final: 0.1972 (m-10) REVERT: D 358 GLU cc_start: 0.4127 (OUTLIER) cc_final: 0.3690 (tm-30) REVERT: D 430 ASN cc_start: 0.5340 (OUTLIER) cc_final: 0.4762 (t0) REVERT: D 493 MET cc_start: -0.0071 (OUTLIER) cc_final: -0.1007 (tpt) REVERT: F 98 PHE cc_start: 0.5498 (OUTLIER) cc_final: 0.3942 (m-80) REVERT: G 141 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7081 (mmt) REVERT: G 302 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7494 (mtmp) REVERT: G 329 PHE cc_start: 0.6308 (OUTLIER) cc_final: 0.6021 (m-80) REVERT: G 340 TRP cc_start: 0.3983 (OUTLIER) cc_final: 0.2234 (m-10) REVERT: H 4 LEU cc_start: 0.2349 (OUTLIER) cc_final: 0.2102 (pp) outliers start: 84 outliers final: 42 residues processed: 196 average time/residue: 0.9108 time to fit residues: 208.1042 Evaluate side-chains 177 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 119 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 21 THR 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 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain 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 31 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 358 GLU 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 D residue 493 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 141 MET Chi-restraints excluded: chain G residue 195 THR 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 296 LYS 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 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 111 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.236753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.184871 restraints weight = 21535.597| |-----------------------------------------------------------------------------| r_work (start): 0.4655 rms_B_bonded: 3.27 r_work: 0.4517 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17145 Z= 0.151 Angle : 0.750 15.514 23247 Z= 0.371 Chirality : 0.046 0.217 2544 Planarity : 0.009 0.350 3012 Dihedral : 9.362 178.521 2490 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.68 % Allowed : 23.06 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.79 (0.18), residues: 2103 helix: 0.04 (0.35), residues: 243 sheet: -0.58 (0.23), residues: 519 loop : -1.75 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 35 HIS 0.005 0.001 HIS G 9 PHE 0.015 0.002 PHE D 329 TYR 0.023 0.001 TYR D 445 ARG 0.030 0.001 ARG A 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 9) link_NAG-ASN : angle 2.02551 ( 27) hydrogen bonds : bond 0.03602 ( 363) hydrogen bonds : angle 5.12241 ( 1017) SS BOND : bond 0.00244 ( 24) SS BOND : angle 1.17821 ( 48) covalent geometry : bond 0.00341 (17106) covalent geometry : angle 0.74610 (23172) Misc. bond : bond 0.00813 ( 6) *********************** 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 202 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 135 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.6326 (OUTLIER) cc_final: 0.5631 (m-80) REVERT: A 340 TRP cc_start: 0.2952 (OUTLIER) cc_final: 0.1730 (m-10) REVERT: A 358 GLU cc_start: 0.4311 (OUTLIER) cc_final: 0.4055 (tm-30) REVERT: A 363 ASP cc_start: 0.3129 (OUTLIER) cc_final: 0.2865 (t0) REVERT: A 441 MET cc_start: 0.5325 (tmt) cc_final: 0.5047 (tmt) REVERT: A 493 MET cc_start: 0.0599 (OUTLIER) cc_final: -0.0136 (tpp) REVERT: B 40 GLN cc_start: 0.5392 (OUTLIER) cc_final: 0.5050 (tp-100) REVERT: C 98 PHE cc_start: 0.5074 (OUTLIER) cc_final: 0.3973 (m-80) REVERT: D 329 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.5712 (m-80) REVERT: D 340 TRP cc_start: 0.3730 (OUTLIER) cc_final: 0.1925 (m-10) REVERT: D 358 GLU cc_start: 0.3973 (OUTLIER) cc_final: 0.3636 (tm-30) REVERT: D 378 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5823 (mt) REVERT: D 493 MET cc_start: -0.0037 (OUTLIER) cc_final: -0.1003 (tpt) REVERT: F 98 PHE cc_start: 0.5585 (OUTLIER) cc_final: 0.4003 (m-80) REVERT: G 105 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7180 (mm-30) REVERT: G 302 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7461 (mtmp) REVERT: G 329 PHE cc_start: 0.5836 (OUTLIER) cc_final: 0.5555 (m-80) REVERT: G 340 TRP cc_start: 