Starting phenix.real_space_refine on Mon Jun 16 06:04:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1c_41809/06_2025/8u1c_41809.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1c_41809/06_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_41809/06_2025/8u1c_41809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1c_41809/06_2025/8u1c_41809.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1c_41809/06_2025/8u1c_41809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1c_41809/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.62, per 1000 atoms: 0.52 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: 4.29 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: 3.05 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: 6.68 Time building geometry restraints manager: 5.12 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: 7.750 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: 0.830 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 41.640 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: 0.010 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.700 ------------------------------------------------------------------------------- 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 : 2.226 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: 1.2042 time to fit residues: 658.8423 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 : 2.209 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119284 restraints weight = 21259.790| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.92 r_work: 0.3282 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 0.00184 ( 4) link_NAG-ASN : angle 0.86285 ( 12) link_BETA1-4 : bond 0.00159 ( 4) link_BETA1-4 : angle 2.25936 ( 12) hydrogen bonds : bond 0.05331 ( 648) hydrogen bonds : angle 6.63903 ( 1584) covalent geometry : bond 0.00449 (18868) covalent geometry : angle 0.71529 (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 : 2.109 Fit side-chains REVERT: L 21 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6833 (mm) REVERT: A 284 LYS cc_start: 0.8315 (mttm) cc_final: 0.7656 (mttp) REVERT: A 360 ILE cc_start: 0.8250 (mt) cc_final: 0.7760 (tp) REVERT: A 390 SER cc_start: 0.8091 (p) cc_final: 0.7493 (t) REVERT: A 431 ASP cc_start: 0.5775 (t0) cc_final: 0.5457 (p0) REVERT: D 21 LEU cc_start: 0.7158 (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: 0.8218 (mt) cc_final: 0.7756 (tp) REVERT: E 390 SER cc_start: 0.8080 (p) cc_final: 0.7473 (t) REVERT: E 431 ASP cc_start: 0.5799 (t0) cc_final: 0.5473 (p0) REVERT: I 21 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6847 (mm) REVERT: J 218 ASN cc_start: 0.7502 (m-40) cc_final: 0.7270 (m-40) REVERT: J 284 LYS cc_start: 0.8316 (mttm) cc_final: 0.7660 (mttp) REVERT: J 390 SER cc_start: 0.8081 (p) cc_final: 0.7474 (t) REVERT: J 431 ASP cc_start: 0.5839 (t0) cc_final: 0.5483 (p0) REVERT: N 21 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6831 (mm) REVERT: O 284 LYS cc_start: 0.8323 (mttm) cc_final: 0.7668 (mttp) REVERT: O 390 SER cc_start: 0.8080 (p) cc_final: 0.7472 (t) REVERT: O 431 ASP cc_start: 0.5784 (t0) cc_final: 0.5465 (p0) outliers start: 88 outliers final: 49 residues processed: 376 average time/residue: 1.1120 time to fit residues: 477.4427 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 : 2.387 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 2.9990 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: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.140343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109669 restraints weight = 21583.179| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.91 r_work: 0.3124 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 18876 Z= 0.352 Angle : 0.755 7.940 25564 Z= 0.407 Chirality : 0.052 0.200 2708 Planarity : 0.006 0.075 3252 Dihedral : 5.884 25.498 2724 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.65 % Favored : 95.17 % Rotamer: Outliers : 6.06 % Allowed : 13.80 % Favored : 80.14 % 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: -0.93 (0.16), residues: 2300 helix: None (None), residues: 0 sheet: 0.38 (0.17), residues: 896 loop : -1.36 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 99 HIS 0.005 0.002 HIS N 90 PHE 0.019 0.003 PHE E 118 TYR 0.020 0.002 TYR D 32 ARG 0.004 0.001 ARG O 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 4) link_NAG-ASN : angle 1.42271 ( 12) link_BETA1-4 : bond 0.00653 ( 4) link_BETA1-4 : angle 1.46211 ( 12) hydrogen bonds : bond 0.05727 ( 648) hydrogen bonds : angle 6.17776 ( 1584) covalent geometry : bond 0.00829 (18868) covalent geometry : angle 0.75357 (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 421 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 302 time to evaluate : 2.105 Fit side-chains REVERT: A 78 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7113 (tp30) REVERT: A 170 ILE cc_start: 0.8763 (mt) cc_final: 0.8490 (mp) REVERT: A 284 LYS cc_start: 0.8442 (mttm) cc_final: 0.7771 (mttp) REVERT: A 390 SER cc_start: 0.8262 (p) cc_final: 0.7567 (t) REVERT: A 403 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8157 (pttt) REVERT: E 78 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7118 (tp30) REVERT: E 170 ILE cc_start: 0.8760 (mt) cc_final: 0.8488 (mp) REVERT: E 284 LYS cc_start: 0.8447 (mttm) cc_final: 0.7773 (mttp) REVERT: E 359 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7390 (ttpp) REVERT: E 390 SER cc_start: 0.8247 (p) cc_final: 0.7562 (t) REVERT: E 403 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8159 (pttt) REVERT: J 78 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7124 (tp30) REVERT: J 170 ILE cc_start: 0.8760 (mt) cc_final: 0.8487 (mp) REVERT: J 284 LYS cc_start: 0.8445 (mttm) cc_final: 0.7773 (mttp) REVERT: J 390 SER cc_start: 0.8259 (p) cc_final: 0.7576 (t) REVERT: J 403 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8147 (pttt) REVERT: O 78 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7120 (tp30) REVERT: O 170 ILE cc_start: 0.8758 (mt) cc_final: 0.8484 (mp) REVERT: O 284 LYS cc_start: 0.8437 (mttm) cc_final: 0.7765 (mttp) REVERT: O 291 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8009 (ttt180) REVERT: O 359 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7454 (ttpp) REVERT: O 390 SER cc_start: 0.8271 (p) cc_final: 0.7591 (t) REVERT: O 403 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8139 (pttt) outliers start: 119 outliers final: 52 residues processed: 365 average time/residue: 1.0498 time to fit residues: 441.5083 Evaluate side-chains 332 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 273 time to evaluate : 2.019 ------------------------------------------------------------------------------- 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 215 SER 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 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 215 SER 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 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 215 SER 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 215 SER 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 359 LYS 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: 1.9990 chunk 49 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 213 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 124 optimal weight: 0.3980 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 = 0.3675 r_free = 0.3675 target = 0.145624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115451 restraints weight = 21242.575| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.91 r_work: 0.3226 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4070 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= 0.141 Angle : 0.589 5.780 25564 Z= 0.318 Chirality : 0.045 0.146 2708 Planarity : 0.004 0.033 3252 Dihedral : 5.376 26.299 2724 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.65 % Favored : 96.17 % Rotamer: Outliers : 5.40 % Allowed : 14.97 % 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: -1.07 (0.16), residues: 2300 helix: None (None), residues: 0 sheet: 0.23 (0.17), residues: 924 loop : -1.44 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 100F HIS 0.002 0.001 HIS J 128 PHE 0.012 0.002 PHE A 118 TYR 0.011 0.001 TYR O 321 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00081 ( 4) link_NAG-ASN : angle 0.53131 ( 12) link_BETA1-4 : bond 0.00437 ( 4) link_BETA1-4 : angle 1.26011 ( 12) hydrogen bonds : bond 0.04123 ( 648) hydrogen bonds : angle 5.73917 ( 1584) covalent geometry : bond 0.00317 (18868) covalent geometry : angle 0.58838 (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 387 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 281 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 92 CYS cc_start: 0.7603 (OUTLIER) cc_final: 0.6931 (p) REVERT: H 97 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: L 69 THR cc_start: 0.8091 (p) cc_final: 0.7541 (m) REVERT: L 93 THR cc_start: 0.8702 (p) cc_final: 0.8441 (m) REVERT: A 78 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7148 (tp30) REVERT: A 170 ILE cc_start: 0.8747 (mt) cc_final: 0.8474 (mp) REVERT: A 284 LYS cc_start: 0.8474 (mttm) cc_final: 0.7789 (mttp) REVERT: A 307 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: A 390 SER cc_start: 0.8257 (p) cc_final: 0.7634 (t) REVERT: A 403 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8133 (pttt) REVERT: C 92 CYS cc_start: 0.7602 (OUTLIER) cc_final: 0.6928 (p) REVERT: C 97 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: D 69 THR cc_start: 0.8096 (p) cc_final: 0.7545 (m) REVERT: D 93 THR cc_start: 0.8704 (p) cc_final: 0.8443 (m) REVERT: E 78 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7150 (tp30) REVERT: E 170 ILE cc_start: 0.8751 (mt) cc_final: 0.8477 (mp) REVERT: E 284 LYS cc_start: 0.8474 (mttm) cc_final: 0.7791 (mttp) REVERT: E 307 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: E 390 SER cc_start: 0.8272 (p) cc_final: 0.7648 (t) REVERT: E 403 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8140 (pttt) REVERT: G 92 CYS cc_start: 0.7609 (OUTLIER) cc_final: 0.6922 (p) REVERT: G 97 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: I 69 THR cc_start: 0.8111 (p) cc_final: 0.7555 (m) REVERT: I 93 THR cc_start: 0.8702 (p) cc_final: 0.8437 (m) REVERT: J 78 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7146 (tp30) REVERT: J 170 ILE cc_start: 0.8753 (mt) cc_final: 0.8477 (mp) REVERT: J 284 LYS cc_start: 0.8477 (mttm) cc_final: 0.7797 (mttp) REVERT: J 307 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: J 360 ILE cc_start: 0.8346 (mt) cc_final: 0.8145 (tp) REVERT: J 390 SER cc_start: 0.8269 (p) cc_final: 0.7651 (t) REVERT: J 403 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8138 (pttt) REVERT: M 92 CYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6920 (p) REVERT: M 97 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: N 69 THR cc_start: 0.8108 (p) cc_final: 0.7553 (m) REVERT: N 93 THR cc_start: 0.8708 (p) cc_final: 0.8446 (m) REVERT: O 78 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7141 (tp30) REVERT: O 170 ILE cc_start: 0.8754 (mt) cc_final: 0.8480 (mp) REVERT: O 218 ASN cc_start: 0.8179 (m-40) cc_final: 0.7951 (m-40) REVERT: O 284 