Starting phenix.real_space_refine on Sun Jun 15 01:57:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuy_35733/06_2025/8iuy_35733.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuy_35733/06_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_35733/06_2025/8iuy_35733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuy_35733/06_2025/8iuy_35733.map" model { file = "/net/cci-nas-00/data/ceres_data/8iuy_35733/06_2025/8iuy_35733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuy_35733/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 4.30 Conformation dependent library (CDL) restraints added in 2.4 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: 2.51 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: 6.15 Time building geometry restraints manager: 5.13 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: 0.12 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: 2.770 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: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 41.580 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.790 ------------------------------------------------------------------------------- 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 : 1.736 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: 0.9974 time to fit residues: 316.7029 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 : 1.707 ------------------------------------------------------------------------------- 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 = 0.248179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.202482 restraints weight = 23533.274| |-----------------------------------------------------------------------------| r_work (start): 0.4735 rms_B_bonded: 2.96 r_work: 0.4633 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 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 : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4074 (tt0) cc_final: 0.3807 (tp30) REVERT: A 430 ASN cc_start: 0.4905 (OUTLIER) cc_final: 0.4268 (t0) REVERT: A 435 ASP cc_start: 0.6005 (p0) cc_final: 0.5455 (p0) REVERT: D 312 MET cc_start: 0.5283 (ttt) cc_final: 0.4913 (tmt) REVERT: D 430 ASN cc_start: 0.5144 (OUTLIER) cc_final: 0.4521 (t0) REVERT: D 435 ASP cc_start: 0.5734 (p0) cc_final: 0.5463 (p0) REVERT: E 4 LEU cc_start: 0.3618 (OUTLIER) cc_final: 0.3321 (pp) REVERT: G 264 GLN cc_start: 0.5209 (OUTLIER) cc_final: 0.4771 (pp30) REVERT: G 312 MET cc_start: 0.5641 (tmt) cc_final: 0.5199 (tmt) REVERT: G 430 ASN cc_start: 0.4847 (OUTLIER) cc_final: 0.4451 (t0) REVERT: G 435 ASP cc_start: 0.5863 (p0) cc_final: 0.5602 (p0) REVERT: H 4 LEU cc_start: 0.3177 (OUTLIER) cc_final: 0.2735 (pp) outliers start: 69 outliers final: 23 residues processed: 196 average time/residue: 0.9492 time to fit residues: 215.6533 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 : 1.775 ------------------------------------------------------------------------------- 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: 0.0770 chunk 125 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 373 GLN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.5217 r_free = 0.5217 target = 0.243874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.193581 restraints weight = 22717.072| |-----------------------------------------------------------------------------| r_work (start): 0.4714 rms_B_bonded: 3.10 r_work: 0.4606 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17145 Z= 0.146 Angle : 0.725 15.258 23247 Z= 0.375 Chirality : 0.046 0.217 2544 Planarity : 0.006 0.084 3012 Dihedral : 9.480 176.863 2490 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 5.38 % Allowed : 16.04 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.16), residues: 2103 helix: -0.21 (0.37), residues: 219 sheet: -0.95 (0.24), residues: 405 loop : -2.21 (0.14), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 143 HIS 0.005 0.002 HIS G 9 PHE 0.030 0.002 PHE D 137 TYR 0.010 0.001 TYR A 300 ARG 0.010 0.001 ARG G 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 9) link_NAG-ASN : angle 2.22846 ( 27) hydrogen