Starting phenix.real_space_refine on Mon May 19 09:14:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1c_41809/05_2025/8u1c_41809.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1c_41809/05_2025/8u1c_41809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u1c_41809/05_2025/8u1c_41809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1c_41809/05_2025/8u1c_41809.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1c_41809/05_2025/8u1c_41809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1c_41809/05_2025/8u1c_41809.cif" } resolution = 2.89 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= 0.022 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 140 5.16 5 C 11632 2.51 5 N 3144 2.21 5 O 3464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18380 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2757 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 16, 'TRANS': 337} Chain breaks: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 10, 'TRANS': 115} Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Restraints were copied for chains: G, H, M, I, L, N, F, K, P, E, J, O Time building chain proxies: 10.27, per 1000 atoms: 0.56 Number of scatterers: 18380 At special positions: 0 Unit cell: (157.325, 157.325, 99.325, 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 140 16.00 O 3464 8.00 N 3144 7.00 C 11632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG K 1 " - " NAG K 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG B 1 " - " ASN A 283 " " NAG F 1 " - " ASN E 283 " " NAG K 1 " - " ASN J 283 " " NAG P 1 " - " ASN O 283 " Time building additional restraints: 4.76 Conformation dependent library (CDL) restraints added in 2.2 seconds 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 52 sheets defined 5.3% alpha, 46.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 100 through 100D Processing helix chain 'L' and resid 28 through 31 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.999A pdb=" N PHE A 102 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 100 through 100D Processing helix chain 'D' and resid 28 through 31 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.999A pdb=" N PHE E 102 " --> pdb=" O PRO E 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 100 through 100D Processing helix chain 'I' and resid 28 through 31 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 98 through 102 removed outlier: 3.999A pdb=" N PHE J 102 " --> pdb=" O PRO J 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 73 through 75 No H-bonds generated for 'chain 'M' and resid 73 through 75' Processing helix chain 'M' and resid 100 through 100D Processing helix chain 'N' and resid 28 through 31 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'O' and resid 98 through 102 removed outlier: 3.999A pdb=" N PHE O 102 " --> pdb=" O PRO O 99 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=2, first strand: chain 'H' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'H' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=5, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 91 through 97 removed outlier: 6.785A pdb=" N ILE A 444 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU A 96 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 442 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 113 through 122 removed outlier: 6.981A pdb=" N ILE A 114 " --> pdb=" O HIS A 133 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS A 133 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU A 116 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 131 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS A 154 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 155 " --> pdb=" O HIS A 172 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 177 through 182 removed outlier: 6.394A pdb=" N LEU A 201 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 212 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL A 203 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 221 through 223 Processing sheet with id=11, first strand: chain 'A' and resid 221 through 223 removed outlier: 6.598A pdb=" N ARG A 256 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.578A pdb=" N THR A 267 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N LEU A 315 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR A 285 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE A 280 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU A 287 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS A 278 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA A 289 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N CYS A 276 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 351 through 356 removed outlier: 7.961A pdb=" N MET A 374 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL A 400 " --> pdb=" O MET A 374 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N MET A 376 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL A 398 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 378 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=15, first strand: chain 'C' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=18, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 91 through 97 removed outlier: 6.785A pdb=" N ILE E 444 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU E 96 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR E 442 " --> pdb=" O LEU E 96 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'E' and resid 113 through 122 removed outlier: 6.981A pdb=" N ILE E 114 " --> pdb=" O HIS E 133 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS E 133 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU E 116 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU E 131 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS E 154 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU E 155 " --> pdb=" O HIS E 172 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 177 through 182 removed outlier: 6.394A pdb=" N LEU E 201 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR E 212 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL E 203 " --> pdb=" O THR E 210 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 221 through 223 Processing sheet with id=24, first strand: chain 'E' and resid 221 through 223 removed outlier: 6.598A pdb=" N ARG E 256 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 267 through 268 removed outlier: 6.578A pdb=" N THR E 267 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N LEU E 315 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR E 285 " --> pdb=" O PHE E 280 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE E 280 " --> pdb=" O THR E 285 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU E 287 " --> pdb=" O CYS E 278 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS E 278 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA E 289 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N CYS E 276 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 351 through 356 removed outlier: 7.961A pdb=" N MET E 374 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL E 400 " --> pdb=" O MET E 374 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N MET E 376 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL E 