LYS cc_start: 0.8469 (mttm) cc_final: 0.7785 (mttp) REVERT: O 307 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: O 360 ILE cc_start: 0.8362 (mt) cc_final: 0.8161 (tp) REVERT: O 390 SER cc_start: 0.8277 (p) cc_final: 0.7654 (t) REVERT: O 403 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8129 (pttt) outliers start: 106 outliers final: 37 residues processed: 349 average time/residue: 0.9390 time to fit residues: 381.9809 Evaluate side-chains 330 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 277 time to evaluate : 1.898 ------------------------------------------------------------------------------- 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 223 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 307 GLU 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 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 223 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 336 CYS 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 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 223 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 223 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 307 GLU Chi-restraints excluded: chain O residue 336 CYS 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: 0.9990 chunk 48 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 102 optimal weight: 0.0030 chunk 209 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 GLN ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3669 r_free = 0.3669 target = 0.145186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114683 restraints weight = 21526.235| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.97 r_work: 0.3206 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4230 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= 0.149 Angle : 0.564 5.908 25564 Z= 0.304 Chirality : 0.044 0.147 2708 Planarity : 0.004 0.034 3252 Dihedral : 5.207 24.761 2724 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.22 % Favored : 94.61 % Rotamer: Outliers : 5.75 % Allowed : 14.41 % Favored : 79.84 % 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: 0.34 (0.17), residues: 936 loop : -1.34 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 100F HIS 0.003 0.001 HIS I 90 PHE 0.011 0.002 PHE J 118 TYR 0.010 0.001 TYR O 321 ARG 0.004 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 4) link_NAG-ASN : angle 0.85554 ( 12) link_BETA1-4 : bond 0.00451 ( 4) link_BETA1-4 : angle 1.28623 ( 12) hydrogen bonds : bond 0.04047 ( 648) hydrogen bonds : angle 5.62565 ( 1584) covalent geometry : bond 0.00339 (18868) covalent geometry : angle 0.56314 (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 390 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 277 time to evaluate : 1.999 Fit side-chains REVERT: H 92 CYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6918 (p) REVERT: H 97 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8190 (mm-30) REVERT: L 56 THR cc_start: 0.7964 (m) cc_final: 0.7570 (p) REVERT: L 69 THR cc_start: 0.8155 (p) cc_final: 0.7599 (m) REVERT: A 78 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7212 (tp30) REVERT: A 170 ILE cc_start: 0.8791 (mt) cc_final: 0.8527 (mp) REVERT: A 193 ASP cc_start: 0.7342 (t70) cc_final: 0.7121 (t70) REVERT: A 284 LYS cc_start: 0.8503 (mttm) cc_final: 0.7828 (mttp) REVERT: A 291 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7417 (ttt180) REVERT: A 390 SER cc_start: 0.8354 (p) cc_final: 0.7765 (t) REVERT: A 403 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8092 (pttt) REVERT: C 92 CYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6931 (p) REVERT: C 97 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8199 (mm-30) REVERT: D 56 THR cc_start: 0.7970 (m) cc_final: 0.7571 (p) REVERT: D 69 THR cc_start: 0.8156 (p) cc_final: 0.7595 (m) REVERT: E 78 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7227 (tp30) REVERT: E 170 ILE cc_start: 0.8785 (mt) cc_final: 0.8522 (mp) REVERT: E 193 ASP cc_start: 0.7355 (t70) cc_final: 0.7149 (OUTLIER) REVERT: E 284 LYS cc_start: 0.8503 (mttm) cc_final: 0.7830 (mttp) REVERT: E 291 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.7399 (ttt180) REVERT: E 390 SER cc_start: 0.8350 (p) cc_final: 0.7759 (t) REVERT: E 403 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8089 (pttt) REVERT: G 92 CYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6913 (p) REVERT: G 97 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8168 (mm-30) REVERT: I 56 THR cc_start: 0.7960 (m) cc_final: 0.7576 (p) REVERT: I 69 THR cc_start: 0.8164 (p) cc_final: 0.7600 (m) REVERT: J 78 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7213 (tp30) REVERT: J 170 ILE cc_start: 0.8790 (mt) cc_final: 0.8527 (mp) REVERT: J 193 ASP cc_start: 0.7348 (t70) cc_final: 0.7136 (t70) REVERT: J 284 LYS cc_start: 0.8510 (mttm) cc_final: 0.7835 (mttp) REVERT: J 390 SER cc_start: 0.8355 (p) cc_final: 0.7762 (t) REVERT: J 403 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8095 (pttt) REVERT: M 92 CYS cc_start: 0.7582 (OUTLIER) cc_final: 0.6915 (p) REVERT: M 97 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8181 (mm-30) REVERT: N 56 THR cc_start: 0.7961 (m) cc_final: 0.7578 (p) REVERT: N 69 THR cc_start: 0.8170 (p) cc_final: 0.7602 (m) REVERT: O 78 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7224 (tp30) REVERT: O 170 ILE cc_start: 0.8801 (mt) cc_final: 0.8539 (mp) REVERT: O 193 ASP cc_start: 0.7352 (t70) cc_final: 0.7134 (t70) REVERT: O 284 LYS cc_start: 0.8511 (mttm) cc_final: 0.7831 (mttp) REVERT: O 390 SER cc_start: 0.8399 (p) cc_final: 0.7812 (t) REVERT: O 403 