bonds : bond 0.04375 ( 363) hydrogen bonds : angle 5.85185 ( 1017) SS BOND : bond 0.00260 ( 24) SS BOND : angle 0.77785 ( 48) covalent geometry : bond 0.00318 (17106) covalent geometry : angle 0.72178 (23172) Misc. bond : bond 0.00393 ( 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 233 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 135 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6753 (pt0) REVERT: A 329 PHE cc_start: 0.5627 (OUTLIER) cc_final: 0.4396 (m-80) REVERT: A 340 TRP cc_start: 0.3676 (OUTLIER) cc_final: 0.1983 (m-10) REVERT: D 202 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6876 (pt0) REVERT: D 312 MET cc_start: 0.5575 (ttt) cc_final: 0.5082 (tmt) REVERT: D 314 ASN cc_start: 0.2430 (OUTLIER) cc_final: 0.2110 (t0) REVERT: D 329 PHE cc_start: 0.5107 (OUTLIER) cc_final: 0.4352 (m-80) REVERT: D 340 TRP cc_start: 0.3847 (OUTLIER) cc_final: 0.2459 (m-10) REVERT: D 430 ASN cc_start: 0.4685 (OUTLIER) cc_final: 0.4340 (t0) REVERT: D 446 GLU cc_start: 0.5235 (OUTLIER) cc_final: 0.4803 (mt-10) REVERT: E 88 THR cc_start: 0.7152 (t) cc_final: 0.6949 (m) REVERT: G 110 ASP cc_start: 0.6809 (t0) cc_final: 0.6515 (t70) REVERT: G 114 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6645 (mtm) REVERT: G 121 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6289 (pt) REVERT: G 312 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.5087 (tmt) REVERT: G 329 PHE cc_start: 0.5407 (OUTLIER) cc_final: 0.5033 (t80) REVERT: G 340 TRP cc_start: 0.3762 (OUTLIER) cc_final: 0.2123 (m-10) REVERT: G 435 ASP cc_start: 0.6269 (p0) cc_final: 0.6066 (p0) REVERT: G 446 GLU cc_start: 0.5115 (OUTLIER) cc_final: 0.4887 (mt-10) REVERT: G 493 MET cc_start: 0.0079 (OUTLIER) cc_final: -0.0171 (ppp) outliers start: 98 outliers final: 29 residues processed: 203 average time/residue: 0.9563 time to fit residues: 224.9880 Evaluate side-chains 159 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 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 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 193 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 312 MET Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 46 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 28 optimal weight: 0.0570 chunk 200 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.3702 ------------------------------------------------------------------------------- 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** C 55 HIS C 90 GLN D 191 ASN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS ** G 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5150 r_free = 0.5150 target = 0.236843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.185772 restraints weight = 22820.670| |-----------------------------------------------------------------------------| r_work (start): 0.4631 rms_B_bonded: 3.14 r_work: 0.4517 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 17145 Z= 0.209 Angle : 0.823 15.030 23247 Z= 0.420 Chirality : 0.049 0.238 2544 Planarity : 0.010 0.403 3012 Dihedral : 9.389 177.481 2490 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 6.15 % Allowed : 17.08 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.45 (0.17), residues: 2103 helix: -0.49 (0.34), residues: 234 sheet: -1.15 (0.22), residues: 480 loop : -2.13 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 32 HIS 0.008 0.002 HIS G 9 PHE 0.018 0.003 PHE D 329 TYR 0.018 0.002 TYR D 445 ARG 0.027 0.001 ARG A 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 9) link_NAG-ASN : angle 2.15192 ( 27) hydrogen bonds : bond 0.04496 ( 363) hydrogen bonds : angle 5.71502 ( 1017) SS BOND : bond 0.00290 ( 24) SS BOND : angle 1.08418 ( 48) covalent geometry : bond 0.00469 (17106) covalent geometry : angle 0.81994 (23172) Misc. bond : bond 0.00773 ( 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 244 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 132 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7529 (mmtt) cc_final: 0.7235 (mtmp) REVERT: A 329 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.5067 (m-80) REVERT: A 340 TRP cc_start: 0.3161 (OUTLIER) cc_final: 0.2156 (m-10) REVERT: A 358 GLU cc_start: 0.4251 (OUTLIER) cc_final: 0.3903 (tm-30) REVERT: A 430 ASN cc_start: 0.4855 (OUTLIER) cc_final: 0.4089 (t0) REVERT: A 465 GLU cc_start: 0.5762 (pp20) cc_final: 0.5383 (pp20) REVERT: A 493 MET cc_start: 0.0320 (OUTLIER) cc_final: -0.0061 (ppp) REVERT: B 40 GLN cc_start: 0.5286 (OUTLIER) cc_final: 0.4990 (tp-100) REVERT: D 202 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.6802 (pt0) REVERT: D 329 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.5477 (m-80) REVERT: D 340 TRP cc_start: 0.4153 (OUTLIER) cc_final: 0.2378 (m-10) REVERT: D 358 GLU cc_start: 0.4222 (OUTLIER) cc_final: 0.3762 (tm-30) REVERT: D 446 GLU cc_start: 0.5720 (OUTLIER) cc_final: 0.5483 (mt-10) REVERT: E 40 GLN cc_start: 0.5384 (OUTLIER) cc_final: 0.5173 (tp-100) REVERT: G 114 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6930 (mtm) REVERT: G 329 PHE cc_start: 0.6255 (OUTLIER) cc_final: 0.5792 (t80) REVERT: G 340 TRP cc_start: 0.4022 (OUTLIER) cc_final: 0.2443 (m-10) REVERT: G 358 GLU cc_start: 0.4390 (OUTLIER) cc_final: 0.3990 (tm-30) REVERT: G 429 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6738 (mp0) REVERT: G 446 GLU cc_start: 0.5369 (OUTLIER) cc_final: 0.5134 (mt-10) REVERT: G 493 MET cc_start: 0.0081 (OUTLIER) cc_final: -0.0193 (tmt) REVERT: H 4 LEU cc_start: 0.2699 (OUTLIER) cc_final: 0.2439 (pp) REVERT: H 40 GLN cc_start: 0.5204 (OUTLIER) cc_final: 0.5002 (tp-100) outliers start: 112 outliers final: 43 residues processed: 212 average time/residue: 0.9055 time to fit residues: 223.3133 Evaluate side-chains 168 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 105 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 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 358 GLU 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 4 LEU 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 21 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 40 GLN 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 25 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 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 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 446 GLU 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 40 GLN 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: 0.9990 chunk 205 optimal weight: 4.9990 chunk 170 optimal weight: 0.0000 chunk 40 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5162 r_free = 0.5162 target = 0.237771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.185292 restraints weight = 22037.826| |-----------------------------------------------------------------------------| r_work (start): 0.4667 rms_B_bonded: 3.70 r_work: 0.4525 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17145 Z= 0.162 Angle : 0.777 14.338 23247 Z= 0.386 Chirality : 0.046 0.214 2544 Planarity : 0.011 0.438 3012 Dihedral : 8.792 174.067 2490 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.67 % Allowed : 20.65 % Favored : 74.68 % 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: -2.19 (0.17), residues: 2103 helix: 0.35 (0.37), residues: 201 sheet: -1.08 (0.22), residues: 471 loop : -1.97 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 35 HIS 0.006 0.002 HIS G 9 PHE 0.017 0.002 PHE A 116 TYR 0.022 0.001 TYR D 445 ARG 0.067 0.001 ARG D 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 9) link_NAG-ASN : angle 1.86788 ( 27) hydrogen bonds : bond 0.03962 ( 363) hydrogen bonds : angle 5.41443 ( 1017) SS BOND : bond 0.00285 ( 24) SS BOND : angle 0.90340 ( 48) covalent geometry : bond 0.00364 (17106) covalent geometry : angle 0.77501 (23172) Misc. bond : bond 0.00857 ( 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 218 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 133 time to evaluate : 1.695 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 302 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7262 (mtmp) REVERT: A 329 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.5230 (m-80) REVERT: A 340 TRP cc_start: 0.2926 (OUTLIER) cc_final: 