0.3785 (OUTLIER) cc_final: 0.2023 (m-10) REVERT: G 493 MET cc_start: 0.0071 (tmt) cc_final: -0.1280 (tpp) REVERT: H 4 LEU cc_start: 0.2304 (OUTLIER) cc_final: 0.2093 (pp) outliers start: 67 outliers final: 35 residues processed: 187 average time/residue: 0.8945 time to fit residues: 196.1682 Evaluate side-chains 171 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 120 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain 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 31 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 182 optimal weight: 3.9990 chunk 8 optimal weight: 0.0170 chunk 39 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 166 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 202 optimal weight: 0.0670 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5175 r_free = 0.5175 target = 0.239447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.187673 restraints weight = 21755.868| |-----------------------------------------------------------------------------| r_work (start): 0.4681 rms_B_bonded: 3.34 r_work: 0.4546 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.6921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17145 Z= 0.125 Angle : 0.727 14.380 23247 Z= 0.356 Chirality : 0.044 0.209 2544 Planarity : 0.007 0.286 3012 Dihedral : 9.397 178.750 2490 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.08 % Allowed : 24.00 % Favored : 72.93 % 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: -1.61 (0.18), residues: 2103 helix: 0.22 (0.36), residues: 243 sheet: -0.42 (0.23), residues: 519 loop : -1.67 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 35 HIS 0.003 0.001 HIS G 9 PHE 0.016 0.002 PHE G 335 TYR 0.020 0.001 TYR D 445 ARG 0.018 0.001 ARG D 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 9) link_NAG-ASN : angle 1.87753 ( 27) hydrogen bonds : bond 0.03358 ( 363) hydrogen bonds : angle 4.97569 ( 1017) SS BOND : bond 0.00240 ( 24) SS BOND : angle 1.02927 ( 48) covalent geometry : bond 0.00283 (17106) covalent geometry : angle 0.72335 (23172) Misc. bond : bond 0.00730 ( 6) *********************** 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 184 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 128 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5557 (m-80) REVERT: A 340 TRP cc_start: 0.2903 (OUTLIER) cc_final: 0.1749 (m-10) REVERT: A 430 ASN cc_start: 0.4996 (m110) cc_final: 0.4644 (t0) REVERT: A 493 MET cc_start: 0.0783 (OUTLIER) cc_final: -0.0092 (tpp) REVERT: B 40 GLN cc_start: 0.5325 (OUTLIER) cc_final: 0.5005 (tp-100) REVERT: D 329 PHE cc_start: 0.6334 (OUTLIER) cc_final: 0.5539 (m-80) REVERT: D 340 TRP cc_start: 0.3995 (OUTLIER) cc_final: 0.2365 (m-10) REVERT: D 493 MET cc_start: 0.0685 (OUTLIER) cc_final: -0.0868 (tpt) REVERT: F 98 PHE cc_start: 0.5433 (OUTLIER) cc_final: 0.3872 (m-80) REVERT: G 105 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7133 (mm-30) REVERT: G 114 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7173 (mtp) REVERT: G 302 LYS cc_start: 0.7695 (mmtt) cc_final: 0.7485 (mtmp) REVERT: G 329 PHE cc_start: 0.5620 (OUTLIER) cc_final: 0.5401 (m-80) REVERT: G 340 TRP cc_start: 0.4079 (OUTLIER) cc_final: 0.2173 (m-10) REVERT: G 493 MET cc_start: -0.0229 (tmt) cc_final: -0.1509 (tpp) REVERT: H 4 LEU cc_start: 0.2308 (OUTLIER) cc_final: 0.2064 (pp) REVERT: H 103 TYR cc_start: 0.2839 (OUTLIER) cc_final: -0.0336 (m-80) outliers start: 56 outliers final: 29 residues processed: 172 average time/residue: 0.8234 time to fit residues: 167.6163 Evaluate side-chains 163 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 103 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 160 optimal weight: 0.6980 chunk 143 optimal weight: 0.4980 chunk 153 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5176 r_free = 0.5176 target = 0.239373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.187423 restraints weight = 22065.279| |-----------------------------------------------------------------------------| r_work (start): 0.4667 rms_B_bonded: 3.69 r_work: 0.4533 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17145 Z= 0.128 Angle : 0.731 14.541 23247 Z= 0.359 Chirality : 0.044 0.203 2544 Planarity : 0.007 0.212 3012 Dihedral : 9.986 179.368 2490 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.47 % Allowed : 24.88 % Favored : 72.65 % 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: -1.51 (0.18), residues: 2103 helix: 0.51 (0.37), residues: 231 sheet: -0.50 (0.22), residues: 567 loop : -1.58 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 35 HIS 0.004 0.001 HIS A 176 PHE 0.015 0.002 PHE E 80 TYR 0.022 0.001 TYR G 445 ARG 0.012 0.001 ARG D 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 9) link_NAG-ASN : angle 1.89253 ( 27) hydrogen bonds : bond 0.03397 ( 363) hydrogen bonds : angle 4.87815 ( 1017) SS BOND : bond 0.00216 ( 24) SS BOND : angle 0.99012 ( 48) covalent geometry : bond 0.00289 (17106) covalent geometry : angle 0.72829 (23172) Misc. bond : bond 0.00731 ( 6) ********************** 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 171 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 1.668 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 329 PHE cc_start: 0.6237 (OUTLIER) cc_final: 0.5578 (m-80) REVERT: A 340 TRP cc_start: 0.2782 (OUTLIER) cc_final: 0.1581 (m-10) REVERT: A 430 ASN cc_start: 0.4935 (m110) cc_final: 0.4601 (t0) REVERT: A 493 MET cc_start: 0.0655 (OUTLIER) cc_final: -0.0209 (tpp) REVERT: B 40 GLN cc_start: 0.5211 (OUTLIER) cc_final: 0.4940 (tp-100) REVERT: D 329 PHE cc_start: 0.6299 (OUTLIER) cc_final: 0.5511 (m-80) REVERT: D 340 TRP cc_start: 0.4013 (OUTLIER) cc_final: 0.2352 (m-10) REVERT: D 493 MET cc_start: 0.0587 (OUTLIER) cc_final: -0.0888 (tpt) REVERT: F 98 PHE cc_start: 0.5018 (OUTLIER) cc_final: 0.3559 (m-80) REVERT: G 105 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7131 (mm-30) REVERT: G 114 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.7179 (mtp) REVERT: G 302 LYS cc_start: 0.7750 (mmtt) cc_final: 0.7504 (mtmp) REVERT: G 329 PHE cc_start: 0.5756 (OUTLIER) cc_final: 0.5178 (m-80) REVERT: G 340 TRP cc_start: 0.3882 (OUTLIER) cc_final: 0.1961 (m-10) REVERT: G 493 MET cc_start: -0.0611 (tmt) cc_final: -0.1694 (tpp) REVERT: H 4 LEU cc_start: 0.1963 (OUTLIER) cc_final: 0.1745 (pp) REVERT: H 103 TYR cc_start: 0.2538 (OUTLIER) cc_final: -0.0533 (m-80) outliers start: 45 outliers final: 26 residues processed: 161 average time/residue: 0.8210 time to fit residues: 156.3402 Evaluate side-chains 158 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain 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 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 D residue 493 MET Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 103 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 121 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.237462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.186571 restraints weight = 22157.816| |-----------------------------------------------------------------------------| r_work (start): 0.4659 rms_B_bonded: 3.48 r_work: 0.4514 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.7276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17145 Z= 0.147 Angle : 0.755 22.708 23247 Z= 0.372 Chirality : 0.045 0.208 2544 Planarity : 0.006 0.227 3012 Dihedral : 8.858 179.262 2490 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.86 % Allowed : 24.60 % Favored : 72.54 % 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: -1.55 (0.18), residues: 2103 helix: 0.44 (0.37), residues: 231 sheet: -0.56 (0.22), residues: 567 loop : -1.58 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 35 HIS 0.005 0.001 HIS D 352 PHE 0.015 0.002 PHE D 329 TYR 0.023 0.001 TYR D 445 ARG 0.011 0.001 ARG G 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 9) link_NAG-ASN : angle 2.01373 ( 27) hydrogen bonds : bond 0.03503 ( 363) hydrogen bonds : angle 4.92482 ( 1017) SS BOND : bond 0.00230 ( 24) SS BOND : angle 1.01972 ( 48) covalent geometry : bond 0.00332 (17106) covalent geometry : angle 0.75169 (23172) Misc. bond : bond 0.00854 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13526.75 seconds wall clock time: 233 minutes 23.82 seconds (14003.82 seconds total)