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8089 (pttt) outliers start: 113 outliers final: 60 residues processed: 345 average time/residue: 0.9037 time to fit residues: 365.9889 Evaluate side-chains 319 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 246 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 H residue 97 GLU 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 215 SER 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 324 THR 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 C residue 97 GLU 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 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 291 ARG Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 356 MET 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 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 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 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 344 SER Chi-restraints excluded: chain O residue 356 MET 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: 6.9990 chunk 219 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108917 restraints weight = 21451.582| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.90 r_work: 0.3149 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 18876 Z= 0.303 Angle : 0.675 5.736 25564 Z= 0.360 Chirality : 0.048 0.149 2708 Planarity : 0.006 0.060 3252 Dihedral : 5.578 24.354 2724 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.65 % Favored : 94.17 % Rotamer: Outliers : 6.11 % Allowed : 14.92 % Favored : 78.97 % 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: 0.14 (0.17), residues: 924 loop : -1.42 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP H 100F HIS 0.007 0.002 HIS N 91 PHE 0.015 0.002 PHE J 118 TYR 0.013 0.002 TYR G 32 ARG 0.007 0.001 ARG J 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00732 ( 4) link_NAG-ASN : angle 1.26754 ( 12) link_BETA1-4 : bond 0.00474 ( 4) link_BETA1-4 : angle 1.40524 ( 12) hydrogen bonds : bond 0.04857 ( 648) hydrogen bonds : angle 5.83336 ( 1584) covalent geometry : bond 0.00723 (18868) covalent geometry : angle 0.67425 (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 391 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 271 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.7829 (mmt180) cc_final: 0.7533 (mmt180) REVERT: L 56 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7759 (p) REVERT: L 69 THR cc_start: 0.8369 (p) cc_final: 0.7853 (m) REVERT: A 78 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7562 (tp30) REVERT: A 170 ILE cc_start: 0.8982 (mt) cc_final: 0.8780 (mp) REVERT: A 193 ASP cc_start: 0.7644 (t70) cc_final: 0.7406 (t70) REVERT: A 284 LYS cc_start: 0.8645 (mttm) cc_final: 0.8123 (mttp) REVERT: A 291 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.7866 (ttm170) REVERT: A 390 SER cc_start: 0.8693 (p) cc_final: 0.8135 (t) REVERT: A 403 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8234 (pttt) REVERT: A 419 CYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8094 (p) REVERT: D 24 ARG cc_start: 0.7836 (mmt180) cc_final: 0.7542 (mmt180) REVERT: D 56 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7748 (p) REVERT: D 69 THR cc_start: 0.8375 (p) cc_final: 0.7863 (m) REVERT: E 78 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7540 (tp30) REVERT: E 170 ILE cc_start: 0.8986 (mt) cc_final: 0.8784 (mp) REVERT: E 193 ASP cc_start: 0.7699 (t70) cc_final: 0.7456 (t70) REVERT: E 284 LYS cc_start: 0.8645 (mttm) cc_final: 0.8120 (mttp) REVERT: E 291 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.7859 (ttm170) REVERT: E 390 SER cc_start: 0.8702 (p) cc_final: 0.8147 (t) REVERT: E 403 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8236 (pttt) REVERT: E 419 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8047 (p) REVERT: I 24 ARG cc_start: 0.7816 (mmt180) cc_final: 0.7516 (mmt180) REVERT: I 56 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7762 (p) REVERT: I 69 THR cc_start: 0.8370 (p) cc_final: 0.7850 (m) REVERT: J 78 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7550 (tp30) REVERT: J 193 ASP cc_start: 0.7665 (t70) cc_final: 0.7420 (t70) REVERT: J 284 LYS cc_start: 0.8663 (mttm) cc_final: 0.8142 (mttp) REVERT: J 390 SER cc_start: 0.8695 (p) cc_final: 0.8132 (t) REVERT: J 403 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8251 (pttt) REVERT: J 419 CYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8135 (p) REVERT: N 24 ARG cc_start: 0.7816 (mmt180) cc_final: 0.7518 (mmt180) REVERT: N 56 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7761 (p) REVERT: N 69 THR cc_start: 0.8365 (p) cc_final: 0.7851 (m) REVERT: O 78 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7559 (tp30) REVERT: O 170 ILE cc_start: 0.8987 (mt) cc_final: 0.8785 (mp) REVERT: O 193 ASP cc_start: 0.7644 (t70) cc_final: 0.7404 (t70) REVERT: O 284 LYS cc_start: 0.8635 (mttm) cc_final: 0.8111 (mttp) REVERT: O 390 SER cc_start: 0.8699 (p) cc_final: 0.8136 (t) REVERT: O 403 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8248 (pttt) REVERT: O 419 CYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8067 (p) outliers start: 120 outliers final: 60 residues processed: 345 average time/residue: 1.0390 time to fit residues: 414.4466 Evaluate side-chains 333 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 259 time to evaluate : 2.030 ------------------------------------------------------------------------------- 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 56 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 166 VAL 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 291 