0.1984 (m-10) REVERT: A 475 MET cc_start: -0.3074 (mtp) cc_final: -0.3323 (mtm) REVERT: A 493 MET cc_start: 0.0007 (OUTLIER) cc_final: -0.0405 (ppp) REVERT: B 40 GLN cc_start: 0.5446 (OUTLIER) cc_final: 0.5242 (tp-100) REVERT: D 114 MET cc_start: 0.7618 (mmm) cc_final: 0.7088 (mtm) REVERT: D 329 PHE cc_start: 0.6227 (OUTLIER) cc_final: 0.5553 (m-80) REVERT: D 340 TRP cc_start: 0.3791 (OUTLIER) cc_final: 0.2039 (m-10) REVERT: D 430 ASN cc_start: 0.5234 (OUTLIER) cc_final: 0.4818 (t0) REVERT: G 203 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7559 (tp40) REVERT: G 296 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7281 (mptp) REVERT: G 329 PHE cc_start: 0.6136 (OUTLIER) cc_final: 0.5842 (t80) REVERT: G 340 TRP cc_start: 0.4021 (OUTLIER) cc_final: 0.2292 (m-10) REVERT: G 429 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6794 (mp0) REVERT: G 430 ASN cc_start: 0.5163 (OUTLIER) cc_final: 0.4563 (t0) REVERT: G 493 MET cc_start: 0.0046 (OUTLIER) cc_final: -0.0213 (tmt) REVERT: H 4 LEU cc_start: 0.2417 (OUTLIER) cc_final: 0.2128 (pp) REVERT: H 40 GLN cc_start: 0.5292 (OUTLIER) cc_final: 0.5083 (tp-100) outliers start: 85 outliers final: 36 residues processed: 193 average time/residue: 1.0511 time to fit residues: 230.9366 Evaluate side-chains 161 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 110 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 127 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 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 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 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 312 MET Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP 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 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 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 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 343 LEU 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 40 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 156 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 103 optimal weight: 0.1980 chunk 206 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** E 78 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5163 r_free = 0.5163 target = 0.237978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.184266 restraints weight = 21767.328| |-----------------------------------------------------------------------------| r_work (start): 0.4651 rms_B_bonded: 3.67 r_work: 0.4522 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17145 Z= 0.150 Angle : 0.742 13.319 23247 Z= 0.370 Chirality : 0.046 0.197 2544 Planarity : 0.008 0.278 3012 Dihedral : 8.527 176.762 2490 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.50 % Allowed : 21.64 % Favored : 73.86 % 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: -2.04 (0.17), residues: 2103 helix: -0.21 (0.35), residues: 243 sheet: -0.82 (0.22), residues: 546 loop : -1.90 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 35 HIS 0.006 0.002 HIS G 9 PHE 0.017 0.002 PHE A 116 TYR 0.018 0.001 TYR D 445 ARG 0.038 0.001 ARG A 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 9) link_NAG-ASN : angle 2.14604 ( 27) hydrogen bonds : bond 0.03807 ( 363) hydrogen bonds : angle 5.30297 ( 1017) SS BOND : bond 0.00253 ( 24) SS BOND : angle 0.86296 ( 48) covalent geometry : bond 0.00330 (17106) covalent geometry : angle 0.73867 (23172) Misc. bond : bond 0.00882 ( 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 : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7604 (mmtt) cc_final: 0.7299 (mtmp) REVERT: A 329 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.5506 (m-80) REVERT: A 340 TRP cc_start: 0.2897 (OUTLIER) cc_final: 0.1920 (m-10) REVERT: A 358 GLU cc_start: 0.3922 (OUTLIER) cc_final: 0.3603 (tm-30) REVERT: A 378 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5659 (mt) REVERT: A 465 GLU cc_start: 0.5517 (pp20) cc_final: 0.5174 (pp20) REVERT: A 493 MET cc_start: 0.0021 (OUTLIER) cc_final: -0.0369 (ppp) REVERT: B 40 GLN cc_start: 0.5304 (OUTLIER) cc_final: 0.5095 (tp-100) REVERT: D 114 MET cc_start: 0.7554 (mmm) cc_final: 0.7017 (mtm) REVERT: D 329 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.5708 (m-80) REVERT: D 340 TRP cc_start: 0.3864 (OUTLIER) cc_final: 0.2084 (m-10) REVERT: D 358 GLU cc_start: 0.3944 (OUTLIER) cc_final: 0.3660 (tm-30) REVERT: D 430 ASN cc_start: 0.5284 (OUTLIER) cc_final: 0.4818 (t0) REVERT: D 493 MET cc_start: 0.0267 (OUTLIER) cc_final: -0.0548 (tpt) REVERT: G 203 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7603 (tp40) REVERT: G 296 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7289 (mptp) REVERT: G 329 PHE cc_start: 0.6148 (OUTLIER) cc_final: 0.5751 (t80) REVERT: G 340 TRP cc_start: 0.3984 (OUTLIER) cc_final: 0.2243 (m-10) REVERT: G 358 GLU cc_start: 0.4278 (OUTLIER) cc_final: 0.3926 (tm-30) REVERT: G 429 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6701 (mp0) REVERT: G 430 ASN cc_start: 0.5204 (OUTLIER) cc_final: 0.4586 (t0) REVERT: G 493 MET cc_start: 0.0048 (OUTLIER) cc_final: -0.0209 (tmt) REVERT: H 4 LEU cc_start: 0.2282 (OUTLIER) cc_final: 0.1987 (pp) outliers start: 82 outliers final: 38 residues processed: 194 average time/residue: 0.9429 time to fit residues: 212.0000 Evaluate side-chains 177 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 120 time to evaluate : 1.951 ------------------------------------------------------------------------------- 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 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 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 312 MET 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 72 ARG Chi-restraints excluded: chain E residue 78 GLN 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 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 358 GLU 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 72 ARG Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 109 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 159 optimal weight: 0.0070 chunk 66 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 GLN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 379 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 = 0.5150 r_free = 0.5150 target = 0.236448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.184334 restraints weight = 21704.626| |-----------------------------------------------------------------------------| r_work (start): 0.4651 rms_B_bonded: 3.33 r_work: 0.4516 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 17145 Z= 0.163 Angle : 0.748 12.970 23247 Z= 0.375 Chirality : 0.047 0.235 2544 Planarity : 0.007 0.192 3012 Dihedral : 8.433 175.142 2490 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.67 % Allowed : 22.95 % Favored : 72.38 % 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: -1.95 (0.17), residues: 2103 helix: -0.13 (0.35), residues: 243 sheet: -0.71 (0.23), residues: 525 loop : -1.85 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 35 HIS 0.006 0.002 HIS G 9 PHE 0.024 0.002 PHE E 79 TYR 0.026 0.001 TYR D 445 ARG 0.017 0.001 ARG G 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 9) link_NAG-ASN : angle 2.15194 ( 27) hydrogen bonds : bond 0.03824 ( 363) hydrogen bonds : angle 5.32313 ( 1017) SS BOND : bond 0.00249 ( 24) SS BOND : angle 1.10763 ( 48) covalent geometry : bond 0.00370 (17106) covalent geometry : angle 0.74437 (23172) Misc. bond : bond 0.00874 ( 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 217 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 132 time to evaluate : 1.952 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 302 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7310 (mtmp) REVERT: A 329 PHE cc_start: 0.6371 (OUTLIER) cc_final: 0.5581 (m-80) REVERT: A 340 TRP cc_start: 0.2870 (OUTLIER) cc_final: 0.1765 (m-10) REVERT: A 378 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5697 (mt) REVERT: A 441 MET cc_start: 0.5199 (tmt) cc_final: 0.4890 (tmt) REVERT: A 493 MET cc_start: 0.0319 (OUTLIER) cc_final: -0.0477 (tpp) REVERT: B 40 GLN cc_start: 0.5431 (OUTLIER) cc_final: 0.5135 (tp-100) REVERT: D 329 