398 " --> pdb=" O MET E 376 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU E 378 " --> pdb=" O SER E 396 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=28, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=31, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'J' and resid 91 through 97 removed outlier: 6.785A pdb=" N ILE J 444 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU J 96 " --> pdb=" O THR J 442 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR J 442 " --> pdb=" O LEU J 96 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'J' and resid 113 through 122 removed outlier: 6.981A pdb=" N ILE J 114 " --> pdb=" O HIS J 133 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS J 133 " --> pdb=" O ILE J 114 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU J 116 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU J 131 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS J 154 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU J 155 " --> pdb=" O HIS J 172 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'J' and resid 177 through 182 removed outlier: 6.394A pdb=" N LEU J 201 " --> pdb=" O THR J 212 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR J 212 " --> pdb=" O LEU J 201 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL J 203 " --> pdb=" O THR J 210 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'J' and resid 221 through 223 Processing sheet with id=37, first strand: chain 'J' and resid 221 through 223 removed outlier: 6.598A pdb=" N ARG J 256 " --> pdb=" O ILE J 260 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE J 260 " --> pdb=" O ARG J 256 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'J' and resid 267 through 268 removed outlier: 6.578A pdb=" N THR J 267 " --> pdb=" O ILE J 313 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N LEU J 315 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR J 285 " --> pdb=" O PHE J 280 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE J 280 " --> pdb=" O THR J 285 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU J 287 " --> pdb=" O CYS J 278 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS J 278 " --> pdb=" O GLU J 287 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA J 289 " --> pdb=" O CYS J 276 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N CYS J 276 " --> pdb=" O ALA J 289 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'J' and resid 351 through 356 removed outlier: 7.961A pdb=" N MET J 374 " --> pdb=" O VAL J 400 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL J 400 " --> pdb=" O MET J 374 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N MET J 376 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL J 398 " --> pdb=" O MET J 376 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU J 378 " --> pdb=" O SER J 396 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=41, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=44, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'O' and resid 91 through 97 removed outlier: 6.785A pdb=" N ILE O 444 " --> pdb=" O ALA O 94 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU O 96 " --> pdb=" O THR O 442 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR O 442 " --> pdb=" O LEU O 96 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'O' and resid 113 through 122 removed outlier: 6.981A pdb=" N ILE O 114 " --> pdb=" O HIS O 133 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS O 133 " --> pdb=" O ILE O 114 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU O 116 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU O 131 " --> pdb=" O GLU O 116 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS O 154 " --> pdb=" O THR O 132 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU O 155 " --> pdb=" O HIS O 172 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'O' and resid 177 through 182 removed outlier: 6.394A pdb=" N LEU O 201 " --> pdb=" O THR O 212 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR O 212 " --> pdb=" O LEU O 201 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL O 203 " --> pdb=" O THR O 210 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'O' and resid 221 through 223 Processing sheet with id=50, first strand: chain 'O' and resid 221 through 223 removed outlier: 6.598A pdb=" N ARG O 256 " --> pdb=" O ILE O 260 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE O 260 " --> pdb=" O ARG O 256 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'O' and resid 267 through 268 removed outlier: 6.578A pdb=" N THR O 267 " --> pdb=" O ILE O 313 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N LEU O 315 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR O 285 " --> pdb=" O PHE O 280 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE O 280 " --> pdb=" O THR O 285 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU O 287 " --> pdb=" O CYS O 278 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS O 278 " --> pdb=" O GLU O 287 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA O 289 " --> pdb=" O CYS O 276 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N CYS O 276 " --> pdb=" O ALA O 289 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'O' and resid 351 through 356 removed outlier: 7.961A pdb=" N MET O 374 " --> pdb=" O VAL O 400 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL O 400 " --> pdb=" O MET O 374 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N MET O 376 " --> pdb=" O VAL O 398 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL O 398 " --> pdb=" O MET O 376 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU O 378 " --> pdb=" O SER O 396 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1584 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: 6.93 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4568 1.32 - 1.46: 6292 1.46 - 1.60: 7788 1.60 - 1.74: 48 1.74 - 1.88: 172 Bond restraints: 18868 Sorted by residual: bond pdb=" CB ILE D 106 " pdb=" CG1 ILE D 106 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" CB ILE L 106 " pdb=" CG1 ILE L 106 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" CB ILE N 106 " pdb=" CG1 ILE N 106 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" CB ILE I 106 " pdb=" CG1 ILE I 106 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" NE ARG J 149 " pdb=" CZ ARG J 149 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.03e+01 ... (remaining 18863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 22448 2.72 - 5.44: 2692 5.44 - 8.15: 368 8.15 - 10.87: 24 10.87 - 13.59: 8 Bond angle restraints: 25540 Sorted by residual: angle pdb=" N ILE G 40 " pdb=" CA ILE G 40 " pdb=" C ILE G 40 " ideal model delta sigma weight residual 108.95 100.35 8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" N ILE H 40 " pdb=" CA ILE H 40 " pdb=" C ILE H 40 " ideal model delta sigma weight residual 108.95 100.35 8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" N ILE C 40 " pdb=" CA ILE C 40 " pdb=" C ILE C 40 " ideal model delta sigma weight residual 108.95 100.35 8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" N ILE M 40 " pdb=" CA ILE M 40 " pdb=" C ILE M 40 " ideal model delta sigma weight residual 108.95 100.35 8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" N