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 SER 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 92 CYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 166 VAL 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 291 ARG Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 356 MET 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 56 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 166 VAL 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 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 56 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain O residue 166 VAL 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 344 SER Chi-restraints excluded: chain O residue 356 MET 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: 0.7980 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 0.0980 chunk 90 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.145788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114462 restraints weight = 20949.967| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.89 r_work: 0.3226 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4609 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= 0.139 Angle : 0.568 6.892 25564 Z= 0.303 Chirality : 0.044 0.145 2708 Planarity : 0.004 0.035 3252 Dihedral : 5.183 24.633 2724 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.74 % Favored : 95.09 % Rotamer: Outliers : 4.38 % Allowed : 17.52 % 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: -1.09 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.11 (0.18), residues: 876 loop : -1.31 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 100F HIS 0.003 0.001 HIS J 353 PHE 0.012 0.001 PHE M 100E TYR 0.011 0.001 TYR E 321 ARG 0.003 0.000 ARG E 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 4) link_NAG-ASN : angle 0.68274 ( 12) link_BETA1-4 : bond 0.00529 ( 4) link_BETA1-4 : angle 1.27578 ( 12) hydrogen bonds : bond 0.03855 ( 648) hydrogen bonds : angle 5.65722 ( 1584) covalent geometry : bond 0.00315 (18868) covalent geometry : angle 0.56744 (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 349 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 263 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 CYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7224 (p) REVERT: L 56 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7812 (p) REVERT: L 69 THR cc_start: 0.8283 (p) cc_final: 0.7863 (m) REVERT: A 78 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7529 (tp30) REVERT: A 170 ILE cc_start: 0.8923 (mt) cc_final: 0.8711 (mp) REVERT: A 284 LYS cc_start: 0.8585 (mttm) cc_final: 0.8039 (mttp) REVERT: A 291 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.7497 (ttm170) REVERT: A 359 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7289 (tttp) REVERT: A 390 SER cc_start: 0.8665 (p) cc_final: 0.8150 (t) REVERT: A 403 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8165 (pttt) REVERT: A 419 CYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7997 (p) REVERT: C 92 CYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7221 (p) REVERT: D 56 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7807 (p) REVERT: D 69 THR cc_start: 0.8289 (p) cc_final: 0.7873 (m) REVERT: E 78 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7517 (tp30) REVERT: E 170 ILE cc_start: 0.8924 (mt) cc_final: 0.8715 (mp) REVERT: E 284 LYS cc_start: 0.8604 (mttm) cc_final: 0.8058 (mttp) REVERT: E 291 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.7525 (ttm170) REVERT: E 356 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8528 (mtm) REVERT: E 359 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7252 (tttp) REVERT: E 390 SER cc_start: 0.8669 (p) cc_final: 0.8155 (t) REVERT: E 403 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8160 (pttt) REVERT: E 419 CYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7996 (p) REVERT: G 92 CYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7207 (p) REVERT: I 56 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7811 (p) REVERT: I 69 THR cc_start: 0.8287 (p) cc_final: 0.7862 (m) REVERT: J 78 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7531 (tp30) REVERT: J 284 LYS cc_start: 0.8604 (mttm) cc_final: 0.8054 (mttp) REVERT: J 359 LYS cc_start: 0.8221 (ttpp) cc_final: 0.7250 (tttp) REVERT: J 390 SER cc_start: 0.8659 (p) cc_final: 0.8142 (t) REVERT: J 403 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8166 (pttt) REVERT: J 419 CYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8015 (p) REVERT: M 92 CYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7212 (p) REVERT: N 56 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7810 (p) REVERT: N 69 THR cc_start: 0.8291 (p) cc_final: 0.7872 (m) REVERT: O 78 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7526 (tp30) REVERT: O 170 ILE cc_start: 0.8928 (mt) cc_final: 0.8717 (mp) REVERT: O 284 LYS cc_start: 0.8576 (mttm) cc_final: 0.8022 (mttp) REVERT: O 356 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8565 (mtm) REVERT: O 359 LYS cc_start: 0.8275 (ttpp) cc_final: 0.7277 (tttp) REVERT: O 390 SER cc_start: 0.8654 (p) cc_final: 0.8134 (t) REVERT: O 403 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8161 (pttt) REVERT: O 419 CYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8002 (p) outliers start: 86 outliers final: 44 residues processed: 307 average time/residue: 1.2443 time to fit residues: 451.0676 Evaluate side-chains 316 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 252 time to evaluate : 2.119 ------------------------------------------------------------------------------- 