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.5896 (m-80) REVERT: D 340 TRP cc_start: 0.3952 (OUTLIER) cc_final: 0.2039 (m-10) REVERT: D 358 GLU cc_start: 0.4306 (OUTLIER) cc_final: 0.4104 (tm-30) REVERT: D 430 ASN cc_start: 0.5397 (OUTLIER) cc_final: 0.4765 (t0) REVERT: D 493 MET cc_start: 0.0189 (OUTLIER) cc_final: -0.0680 (tpt) REVERT: G 203 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7513 (tp40) REVERT: G 296 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7316 (mptp) REVERT: G 329 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.5430 (m-80) REVERT: G 340 TRP cc_start: 0.4035 (OUTLIER) cc_final: 0.2289 (m-10) REVERT: H 4 LEU cc_start: 0.2306 (OUTLIER) cc_final: 0.1988 (pp) outliers start: 85 outliers final: 41 residues processed: 197 average time/residue: 0.9150 time to fit residues: 209.8588 Evaluate side-chains 173 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 1.936 ------------------------------------------------------------------------------- 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 189 SER Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 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 257 MET Chi-restraints excluded: chain D residue 312 MET 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 403 ILE 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 72 ARG Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 128 SER 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: 4.9990 chunk 185 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ** 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 = 0.5159 r_free = 0.5159 target = 0.237335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.185228 restraints weight = 21643.922| |-----------------------------------------------------------------------------| r_work (start): 0.4663 rms_B_bonded: 3.38 r_work: 0.4524 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17145 Z= 0.151 Angle : 0.783 19.712 23247 Z= 0.389 Chirality : 0.046 0.298 2544 Planarity : 0.010 0.369 3012 Dihedral : 9.001 176.337 2490 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.73 % Allowed : 23.94 % Favored : 72.32 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.81 (0.18), residues: 2103 helix: 0.01 (0.35), residues: 243 sheet: -0.64 (0.22), residues: 555 loop : -1.77 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 35 HIS 0.005 0.002 HIS G 9 PHE 0.015 0.002 PHE D 329 TYR 0.021 0.001 TYR G 445 ARG 0.049 0.001 ARG G 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 9) link_NAG-ASN : angle 2.01783 ( 27) hydrogen bonds : bond 0.03657 ( 363) hydrogen bonds : angle 5.08790 ( 1017) SS BOND : bond 0.00244 ( 24) SS BOND : angle 1.17256 ( 48) covalent geometry : bond 0.00335 (17106) covalent geometry : angle 0.77913 (23172) Misc. bond : bond 0.01082 ( 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 198 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 130 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7325 (mtmp) REVERT: A 329 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.5562 (m-80) REVERT: A 340 TRP cc_start: 0.3146 (OUTLIER) cc_final: 0.1884 (m-10) REVERT: A 493 MET cc_start: 0.0515 (OUTLIER) cc_final: -0.0215 (tpp) REVERT: B 40 GLN cc_start: 0.5458 (OUTLIER) cc_final: 0.5143 (tp-100) REVERT: D 329 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.5823 (m-80) REVERT: D 340 TRP cc_start: 0.3997 (OUTLIER) cc_final: 0.2067 (m-10) REVERT: D 358 GLU cc_start: 0.4203 (OUTLIER) cc_final: 0.3869 (tm-30) REVERT: D 493 MET cc_start: 0.0053 (OUTLIER) cc_final: -0.1007 (tpt) REVERT: G 296 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7353 (mptp) REVERT: G 329 PHE cc_start: 0.6211 (OUTLIER) cc_final: 0.5375 (m-80) REVERT: G 340 TRP cc_start: 0.4133 (OUTLIER) cc_final: 0.2309 (m-10) REVERT: G 493 MET cc_start: 0.0027 (tmt) cc_final: -0.1419 (tpp) REVERT: H 4 LEU cc_start: 0.2347 (OUTLIER) cc_final: 0.2036 (pp) outliers start: 68 outliers final: 37 residues processed: 181 average time/residue: 0.9552 time to fit residues: 202.9506 Evaluate side-chains 165 