PRO G 52A" pdb=" CA PRO G 52A" pdb=" C PRO G 52A" ideal model delta sigma weight residual 111.21 97.62 13.59 1.59e+00 3.96e-01 7.30e+01 ... (remaining 25535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 10752 17.04 - 34.09: 316 34.09 - 51.13: 56 51.13 - 68.17: 28 68.17 - 85.22: 16 Dihedral angle restraints: 11168 sinusoidal: 4524 harmonic: 6644 Sorted by residual: dihedral pdb=" N THR J 324 " pdb=" C THR J 324 " pdb=" CA THR J 324 " pdb=" CB THR J 324 " ideal model delta harmonic sigma weight residual 123.40 133.38 -9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" N THR E 324 " pdb=" C THR E 324 " pdb=" CA THR E 324 " pdb=" CB THR E 324 " ideal model delta harmonic sigma weight residual 123.40 133.38 -9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" N THR O 324 " pdb=" C THR O 324 " pdb=" CA THR O 324 " pdb=" CB THR O 324 " ideal model delta harmonic sigma weight residual 123.40 133.38 -9.98 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 11165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1896 0.102 - 0.203: 636 0.203 - 0.305: 124 0.305 - 0.407: 32 0.407 - 0.508: 20 Chirality restraints: 2708 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 2705 not shown) Planarity restraints: 3256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 99 " -0.060 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP M 99 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP M 99 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP M 99 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP M 99 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 99 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP M 99 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 99 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 99 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP M 99 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 99 " -0.060 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP H 99 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP H 99 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP H 99 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP H 99 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 99 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP H 99 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 99 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 99 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 99 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 99 " -0.060 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP C 99 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP C 99 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 99 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP C 99 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 99 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 99 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 99 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 99 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 99 " -0.034 2.00e-02 2.50e+03 ... (remaining 3253 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 236 2.59 - 3.17: 14876 3.17 - 3.75: 29120 3.75 - 4.32: 45236 4.32 - 4.90: 73432 Nonbonded interactions: 162900 Sorted by model distance: nonbonded pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " model vdw 2.013 3.760 nonbonded pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " model vdw 2.013 3.760 nonbonded pdb=" SG CYS G 22 " pdb=" SG CYS G 92 " model vdw 2.013 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " model vdw 2.013 3.760 nonbonded pdb=" SG CYS A 276 " pdb=" SG CYS A 290 " model vdw 2.017 3.760 ... (remaining 162895 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: 0.13 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'J' selection = chain 'O' } 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: 6.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 42.320 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.023 0.159 18876 Z= 1.221 Angle : 1.850 13.590 25564 Z= 1.228 Chirality : 0.109 0.508 2708 Planarity : 0.010 0.055 3252 Dihedral : 10.037 85.218 6960 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.52 % Favored : 95.13 % Rotamer: Outliers : 0.20 % Allowed : 1.63 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.02 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.65 (0.17), residues: 892 loop : -0.38 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.013 TRP C 99 HIS 0.014 0.003 HIS H 100C PHE 0.028 0.006 PHE L 98 TYR 0.055 0.009 TYR E 321 ARG 0.009 0.001 ARG A 326 Details of bonding type rmsd link_NAG-ASN : bond 0.06197 ( 4) link_NAG-ASN : angle 2.09504 ( 12) link_BETA1-4 : bond 0.06925 ( 4) link_BETA1-4 : angle 5.02179 ( 12) hydrogen bonds : bond 0.17232 ( 648) hydrogen bonds : angle 8.45131 ( 1584) covalent geometry : bond 0.02316 (18868) covalent geometry : angle 1.84663 (25540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 480 time to evaluate : 2.026 Fit side-chains REVERT: J 417 LYS cc_start: 0.7185 (mmtt) cc_final: 0.6970 (mppt) outliers start: 4 outliers final: 4 residues processed: 484 average time/residue: 1.2289 time to fit residues: 669.5251 Evaluate side-chains 296 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 292 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain M residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 272 HIS E 133 HIS E 272 HIS J 133 HIS J 272 HIS O 133 HIS O 272 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119291 restraints weight = 21259.638| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.92 r_work: 0.3284 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18876 Z= 0.198 Angle : 0.717 9.111 25564 Z= 0.389 Chirality : 0.049 0.155 2708 Planarity : 0.005 0.035 3252 Dihedral : 5.980 27.878 2728 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.96 % Favored : 96.87 % Rotamer: Outliers : 4.48 % Allowed : 11.41 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.68 (0.16), residues: 2300 helix: None (None), residues: 0 sheet: 0.40 (0.17), residues: 884 loop : -1.05 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 47 HIS 0.004 0.001 HIS N 91 PHE 0.016 0.002 PHE D 83 TYR 0.017 0.002 TYR A 321 ARG 0.004 0.001 ARG I 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 4) link_NAG-ASN : angle 0.86282 ( 12) link_BETA1-4 : bond 0.00159 ( 4) link_BETA1-4 : angle 2.25965 ( 12) hydrogen bonds : bond 0.05331 ( 648) hydrogen bonds : angle 6.63908 ( 1584) covalent geometry : bond 0.00449 (18868) covalent geometry : angle 0.71528 (25540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 340 time to evaluate : 1.963 Fit side-chains REVERT: L 21 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6833 (mm) REVERT: A 284 LYS cc_start: 0.8316 (mttm) cc_final: 0.7657 (mttp) REVERT: A 360 ILE cc_start: 0.8251 (mt) cc_final: 0.7761 (tp) REVERT: A 390 SER cc_start: 0.8093 (p) cc_final: 0.7495 (t) REVERT: A 431 ASP cc_start: 0.5775 (t0) cc_final: 0.5459 (p0) REVERT: D 21 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6844 (mm) REVERT: E 284 LYS cc_start: 0.8312 (mttm) cc_final: 0.7656 (mttp) REVERT: E 360 ILE cc_start: 0.8220 (mt) cc_final: 0.7758 (tp) REVERT: E 390 SER cc_start: 0.8078 (p) cc_final: 0.7467 (t) REVERT: E 431 ASP cc_start: 0.5798 (t0) cc_final: 0.5473 (p0) REVERT: I 21 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6849 (mm) REVERT: J 218 ASN cc_start: 0.7501 (m-40) cc_final: 0.7269 (m-40) REVERT: J 284 LYS cc_start: 0.8317 (mttm) cc_final: 0.7663 (mttp) REVERT: J 390 SER cc_start: 0.8083 (p) cc_final: 0.7477 (t) REVERT: J 431 ASP cc_start: 0.5838 (t0) cc_final: 0.5483 (p0) REVERT: N 21 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6832 (mm) REVERT: O 284 LYS cc_start: 0.8325 (mttm) cc_final: 0.7670 (mttp) REVERT: O 390 SER cc_start: 0.8084 (p) cc_final: 0.7477 (t) REVERT: O 431 ASP cc_start: 0.5784 (t0) cc_final: 0.5466 (p0) outliers start: 88 outliers final: 49 residues processed: 376 average time/residue: 1.1119 time to fit residues: 476.8244 Evaluate side-chains 329 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 276 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 124 ASN Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 336 CYS Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 359 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 73 LYS Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 124 ASN Chi-restraints excluded: chain O residue 125 GLU Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 336 CYS Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 87 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 GLN L 90 HIS L 91 HIS A 100 HIS D 42 GLN D 90 HIS D 91 HIS E 100 HIS I 42 GLN I 90 HIS I 91 HIS J 100 HIS N 42 GLN N 90 HIS N 91 HIS O 100 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111034 restraints weight = 21497.425| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.91 r_work: 0.3163 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 18876 Z= 0.297 Angle : 0.723 7.272 25564 Z= 0.391 Chirality : 0.050 0.174 2708 Planarity : 0.006 0.071 3252 Dihedral : 5.759 25.306 2724 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.35 % Rotamer: Outliers : 6.06 % Allowed : 13.90 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.90 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.39 (0.17), residues: 900 loop : -1.33 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 99 HIS 0.006 0.002 HIS O 272 PHE 0.017 0.003 PHE E 118 TYR 0.019 0.002 TYR L 32 ARG 0.003 0.001 ARG O 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 4) link_NAG-ASN : angle 1.35464 ( 12) link_BETA1-4 : bond 0.00509 ( 4) link_BETA1-4 : angle 1.46090 ( 12) hydrogen bonds : bond 0.05483 ( 648) hydrogen bonds : angle 6.05015 ( 1584) covalent geometry : bond 0.00694 (18868) covalent geometry : angle 0.72206 (25540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 307 time to evaluate : 1.936 Fit side-chains REVERT: A 78 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7116 (tp30) REVERT: A 167 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: A 170 ILE cc_start: 0.8742 (mt) cc_final: 0.8467 (mp) REVERT: A 284 LYS cc_start: 0.8437 (mttm) cc_final: 0.7771 (mttp) REVERT: A 291 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.7951 (ttt180) REVERT: A 359 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7462 (ttpp) REVERT: A 390 SER cc_start: 0.8266 (p) cc_final: 0.7587 (t) REVERT: A 403 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8155 (pttt) REVERT: E 78 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7121 (tp30) REVERT: E 167 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: E 170 ILE cc_start: 0.8736 (mt) cc_final: 0.8460 (mp) REVERT: E 284 LYS cc_start: 0.8443 (mttm) cc_final: 0.7776 (mttp) REVERT: E 291 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.7957 (ttt180) REVERT: E 359 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7449 (ttpp) REVERT: E 390 SER cc_start: 0.8245 (p) cc_final: 0.7572 (t) REVERT: E 403 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8156 (pttt) REVERT: J 78 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7122 (tp30) REVERT: J 167 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: J 170 ILE cc_start: 0.8738 (mt) cc_final: 0.8464 (mp) REVERT: J 284 LYS cc_start: 0.8444 (mttm) cc_final: 0.7773 (mttp) REVERT: J 360 ILE cc_start: 0.8363 (mt) cc_final: 0.7967 (tp) REVERT: J 390 SER cc_start: 0.8252 (p) cc_final: 0.7578 (t) REVERT: J 403 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8152 (pttt) REVERT: O 78 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7118 (tp30) REVERT: O 167 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: O 170 ILE cc_start: 0.8736 (mt) cc_final: 0.8461 (mp) REVERT: O 284 LYS cc_start: 0.8423 (mttm) cc_final: 0.7754 (mttp) REVERT: O 291 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.7963 (ttt180) REVERT: O 360 ILE cc_start: 0.8363 (mt) cc_final: 0.7968 (tp) REVERT: O 390 SER cc_start: 0.8267 (p) cc_final: 0.7596 (t) REVERT: O 403 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8146 (pttt) outliers start: 119 outliers final: 56 residues processed: 370 average time/residue: 1.0449 time to fit residues: 446.5409 Evaluate side-chains 346 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 277 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 73 LYS Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 125 GLU Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 291 ARG Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 213 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN C 81 GLN G 81 GLN M 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116200 restraints weight = 21275.397| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.91 r_work: 0.3232 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18876 Z= 0.136 Angle : 0.582 5.856 25564 Z= 0.313 Chirality : 0.045 0.146 2708 Planarity : 0.004 0.033 3252 Dihedral : 5.324 26.099 2724 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.48 % Favored : 96.35 % Rotamer: Outliers : 5.35 % Allowed : 15.89 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.98 (0.16), residues: 2300 helix: None (None), residues: 0 sheet: 0.31 (0.17), residues: 940 loop : -1.41 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 100F HIS 0.002 0.001 HIS J 128 PHE 0.011 0.002 PHE M 29 TYR 0.010 0.001 TYR E 364 ARG 0.003 0.000 ARG O 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 4) link_NAG-ASN : angle 0.54489 ( 12) link_BETA1-4 : bond 0.00389 ( 4) link_BETA1-4 : angle 1.21207 ( 12) hydrogen bonds : bond 0.04074 ( 648) hydrogen bonds : angle 5.72380 ( 1584) covalent geometry : bond 0.00303 (18868) covalent geometry : angle 0.58137 (25540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 271 time to evaluate : 2.282 Fit side-chains REVERT: H 92 CYS cc_start: 0.7586 (OUTLIER) cc_final: 0.6879 (p) REVERT: H 97 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: L 69 THR cc_start: 0.8065 (p) cc_final: 0.7519 (m) REVERT: L 93 THR cc_start: 0.8663 (p) cc_final: 0.8414 (m) REVERT: A 78 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7115 (tp30) REVERT: A 170 ILE cc_start: 0.8744 (mt) cc_final: 0.8464 (mp) REVERT: A 284 LYS cc_start: 0.8450 (mttm) cc_final: 0.7747 (mttp) REVERT: A 360 ILE cc_start: 0.8337 (mt) cc_final: 0.8124 (tp) REVERT: A 390 SER cc_start: 0.8239 (p) cc_final: 0.7612 (t) REVERT: A 403 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8097 (pttt) REVERT: C 92 CYS cc_start: 0.7590 (OUTLIER) cc_final: 0.6880 (p) REVERT: C 97 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: D 69 THR cc_start: 0.8052 (p) cc_final: 0.7510 (m) REVERT: D 93 THR cc_start: 0.8682 (p) cc_final: 0.8365 (m) REVERT: E 78 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7111 (tp30) REVERT: E 170 ILE cc_start: 0.8736 (mt) cc_final: 0.8454 (mp) REVERT: E 265 PHE cc_start: 0.9165 (m-80) cc_final: 0.8951 (m-80) REVERT: E 284 LYS cc_start: 0.8456 (mttm) cc_final: 0.7767 (mttp) REVERT: E 307 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: E 360 ILE cc_start: 0.8329 (mt) cc_final: 0.8122 (tp) REVERT: E 390 SER cc_start: 0.8245 (p) cc_final: 0.7614 (t) REVERT: E 403 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8102 (pttt) REVERT: G 92 CYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6886 (p) REVERT: G 97 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: I 69 THR cc_start: 0.8084 (p) cc_final: 0.7514 (m) REVERT: I 93 THR cc_start: 0.8684 (p) cc_final: 0.8367 (m) REVERT: J 78 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7119 (tp30) REVERT: J 170 ILE cc_start: 0.8742 (mt) cc_final: 0.8459 (mp) REVERT: J 265 PHE cc_start: 0.9171 (m-80) cc_final: 0.8958 (m-80) REVERT: J 284 LYS cc_start: 0.8462 (mttm) cc_final: 0.7775 (mttp) REVERT: J 307 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: J 360 ILE cc_start: 0.8290 (mt) cc_final: 0.8040 (tp) REVERT: J 390 SER cc_start: 0.8218 (p) cc_final: 0.7587 (t) REVERT: J 403 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8100 (pttt) REVERT: M 92 CYS cc_start: 0.7584 (OUTLIER) cc_final: 0.6877 (p) REVERT: M 97 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: N 69 THR cc_start: 0.8072 (p) cc_final: 0.7507 (m) REVERT: N 93 THR cc_start: 0.8683 (p) cc_final: 0.8371 (m) REVERT: O 78 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7110 (tp30) REVERT: O 170 ILE cc_start: 0.8752 (mt) cc_final: 0.8471 (mp) REVERT: O 284 LYS cc_start: 0.8447 (mttm) cc_final: 0.7739 (mttp) REVERT: O 360 ILE cc_start: 0.8292 (mt) cc_final: 0.8031 (tp) REVERT: O 390 SER cc_start: 0.8230 (p) cc_final: 0.7608 (t) REVERT: O 403 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8099 (pttt) outliers start: 105 outliers final: 33 residues processed: 334 average time/residue: 0.9742 time to fit residues: 377.5538 Evaluate side-chains 311 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 264 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 102 optimal weight: 0.0170 chunk 209 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 GLN D 42 GLN I 42 GLN N 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114561 restraints weight = 21478.221| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.97 r_work: 0.3206 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18876 Z= 0.154 Angle : 0.566 5.877 25564 Z= 0.304 Chirality : 0.044 0.146 2708 Planarity : 0.004 0.034 3252 Dihedral : 5.195 24.442 2724 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.57 % Favored : 94.26 % Rotamer: Outliers : 5.50 % Allowed : 14.87 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.91 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.33 (0.18), residues: 912 loop : -1.31 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 100F HIS 0.003 0.001 HIS N 90 PHE 0.011 0.002 PHE G 100E TYR 0.010 0.001 TYR I 32 ARG 0.004 0.000 ARG D 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 4) link_NAG-ASN : angle 0.84252 ( 12) link_BETA1-4 : bond 0.00363 ( 4) link_BETA1-4 : angle 1.27903 ( 12) hydrogen bonds : bond 0.04049 ( 648) hydrogen bonds : angle 5.62775 ( 1584) covalent geometry : bond 0.00353 (18868) covalent geometry : angle 0.56482 (25540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 283 time to evaluate : 2.044 Fit side-chains REVERT: H 92 CYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6907 (p) REVERT: L 56 THR cc_start: 0.7949 (m) cc_final: 0.7555 (p) REVERT: L 69 THR cc_start: 0.8148 (p) cc_final: 0.7599 (m) REVERT: A 78 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7197 (tp30) REVERT: A 170 ILE cc_start: 0.8784 (mt) cc_final: 0.8524 (mp) REVERT: A 193 ASP cc_start: 0.7396 (t70) cc_final: 0.7143 (t70) REVERT: A 284 LYS cc_start: 0.8515 (mttm) cc_final: 0.7847 (mttp) REVERT: A 359 LYS cc_start: 0.7960 (ttpp) cc_final: 0.6930 (tttp) REVERT: A 390 SER cc_start: 0.8357 (p) cc_final: 0.7752 (t) REVERT: A 403 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8102 (pttt) REVERT: C 92 CYS cc_start: 0.7600 (OUTLIER) cc_final: 0.6912 (p) REVERT: D 56 THR cc_start: 0.7963 (m) cc_final: 0.7568 (p) REVERT: D 69 THR cc_start: 0.8152 (p) cc_final: 0.7598 (m) REVERT: E 78 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7194 (tp30) REVERT: E 170 ILE cc_start: 0.8782 (mt) cc_final: 0.8520 (mp) REVERT: E 193 ASP cc_start: 0.7428 (t70) cc_final: 0.7142 (t70) REVERT: E 284 LYS cc_start: 0.8497 (mttm) cc_final: 0.7812 (mttp) REVERT: E 359 LYS cc_start: 0.7950 (ttpp) cc_final: 0.6919 (tttp) REVERT: E 390 SER cc_start: 0.8353 (p) cc_final: 0.7747 (t) REVERT: E 403 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8099 (pttt) REVERT: G 92 CYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6897 (p) REVERT: G 97 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: I 56 THR cc_start: 0.7953 (m) cc_final: 0.7562 (p) REVERT: I 69 THR cc_start: 0.8149 (p) cc_final: 0.7588 (m) REVERT: J 78 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7199 (tp30) REVERT: J 170 ILE cc_start: 0.8788 (mt) cc_final: 0.8520 (mp) REVERT: J 193 ASP cc_start: 0.7419 (t70) cc_final: 0.7169 (t70) REVERT: J 284 LYS cc_start: 0.8494 (mttm) cc_final: 0.7809 (mttp) REVERT: J 390 SER cc_start: 0.8369 (p) cc_final: 0.7770 (t) REVERT: J 403 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8091 (pttt) REVERT: M 92 CYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6903 (p) REVERT: M 97 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: N 56 THR cc_start: 0.7946 (m) cc_final: 0.7552 (p) REVERT: N 69 THR cc_start: 0.8144 (p) cc_final: 0.7584 (m) REVERT: O 78 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7203 (tp30) REVERT: O 170 ILE cc_start: 0.8796 (mt) cc_final: 0.8530 (mp) REVERT: O 193 ASP cc_start: 0.7412 (t70) cc_final: 0.7160 (t70) REVERT: O 284 LYS cc_start: 0.8510 (mttm) cc_final: 0.7844 (mttp) REVERT: O 390 SER cc_start: 0.8360 (p) cc_final: 0.7771 (t) REVERT: O 403 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8097 (pttt) outliers start: 108 outliers final: 48 residues processed: 345 average time/residue: 0.8416 time to fit residues: 343.1553 Evaluate side-chains 319 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 261 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 78 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 HIS E 353 HIS E 430 HIS J 353 HIS J 430 HIS O 353 HIS O 430 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107791 restraints weight = 21557.045| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.94 r_work: 0.3130 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 18876 Z= 0.349 Angle : 0.703 6.152 25564 Z= 0.374 Chirality : 0.050 0.156 2708 Planarity : 0.006 0.064 3252 Dihedral : 5.664 24.340 2724 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.83 % Favored : 94.00 % Rotamer: Outliers : 6.11 % Allowed : 15.33 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.11 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.20 (0.17), residues: 