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 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 L residue 94 SER Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 SER 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 22 CYS 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 D residue 94 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 419 CYS 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 I residue 21 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 80 THR 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 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 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 N residue 94 SER Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 356 MET Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 419 CYS 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: 0.3980 chunk 88 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.142365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110565 restraints weight = 21185.390| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.91 r_work: 0.3171 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 18876 Z= 0.237 Angle : 0.613 6.534 25564 Z= 0.326 Chirality : 0.046 0.142 2708 Planarity : 0.005 0.045 3252 Dihedral : 5.313 22.059 2724 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.57 % Favored : 94.26 % Rotamer: Outliers : 4.53 % Allowed : 17.26 % Favored : 78.21 % 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: -1.06 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.17 (0.17), residues: 924 loop : -1.37 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 100F HIS 0.005 0.001 HIS D 91 PHE 0.013 0.002 PHE M 100E TYR 0.010 0.002 TYR H 32 ARG 0.002 0.000 ARG E 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 4) link_NAG-ASN : angle 1.07382 ( 12) link_BETA1-4 : bond 0.00438 ( 4) link_BETA1-4 : angle 1.34906 ( 12) hydrogen bonds : bond 0.04284 ( 648) hydrogen bonds : angle 5.70145 ( 1584) covalent geometry : bond 0.00562 (18868) covalent geometry : angle 0.61239 (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 347 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 258 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 CYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7263 (p) REVERT: L 56 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7829 (p) REVERT: L 69 THR cc_start: 0.8317 (p) cc_final: 0.7869 (m) REVERT: A 78 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7553 (tp30) REVERT: A 170 ILE cc_start: 0.8969 (mt) cc_final: 0.8764 (mp) REVERT: A 193 ASP cc_start: 0.7751 (t70) cc_final: 0.7466 (p0) REVERT: A 284 LYS cc_start: 0.8602 (mttm) cc_final: 0.8050 (mttp) REVERT: A 291 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.7628 (ttm170) REVERT: A 390 SER cc_start: 0.8727 (p) cc_final: 0.8184 (t) REVERT: A 403 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8205 (pttt) REVERT: A 419 CYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8101 (p) REVERT: C 92 CYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7264 (p) REVERT: D 56 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7834 (p) REVERT: D 69 THR cc_start: 0.8326 (p) cc_final: 0.7883 (m) REVERT: E 78 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7548 (tp30) REVERT: E 170 ILE cc_start: 0.8972 (mt) cc_final: 0.8771 (mp) REVERT: E 284 LYS cc_start: 0.8611 (mttm) cc_final: 0.8050 (mttp) REVERT: E 291 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.7607 (ttm170) REVERT: E 390 SER cc_start: 0.8737 (p) cc_final: 0.8194 (t) REVERT: E 403 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8205 (pttt) REVERT: E 419 CYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8098 (p) REVERT: G 92 CYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7257 (p) REVERT: I 56 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7832 (p) REVERT: I 69 THR cc_start: 0.8333 (p) cc_final: 0.7884 (m) REVERT: J 78 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7555 (tp30) REVERT: J 193 ASP cc_start: 0.7761 (t70) cc_final: 0.7476 (p0) REVERT: J 284 LYS cc_start: 0.8627 (mttm) cc_final: 0.8068 (mttp) REVERT: J 359 LYS cc_start: 0.8221 (ttpp) cc_final: 0.7268 (tttp) REVERT: J 390 SER cc_start: 0.8727 (p) cc_final: 0.8179 (t) REVERT: J 403 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8208 (pttt) REVERT: J 419 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8079 (p) REVERT: M 92 CYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7247 (p) REVERT: N 56 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7826 (p) REVERT: N 69 THR cc_start: 0.8318 (p) cc_final: 0.7875 (m) REVERT: O 78 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7560 (tp30) REVERT: O 170 ILE cc_start: 0.8971 (mt) cc_final: 0.8768 (mp) REVERT: O 193 ASP cc_start: 0.7755 (t70) cc_final: 0.7470 (p0) REVERT: O 284 LYS cc_start: 0.8612 (mttm) cc_final: 0.8056 (mttp) REVERT: O 390 SER cc_start: 0.8727 (p) cc_final: 0.8179 (t) REVERT: O 403 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8210 (pttt) REVERT: O 419 CYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8112 (p) outliers start: 89 outliers final: 57 residues processed: 307 average time/residue: 1.0014 time to fit residues: 357.8818 Evaluate side-chains 330 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 255 time to evaluate : 2.105 ------------------------------------------------------------------------------- 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 113 ILE 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 291 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 SER 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 