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 116 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 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 257 MET 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 403 ILE 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 G residue 8 HIS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 296 LYS Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 182 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 155 optimal weight: 0.1980 chunk 114 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 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 = 0.5169 r_free = 0.5169 target = 0.238347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.186232 restraints weight = 21824.962| |-----------------------------------------------------------------------------| r_work (start): 0.4670 rms_B_bonded: 3.36 r_work: 0.4533 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17145 Z= 0.140 Angle : 0.756 18.604 23247 Z= 0.376 Chirality : 0.045 0.272 2544 Planarity : 0.009 0.295 3012 Dihedral : 8.844 175.484 2490 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.02 % Allowed : 24.82 % Favored : 72.16 % 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: -1.67 (0.18), residues: 2103 helix: 0.11 (0.36), residues: 243 sheet: -0.50 (0.22), residues: 555 loop : -1.69 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 35 HIS 0.004 0.001 HIS G 9 PHE 0.015 0.002 PHE D 335 TYR 0.022 0.001 TYR G 445 ARG 0.054 0.001 ARG G 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 9) link_NAG-ASN : angle 1.94155 ( 27) hydrogen bonds : bond 0.03521 ( 363) hydrogen bonds : angle 4.98842 ( 1017) SS BOND : bond 0.00234 ( 24) SS BOND : angle 1.04911 ( 48) covalent geometry : bond 0.00311 (17106) covalent geometry : angle 0.75293 (23172) Misc. bond : bond 0.00938 ( 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 179 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 124 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7317 (mtmp) REVERT: A 329 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.5523 (m-80) REVERT: A 340 TRP cc_start: 0.2963 (OUTLIER) cc_final: 0.1798 (m-10) REVERT: A 493 MET cc_start: 0.0974 (OUTLIER) cc_final: 0.0120 (tpp) REVERT: B 40 GLN cc_start: 0.5423 (OUTLIER) cc_final: 0.5108 (tp-100) REVERT: D 329 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.5677 (m-80) REVERT: D 340 TRP cc_start: 0.3996 (OUTLIER) cc_final: 0.2231 (m-10) REVERT: D 358 GLU cc_start: 0.4069 (OUTLIER) cc_final: 0.3794 (tm-30) REVERT: D 439 SER cc_start: 0.6962 (OUTLIER) cc_final: 0.6410 (m) REVERT: D 493 MET cc_start: 0.0250 (OUTLIER) cc_final: -0.0907 (tpt) REVERT: G 114 MET cc_start: 0.7386 (mtm) cc_final: 0.7153 (mtm) REVERT: G 329 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.5277 (m-80) REVERT: G 340 TRP cc_start: 0.3969 (OUTLIER) cc_final: 0.2033 (m-10) REVERT: G 493 MET cc_start: -0.0152 (tmt) cc_final: -0.1507 (tpp) REVERT: H 4 LEU cc_start: 0.2118 (OUTLIER) cc_final: 0.1850 (pp) outliers start: 55 outliers final: 34 residues processed: 167 average time/residue: 1.0299 time to fit residues: 201.3096 Evaluate side-chains 163 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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 360 THR 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 25 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 257 MET Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 439 SER 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 160 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.5167 r_free = 0.5167 target = 0.238414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.186298 restraints weight = 22059.928| |-----------------------------------------------------------------------------| r_work (start): 0.4659 rms_B_bonded: 3.30 r_work: 0.4530 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.7071 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= 0.142 Angle : 0.749 17.854 23247 Z= 0.370 Chirality : 0.046 0.348 2544 Planarity : 0.009 0.406 3012 Dihedral : 8.378 175.543 2490 