916 loop : -1.45 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP G 100F HIS 0.008 0.002 HIS L 91 PHE 0.016 0.003 PHE A 118 TYR 0.014 0.002 TYR G 32 ARG 0.004 0.001 ARG M 58 Details of bonding type rmsd link_NAG-ASN : bond 0.00831 ( 4) link_NAG-ASN : angle 1.38262 ( 12) link_BETA1-4 : bond 0.00548 ( 4) link_BETA1-4 : angle 1.42147 ( 12) hydrogen bonds : bond 0.05081 ( 648) hydrogen bonds : angle 5.89241 ( 1584) covalent geometry : bond 0.00835 (18868) covalent geometry : angle 0.70238 (25540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 268 time to evaluate : 2.022 Fit side-chains revert: symmetry clash REVERT: H 73 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8036 (ptmm) REVERT: L 24 ARG cc_start: 0.7869 (mmt180) cc_final: 0.7573 (mmt180) REVERT: L 56 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7771 (p) REVERT: L 69 THR cc_start: 0.8392 (p) cc_final: 0.7885 (m) REVERT: A 78 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7556 (tp30) REVERT: A 193 ASP cc_start: 0.7675 (t70) cc_final: 0.7407 (t70) REVERT: A 284 LYS cc_start: 0.8660 (mttm) cc_final: 0.8151 (mttp) REVERT: A 390 SER cc_start: 0.8733 (p) cc_final: 0.8170 (t) REVERT: A 403 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8244 (pttt) REVERT: A 419 CYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8043 (p) REVERT: C 73 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8043 (ptmm) REVERT: D 24 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7577 (mmt180) REVERT: D 56 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7759 (p) REVERT: D 69 THR cc_start: 0.8388 (p) cc_final: 0.7890 (m) REVERT: E 78 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7543 (tp30) REVERT: E 193 ASP cc_start: 0.7693 (t70) cc_final: 0.7408 (t70) REVERT: E 284 LYS cc_start: 0.8647 (mttm) cc_final: 0.8129 (mttp) REVERT: E 390 SER cc_start: 0.8734 (p) cc_final: 0.8173 (t) REVERT: E 403 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8244 (pttt) REVERT: E 419 CYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8036 (p) REVERT: G 73 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8040 (ptmm) REVERT: I 24 ARG cc_start: 0.7837 (mmt180) cc_final: 0.7537 (mmt180) REVERT: I 56 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7765 (p) REVERT: I 69 THR cc_start: 0.8377 (p) cc_final: 0.7869 (m) REVERT: J 78 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7553 (tp30) REVERT: J 193 ASP cc_start: 0.7687 (t70) cc_final: 0.7412 (t70) REVERT: J 284 LYS cc_start: 0.8648 (mttm) cc_final: 0.8119 (mttp) REVERT: J 390 SER cc_start: 0.8717 (p) cc_final: 0.8149 (t) REVERT: J 403 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8247 (pttt) REVERT: J 419 CYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8073 (p) REVERT: M 73 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8043 (ptmm) REVERT: N 24 ARG cc_start: 0.7850 (mmt180) cc_final: 0.7552 (mmt180) REVERT: N 56 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7766 (p) REVERT: N 69 THR cc_start: 0.8370 (p) cc_final: 0.7863 (m) REVERT: O 78 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7557 (tp30) REVERT: O 193 ASP cc_start: 0.7691 (t70) cc_final: 0.7421 (t70) REVERT: O 284 LYS cc_start: 0.8653 (mttm) cc_final: 0.8138 (mttp) REVERT: O 390 SER cc_start: 0.8716 (p) cc_final: 0.8154 (t) REVERT: O 403 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8227 (pttt) REVERT: O 419 CYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8046 (p) outliers start: 120 outliers final: 57 residues processed: 340 average time/residue: 0.9934 time to fit residues: 391.0142 Evaluate side-chains 338 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 265 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 419 CYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 352 VAL Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 419 CYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 73 LYS Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 419 CYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 101 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 chunk 149 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113772 restraints weight = 21044.086| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.89 r_work: 0.3214 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18876 Z= 0.134 Angle : 0.576 6.479 25564 Z= 0.309 Chirality : 0.044 0.149 2708 Planarity : 0.004 0.036 3252 Dihedral : 5.277 24.730 2724 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.78 % Favored : 95.04 % Rotamer: Outliers : 4.58 % Allowed : 17.31 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.08 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.10 (0.18), residues: 876 loop : -1.30 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 100F HIS 0.003 0.001 HIS J 353 PHE 0.012 0.002 PHE C 100E TYR 0.011 0.001 TYR O 321 ARG 0.004 0.000 ARG O 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 4) link_NAG-ASN : angle 0.72704 ( 12) link_BETA1-4 : bond 0.00392 ( 4) link_BETA1-4 : angle 1.21371 ( 12) hydrogen bonds : bond 0.03931 ( 648) hydrogen bonds : angle 5.72674 ( 1584) covalent geometry : bond 0.00297 (18868) covalent geometry : angle 0.57556 (25540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 262 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 CYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7276 (p) REVERT: L 56 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7801 (p) REVERT: L 69 THR cc_start: 0.8331 (p) cc_final: 0.7899 (m) REVERT: A 78 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7533 (tp30) REVERT: A 284 LYS cc_start: 0.8602 (mttm) cc_final: 0.8065 (mttp) REVERT: A 359 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7293 (tttp) REVERT: A 390 SER cc_start: 0.8684 (p) cc_final: 0.8162 (t) REVERT: A 403 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8179 (pttt) REVERT: A 419 CYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8008 (p) REVERT: C 92 CYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7267 (p) REVERT: D 56 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7802 (p) REVERT: D 69 THR cc_start: 0.8336 (p) cc_final: 0.7906 (m) REVERT: E 78 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7522 (tp30) REVERT: E 284 LYS cc_start: 0.8605 (mttm) cc_final: 0.8041 (mttp) REVERT: E 359 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7256 (tttp) REVERT: E 390 SER cc_start: 0.8687 (p) cc_final: 0.8168 (t) REVERT: E 403 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8165 (pttt) REVERT: E 419 CYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8009 (p) REVERT: G 92 CYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7268 (p) REVERT: I 56 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7802 (p) REVERT: I 69 THR cc_start: 0.8336 (p) cc_final: 0.7879 (m) REVERT: J 78 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7535 (tp30) REVERT: J 265 PHE cc_start: 0.9265 (m-80) cc_final: 0.9040 (m-80) REVERT: J 284 LYS cc_start: 0.8592 (mttm) cc_final: 0.8030 (mttp) REVERT: J 359 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7244 (tttp) REVERT: J 390 SER cc_start: 0.8673 (p) cc_final: 0.8149 (t) REVERT: J 419 CYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8020 (p) REVERT: M 92 CYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7262 (p) REVERT: N 56 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7799 (p) REVERT: N 69 THR cc_start: 0.8328 (p) cc_final: 0.7880 (m) REVERT: O 78 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7544 (tp30) REVERT: O 284 LYS cc_start: 0.8620 (mttm) cc_final: 0.8067 (mttp) REVERT: O 359 LYS cc_start: 0.8230 (ttpp) cc_final: 0.7266 (tttp) REVERT: O 390 SER cc_start: 0.8673 (p) cc_final: 0.8152 (t) REVERT: O 403 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8170 (pttt) REVERT: O 419 CYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8014 (p) outliers start: 90 outliers final: 51 residues processed: 309 average time/residue: 0.9421 time to fit residues: 340.5780 Evaluate side-chains 324 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 258 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 419 CYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 419 CYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 193 ASP Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 419 CYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 180 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112581 restraints weight = 21098.781| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.91 r_work: 0.3198 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18876 Z= 0.181 Angle : 0.582 6.529 25564 Z= 0.310 Chirality : 0.045 0.145 2708 Planarity : 0.005 0.036 3252 Dihedral : 5.239 24.185 2724 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.43 % Favored : 94.39 % Rotamer: Outliers : 4.12 % Allowed : 17.72 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.09 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.03 (0.18), residues: 892 loop : -1.27 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 100F HIS 0.003 0.001 HIS N 91 PHE 0.013 0.002 PHE G 100E TYR 0.010 0.001 TYR E 321 ARG 0.002 0.000 ARG A 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 4) link_NAG-ASN : angle 0.92204 ( 12) link_BETA1-4 : bond 0.00456 ( 4) link_BETA1-4 : angle 1.27173 ( 12) hydrogen bonds : bond 0.04100 ( 648) hydrogen bonds : angle 5.64355 ( 1584) covalent geometry : bond 0.00424 (18868) covalent geometry : angle 0.58139 (25540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 259 time to evaluate : 1.979 Fit side-chains revert: symmetry clash REVERT: H 92 CYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7228 (p) REVERT: L 56 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7831 (p) REVERT: L 69 THR cc_start: 0.8280 (p) cc_final: 0.7837 (m) REVERT: A 78 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7545 (tp30) REVERT: A 284 LYS cc_start: 0.8611 (mttm) cc_final: 0.8063 (mttp) REVERT: A 390 SER cc_start: 0.8698 (p) cc_final: 0.8166 (t) REVERT: A 403 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8188 (pttt) REVERT: A 419 CYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8057 (p) REVERT: C 92 CYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7220 (p) REVERT: D 56 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7821 (p) REVERT: D 69 THR cc_start: 0.8287 (p) cc_final: 0.7847 (m) REVERT: E 78 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7540 (tp30) REVERT: E 284 LYS cc_start: 0.8604 (mttm) cc_final: 0.8038 (mttp) REVERT: E 390 SER cc_start: 0.8701 (p) cc_final: 0.8168 (t) REVERT: E 403 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8182 (pttt) REVERT: E 419 CYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8040 (p) REVERT: G 92 CYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7223 (p) REVERT: I 56 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7819 (p) REVERT: I 69 THR cc_start: 0.8284 (p) cc_final: 0.7838 (m) REVERT: J 78 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7541 (tp30) REVERT: J 284 LYS cc_start: 0.8615 (mttm) cc_final: 0.8056 (mttp) REVERT: J 390 SER cc_start: 0.8691 (p) cc_final: 0.8158 (t) REVERT: J 403 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8175 (pttt) REVERT: J 419 CYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8054 (p) REVERT: M 92 CYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7255 (p) REVERT: N 56 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7819 (p) REVERT: N 69 THR cc_start: 0.8275 (p) cc_final: 0.7835 (m) REVERT: O 78 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7556 (tp30) REVERT: O 284 LYS cc_start: 0.8595 (mttm) cc_final: 0.8047 (mttp) REVERT: O 390 SER cc_start: 0.8684 (p) cc_final: 0.8153 (t) REVERT: O 403 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8179 (pttt) REVERT: O 419 CYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8060 (p) outliers start: 81 outliers final: 49 residues processed: 302 average time/residue: 0.9775 time to fit residues: 343.0029 Evaluate side-chains 319 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 254 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 419 CYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 419 CYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 125 GLU Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 419 CYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 161 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN E 328 ASN J 328 ASN O 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112385 restraints weight = 21273.857| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.92 r_work: 0.3193 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18876 Z= 0.184 Angle : 0.588 6.777 25564 Z= 0.312 Chirality : 0.045 0.144 2708 Planarity : 0.005 0.040 3252 Dihedral : 5.185 21.620 2724 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 4.33 % Allowed : 17.31 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.03 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.14 (0.17), residues: 956 loop : -1.35 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 100F HIS 0.004 0.001 HIS L 91 PHE 0.013 0.002 PHE G 100E TYR 0.010 0.001 TYR O 321 ARG 0.002 0.000 ARG E 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 4) link_NAG-ASN : angle 0.91873 ( 12) link_BETA1-4 : bond 0.00428 ( 4) link_BETA1-4 : angle 1.27404 ( 12) hydrogen bonds : bond 0.03976 ( 648) hydrogen bonds : angle 5.63531 ( 1584) covalent geometry : bond 0.00432 (18868) covalent geometry : angle 0.58757 (25540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 252 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 CYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7245 (p) REVERT: L 56 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7844 (p) REVERT: L 69 THR cc_start: 0.8299 (p) cc_final: 0.7859 (m) REVERT: A 78 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7559 (tp30) REVERT: A 284 LYS cc_start: 0.8604 (mttm) cc_final: 0.8058 (mttp) REVERT: A 359 LYS cc_start: 0.8266 (ttpp) cc_final: 0.7053 (ttmt) REVERT: A 390 SER cc_start: 0.8698 (p) cc_final: 0.8164 (t) REVERT: A 403 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8183 (pttt) REVERT: A 419 CYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8047 (p) REVERT: C 92 CYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7250 (p) REVERT: D 56 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7838 (p) REVERT: D 69 THR cc_start: 0.8289 (p) cc_final: 0.7853 (m) REVERT: E 78 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7552 (tp30) REVERT: E 284 LYS cc_start: 0.8595 (mttm) cc_final: 0.8038 (mttp) REVERT: E 359 LYS cc_start: 0.8249 (ttpp) cc_final: 0.7025 (ttmt) REVERT: E 390 SER cc_start: 0.8702 (p) cc_final: 0.8170 (t) REVERT: E 403 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8178 (pttt) REVERT: E 419 CYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8041 (p) REVERT: G 92 CYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7220 (p) REVERT: I 56 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7832 (p) REVERT: I 69 THR cc_start: 0.8294 (p) cc_final: 0.7860 (m) REVERT: J 78 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7563 (tp30) REVERT: J 284 LYS cc_start: 0.8586 (mttm) cc_final: 0.8030 (mttp) REVERT: J 359 LYS cc_start: 0.8241 (ttpp) cc_final: 0.7011 (ttmt) REVERT: J 390 SER cc_start: 0.8696 (p) cc_final: 0.8161 (t) REVERT: J 403 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8189 (pttt) REVERT: J 419 CYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8061 (p) REVERT: M 92 CYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7264 (p) REVERT: N 56 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7845 (p) REVERT: N 69 THR cc_start: 0.8277 (p) cc_final: 0.7846 (m) REVERT: O 78 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7561 (tp30) REVERT: O 284 LYS cc_start: 0.8586 (mttm) cc_final: 0.8042 (mttp) REVERT: O 359 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7029 (ttmt) REVERT: O 390 SER cc_start: 0.8688 (p) cc_final: 0.8151 (t) REVERT: O 403 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8175 (pttt) REVERT: O 419 CYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8064 (p) outliers start: 85 outliers final: 54 residues processed: 299 average time/residue: 0.9378 time to fit residues: 326.7126 Evaluate side-chains 316 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 246 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 419 CYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 371 THR Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 419 CYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 125 GLU Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 419 CYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 5 optimal weight: 0.1980 chunk 189 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 164 optimal weight: 0.6980 chunk 85 optimal weight: 0.0570 chunk 145 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117929 restraints weight = 20971.812| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.93 r_work: 0.3266 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18876 Z= 0.108 Angle : 0.535 7.416 25564 Z= 0.284 Chirality : 0.043 0.145 2708 Planarity : 0.004 0.033 3252 Dihedral : 4.895 21.548 2724 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.70 % Favored : 95.13 % Rotamer: Outliers : 2.75 % Allowed : 18.64 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.95 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.21 (0.17), residues: 932 loop : -1.28 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 100F HIS 0.002 0.001 HIS J 128 PHE 0.013 0.001 PHE C 100E TYR 0.010 0.001 TYR O 364 ARG 0.003 0.000 ARG M 100D Details of bonding type rmsd link_NAG-ASN : bond 0.00024 ( 4) link_NAG-ASN : angle 0.64860 ( 12) link_BETA1-4 : bond 0.00429 ( 4) link_BETA1-4 : angle 1.24167 ( 12) hydrogen bonds : bond 0.03415 ( 648) hydrogen bonds : angle 5.41470 ( 1584) covalent geometry : bond 0.00244 (18868) covalent geometry : angle 0.53427 (25540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 CYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7091 (p) REVERT: L 69 THR cc_start: 0.8272 (p) cc_final: 0.7888 (m) REVERT: A 78 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7533 (tp30) REVERT: A 193 ASP cc_start: 0.7595 (t70) cc_final: 0.7372 (p0) REVERT: A 267 THR cc_start: 0.8847 (p) cc_final: 0.8608 (p) REVERT: A 284 LYS cc_start: 0.8541 (mttm) cc_final: 0.8021 (mttp) REVERT: A 359 LYS cc_start: 0.8245 (ttpp) cc_final: 0.6989 (ttmt) REVERT: A 390 SER cc_start: 0.8630 (p) cc_final: 0.8155 (t) REVERT: C 92 CYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7092 (p) REVERT: D 69 THR cc_start: 0.8289 (p) cc_final: 0.7906 (m) REVERT: E 78 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7529 (tp30) REVERT: E 267 THR cc_start: 0.8847 (p) cc_final: 0.8614 (p) REVERT: E 284 LYS cc_start: 0.8560 (mttm) cc_final: 0.8023 (mttp) REVERT: E 359 LYS cc_start: 0.8232 (ttpp) cc_final: 0.6969 (ttmt) REVERT: E 390 SER cc_start: 0.8623 (p) cc_final: 0.8149 (t) REVERT: G 92 CYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7099 (p) REVERT: I 69 THR cc_start: 0.8289 (p) cc_final: 0.7905 (m) REVERT: J 78 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7541 (tp30) REVERT: J 193 ASP cc_start: 0.7597 (t70) cc_final: 0.7373 (p0) REVERT: J 284 LYS cc_start: 0.8553 (mttm) cc_final: 0.8002 (mttp) REVERT: J 359 LYS cc_start: 0.8250 (ttpp) cc_final: 0.6976 (ttmt) REVERT: J 390 SER cc_start: 0.8623 (p) cc_final: 0.8151 (t) REVERT: J 403 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8110 (pttt) REVERT: J 419 CYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7922 (p) REVERT: M 92 CYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7106 (p) REVERT: N 69 THR cc_start: 0.8271 (p) cc_final: 0.7884 (m) REVERT: N 94 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7784 (m) REVERT: O 78 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7539 (tp30) REVERT: O 193 ASP cc_start: 0.7597 (t70) cc_final: 0.7377 (p0) REVERT: O 267 THR cc_start: 0.8841 (p) cc_final: 0.8608 (p) REVERT: O 284 LYS cc_start: 0.8542 (mttm) cc_final: 0.8024 (mttp) REVERT: O 359 LYS cc_start: 0.8253 (ttpp) cc_final: 0.6985 (ttmt) REVERT: O 390 SER cc_start: 0.8613 (p) cc_final: 0.8142 (t) outliers start: 54 outliers final: 22 residues processed: 299 average time/residue: 1.0522 time to fit residues: 364.6368 Evaluate side-chains 267 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 419 CYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 215 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 134 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.146768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115217 restraints weight = 21080.072| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.92 r_work: 0.3232 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18876 Z= 0.149 Angle : 0.561 6.953 25564 Z= 0.297 Chirality : 0.044 0.144 2708 Planarity : 0.004 0.036 3252 Dihedral : 4.951 21.098 2724 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.35 % Favored : 94.48 % Rotamer: Outliers : 2.14 % Allowed : 19.76 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.91 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.26 (0.17), residues: 932 loop : -1.27 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 100F HIS 0.003 0.001 HIS N 91 PHE 0.013 0.001 PHE G 100E TYR 0.009 0.001 TYR O 321 ARG 0.002 0.000 ARG M 100D Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 4) link_NAG-ASN : angle 0.86985 ( 12) link_BETA1-4 : bond 0.00411 ( 4) link_BETA1-4 : angle 1.24887 ( 12) hydrogen bonds : bond 0.03707 ( 648) hydrogen bonds : angle 5.39750 ( 1584) covalent geometry : bond 0.00346 (18868) covalent geometry : angle 0.56056 (25540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12514.55 seconds wall clock time: 217 minutes 12.06 seconds (13032.06 seconds total)