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 291 ARG Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 356 MET 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 113 ILE 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 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 113 ILE 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 344 SER Chi-restraints excluded: chain O residue 356 MET 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: 0.9990 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 164 optimal weight: 0.3980 chunk 185 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.145139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113586 restraints weight = 21239.525| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.92 r_work: 0.3208 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4772 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= 0.157 Angle : 0.566 6.953 25564 Z= 0.301 Chirality : 0.044 0.143 2708 Planarity : 0.004 0.037 3252 Dihedral : 5.118 22.205 2724 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.87 % Favored : 94.96 % Rotamer: Outliers : 4.02 % Allowed : 17.82 % 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: -1.07 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.11 (0.18), residues: 892 loop : -1.30 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 100F HIS 0.003 0.001 HIS N 91 PHE 0.013 0.002 PHE M 100E TYR 0.010 0.001 TYR E 321 ARG 0.003 0.000 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 4) link_NAG-ASN : angle 0.84098 ( 12) link_BETA1-4 : bond 0.00416 ( 4) link_BETA1-4 : angle 1.26973 ( 12) hydrogen bonds : bond 0.03823 ( 648) hydrogen bonds : angle 5.57119 ( 1584) covalent geometry : bond 0.00364 (18868) covalent geometry : angle 0.56534 (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 336 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 257 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 CYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7233 (p) REVERT: L 56 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7845 (p) REVERT: L 69 THR cc_start: 0.8254 (p) cc_final: 0.7836 (m) REVERT: A 78 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7562 (tp30) REVERT: A 170 ILE cc_start: 0.8928 (mt) cc_final: 0.8728 (mp) REVERT: A 284 LYS cc_start: 0.8581 (mttm) cc_final: 0.8028 (mttp) REVERT: A 291 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7503 (ttm170) REVERT: A 359 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7003 (ttmt) REVERT: A 390 SER cc_start: 0.8698 (p) cc_final: 0.8173 (t) REVERT: A 419 CYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8021 (p) REVERT: C 92 CYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7242 (p) REVERT: D 56 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7845 (p) REVERT: D 69 THR cc_start: 0.8269 (p) cc_final: 0.7854 (m) REVERT: E 78 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7555 (tp30) REVERT: E 284 LYS cc_start: 0.8596 (mttm) cc_final: 0.8046 (mttp) REVERT: E 291 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7487 (ttm170) REVERT: E 390 SER cc_start: 0.8707 (p) cc_final: 0.8185 (t) REVERT: E 419 CYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8002 (p) REVERT: G 92 CYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7223 (p) REVERT: I 56 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7842 (p) REVERT: I 69 THR cc_start: 0.8298 (p) cc_final: 0.7880 (m) REVERT: J 78 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7568 (tp30) REVERT: J 284 LYS cc_start: 0.8611 (mttm) cc_final: 0.8063 (mttp) REVERT: J 359 LYS cc_start: 0.8162 (ttpp) cc_final: 0.7202 (tttp) REVERT: J 390 SER cc_start: 0.8697 (p) cc_final: 0.8171 (t) REVERT: J 419 CYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8047 (p) REVERT: M 92 CYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7225 (p) REVERT: N 56 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7848 (p) REVERT: N 69 THR cc_start: 0.8298 (p) cc_final: 0.7879 (m) REVERT: O 78 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7568 (tp30) REVERT: O 284 LYS cc_start: 0.8575 (mttm) cc_final: 0.8025 (mttp) REVERT: O 390 SER cc_start: 0.8698 (p) cc_final: 0.8179 (t) REVERT: O 419 CYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8018 (p) outliers start: 79 outliers final: 45 residues processed: 300 average time/residue: 0.9985 time to fit residues: 347.6688 Evaluate side-chains 308 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 249 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 215 SER 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 324 THR Chi-restraints excluded: chain A residue 344 SER 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 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 215 SER 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 324 THR Chi-restraints excluded: chain E residue 344 SER 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 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 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 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 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 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: 0.3980 chunk 189 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.141225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109227 restraints weight = 21228.445| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.92 r_work: 0.3152 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 18876 Z= 0.269 Angle : 0.641 6.551 25564 Z= 0.340 Chirality : 0.047 0.144 2708 Planarity : 0.005 0.051 