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.86 % Allowed : 25.21 % Favored : 71.94 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.58 (0.18), residues: 2103 helix: 0.25 (0.36), residues: 243 sheet: -0.46 (0.22), residues: 555 loop : -1.65 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 35 HIS 0.008 0.001 HIS D 352 PHE 0.015 0.002 PHE E 80 TYR 0.022 0.001 TYR G 445 ARG 0.049 0.001 ARG D 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 9) link_NAG-ASN : angle 1.95798 ( 27) hydrogen bonds : bond 0.03547 ( 363) hydrogen bonds : angle 4.97509 ( 1017) SS BOND : bond 0.00224 ( 24) SS BOND : angle 1.02045 ( 48) covalent geometry : bond 0.00316 (17106) covalent geometry : angle 0.74588 (23172) Misc. bond : bond 0.00939 ( 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 181 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 129 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7671 (mmtt) cc_final: 0.7314 (mtmp) REVERT: A 329 PHE cc_start: 0.6354 (OUTLIER) cc_final: 0.5567 (m-80) REVERT: A 340 TRP cc_start: 0.2960 (OUTLIER) cc_final: 0.1764 (m-10) REVERT: A 493 MET cc_start: 0.0809 (OUTLIER) cc_final: -0.0059 (tpp) REVERT: B 40 GLN cc_start: 0.5332 (OUTLIER) cc_final: 0.5012 (tp-100) REVERT: D 329 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.5809 (m-80) REVERT: D 340 TRP cc_start: 0.3945 (OUTLIER) cc_final: 0.2125 (m-10) REVERT: D 439 SER cc_start: 0.6880 (OUTLIER) cc_final: 0.6338 (m) REVERT: D 493 MET cc_start: 0.0698 (OUTLIER) cc_final: -0.0854 (tpt) REVERT: G 114 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7273 (mtm) REVERT: G 329 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.5477 (m-80) REVERT: G 340 TRP cc_start: 0.3754 (OUTLIER) cc_final: 0.1961 (m-10) REVERT: G 493 MET cc_start: -0.0373 (tmt) cc_final: -0.1589 (tpp) REVERT: H 4 LEU cc_start: 0.2081 (OUTLIER) cc_final: 0.1814 (pp) REVERT: H 49 MET cc_start: 0.3575 (mmt) cc_final: 0.3329 (mmm) outliers start: 52 outliers final: 32 residues processed: 168 average time/residue: 0.9652 time to fit residues: 191.6851 Evaluate side-chains 166 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 2.515 ------------------------------------------------------------------------------- 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 360 THR 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 257 MET Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 439 SER 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 G residue 8 HIS Chi-restraints excluded: chain G residue 11 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 121 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 152 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** 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 = 0.5136 r_free = 0.5136 target = 0.235640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.183533 restraints weight = 22242.737| |-----------------------------------------------------------------------------| r_work (start): 0.4615 rms_B_bonded: 3.37 r_work: 0.4482 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17145 Z= 0.173 Angle : 0.791 16.959 23247 Z= 0.394 Chirality : 0.047 0.262 2544 Planarity : 0.008 0.320 3012 Dihedral : 9.213 178.646 2490 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.69 % Allowed : 25.81 % Favored : 71.50 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.74 (0.18), residues: 2103 helix: 0.36 (0.36), residues: 231 sheet: -0.87 (0.21), residues: 627 loop : -1.64 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 35 HIS 0.010 0.002 HIS D 352 PHE 0.018 0.002 PHE D 329 TYR 0.025 0.001 TYR G 445 ARG 0.039 0.001 ARG G 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 9) link_NAG-ASN : angle 2.19854 ( 27) hydrogen bonds : bond 0.03768 ( 363) hydrogen bonds : angle 5.09849 ( 1017) SS BOND : bond 0.00250 ( 24) SS BOND : angle 1.11161 ( 48) covalent geometry : bond 0.00392 (17106) covalent geometry : angle 0.78742 (23172) Misc. bond : bond 0.01128 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15052.59 seconds wall clock time: 260 minutes 15.44 seconds (15615.44 seconds total)