3252 Dihedral : 5.373 22.363 2724 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.39 % Rotamer: Outliers : 3.46 % Allowed : 18.69 % Favored : 77.85 % 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: 0.13 (0.17), residues: 980 loop : -1.44 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP M 100F HIS 0.006 0.001 HIS L 91 PHE 0.014 0.002 PHE J 118 TYR 0.012 0.002 TYR C 32 ARG 0.003 0.000 ARG A 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 4) link_NAG-ASN : angle 1.19077 ( 12) link_BETA1-4 : bond 0.00483 ( 4) link_BETA1-4 : angle 1.36013 ( 12) hydrogen bonds : bond 0.04482 ( 648) hydrogen bonds : angle 5.72301 ( 1584) covalent geometry : bond 0.00640 (18868) covalent geometry : angle 0.63994 (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 291 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 223 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 CYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7245 (p) REVERT: L 69 THR cc_start: 0.8311 (p) cc_final: 0.7863 (m) REVERT: A 78 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7577 (tp30) REVERT: A 97 ILE cc_start: 0.8866 (mp) cc_final: 0.8598 (mm) REVERT: A 170 ILE cc_start: 0.8976 (mt) cc_final: 0.8774 (mp) REVERT: A 265 PHE cc_start: 0.9269 (m-80) cc_final: 0.9021 (m-80) REVERT: A 284 LYS cc_start: 0.8606 (mttm) cc_final: 0.8050 (mttp) REVERT: A 291 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.7782 (ttm170) REVERT: A 337 GLU cc_start: 0.8287 (pm20) cc_final: 0.7903 (pm20) REVERT: A 390 SER cc_start: 0.8753 (p) cc_final: 0.8213 (t) REVERT: A 419 CYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8033 (p) REVERT: C 92 CYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7250 (p) REVERT: D 69 THR cc_start: 0.8312 (p) cc_final: 0.7879 (m) REVERT: E 78 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7571 (tp30) REVERT: E 265 PHE cc_start: 0.9273 (m-80) cc_final: 0.9020 (m-80) REVERT: E 284 LYS cc_start: 0.8619 (mttm) cc_final: 0.8055 (mttp) REVERT: E 291 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.7776 (ttm170) REVERT: E 390 SER cc_start: 0.8754 (p) cc_final: 0.8211 (t) REVERT: E 419 CYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8037 (p) REVERT: G 92 CYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7254 (p) REVERT: I 69 THR cc_start: 0.8306 (p) cc_final: 0.7863 (m) REVERT: J 78 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7577 (tp30) REVERT: J 265 PHE cc_start: 0.9271 (m-80) cc_final: 0.9014 (m-80) REVERT: J 284 LYS cc_start: 0.8628 (mttm) cc_final: 0.8067 (mttp) REVERT: J 359 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7221 (tttp) REVERT: J 390 SER cc_start: 0.8751 (p) cc_final: 0.8206 (t) REVERT: J 419 CYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8089 (p) REVERT: M 92 CYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7252 (p) REVERT: N 69 THR cc_start: 0.8302 (p) cc_final: 0.7868 (m) REVERT: O 78 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7570 (tp30) REVERT: O 265 PHE cc_start: 0.9271 (m-80) cc_final: 0.9020 (m-80) REVERT: O 284 LYS cc_start: 0.8619 (mttm) cc_final: 0.8060 (mttp) REVERT: O 390 SER cc_start: 0.8752 (p) cc_final: 0.8206 (t) REVERT: O 419 CYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8049 (p) outliers start: 68 outliers final: 48 residues processed: 270 average time/residue: 1.1445 time to fit residues: 358.3512 Evaluate side-chains 275 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 2.014 ------------------------------------------------------------------------------- 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 243 SER Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 352 VAL 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 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 215 SER Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 352 VAL 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 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 243 SER Chi-restraints excluded: chain J residue 324 THR 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 243 SER Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 352 VAL 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 215 optimal weight: 0.4980 chunk 117 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 202 optimal weight: 0.4980 chunk 102 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.145539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114014 restraints weight = 21054.493| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.92 r_work: 0.3216 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 0.036 18876 Z= 0.139 Angle : 0.562 7.106 25564 Z= 0.299 Chirality : 0.044 0.144 2708 Planarity : 0.004 0.038 3252 Dihedral : 5.086 20.841 2724 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.65 % Rotamer: Outliers : 3.41 % Allowed : 18.74 % Favored : 77.85 % 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: -1.07 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.12 (0.17), residues: 936 loop : -1.35 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M 100F HIS 0.002 0.001 HIS O 353 PHE 0.013 0.001 PHE M 100E TYR 0.010 0.001 TYR O 364 ARG 0.003 0.000 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 4) link_NAG-ASN : angle 0.75782 ( 12) link_BETA1-4 : bond 0.00423 ( 4) link_BETA1-4 : angle 1.22774 ( 12) hydrogen bonds : bond 0.03711 ( 648) hydrogen bonds : angle 5.57558 ( 1584) covalent geometry : bond 0.00320 (18868) covalent geometry : angle 0.56127 (25540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13757.08 seconds wall clock time: 237 minutes 41.90 seconds (14261.90 seconds total)