Starting phenix.real_space_refine on Sun Aug 24 08:11:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1c_41809/08_2025/8u1c_41809.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1c_41809/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8u1c_41809/08_2025/8u1c_41809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1c_41809/08_2025/8u1c_41809.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u1c_41809/08_2025/8u1c_41809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1c_41809/08_2025/8u1c_41809.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18380 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" 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: "L" 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} 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 Restraints were copied for chains: C, G, M, D, I, N, E, J, O, F, K, P Time building chain proxies: 2.55, per 1000 atoms: 0.14 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=40, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.01 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 181 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 290 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 336 " distance=2.04 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 446 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.01 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.01 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.01 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 86 " - pdb=" SG CYS E 419 " distance=2.04 Simple disulfide: pdb=" SG CYS J 86 " - pdb=" SG CYS J 419 " distance=2.04 Simple disulfide: pdb=" SG CYS O 86 " - pdb=" SG CYS O 419 " distance=2.04 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS J 121 " - pdb=" SG CYS J 126 " distance=2.03 Simple disulfide: pdb=" SG CYS O 121 " - pdb=" SG CYS O 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 181 " - pdb=" SG CYS E 228 " distance=2.03 Simple disulfide: pdb=" SG CYS J 181 " - pdb=" SG CYS J 228 " distance=2.03 Simple disulfide: pdb=" SG CYS O 181 " - pdb=" SG CYS O 228 " distance=2.03 Simple disulfide: pdb=" SG CYS E 230 " - pdb=" SG CYS E 235 " distance=2.03 Simple disulfide: pdb=" SG CYS J 230 " - pdb=" SG CYS J 235 " distance=2.03 Simple disulfide: pdb=" SG CYS O 230 " - pdb=" SG CYS O 235 " distance=2.03 Simple disulfide: pdb=" SG CYS E 276 " - pdb=" SG CYS E 290 " distance=2.02 Simple disulfide: pdb=" SG CYS J 276 " - pdb=" SG CYS J 290 " distance=2.02 Simple disulfide: pdb=" SG CYS O 276 " - pdb=" SG CYS O 290 " distance=2.02 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 288 " distance=2.02 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 288 " distance=2.02 Simple disulfide: pdb=" SG CYS O 278 " - pdb=" SG CYS O 288 " distance=2.02 Simple disulfide: pdb=" SG CYS E 317 " - pdb=" SG CYS E 336 " distance=2.04 Simple disulfide: pdb=" SG CYS J 317 " - pdb=" SG CYS J 336 " distance=2.04 Simple disulfide: pdb=" SG CYS O 317 " - pdb=" SG CYS O 336 " distance=2.04 Simple disulfide: pdb=" SG CYS E 423 " - pdb=" SG CYS E 446 " distance=2.04 Simple disulfide: pdb=" SG CYS J 423 " - pdb=" SG CYS J 446 " distance=2.04 Simple disulfide: pdb=" SG CYS O 423 " - pdb=" SG CYS O 446 " distance=2.04 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: 1.07 Conformation dependent library (CDL) restraints added in 481.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.62 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: 2.89 Time building geometry restraints manager: 1.40 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: 10828 17.04 - 34.09: 348 34.09 - 51.13: 68 51.13 - 68.17: 28 68.17 - 85.22: 16 Dihedral angle restraints: 11288 sinusoidal: 4644 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 11285 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: 2.35 - 2.86: 6668 2.86 - 3.37: 15572 3.37 - 3.88: 33236 3.88 - 4.39: 40212 4.39 - 4.90: 67092 Nonbonded interactions: 162780 Sorted by model distance: nonbonded pdb=" O MET J 399 " pdb=" OH TYR J 445 " model vdw 2.353 3.040 nonbonded pdb=" O MET A 399 " pdb=" OH TYR A 445 " model vdw 2.353 3.040 nonbonded pdb=" O MET E 399 " pdb=" OH TYR E 445 " model vdw 2.353 3.040 nonbonded pdb=" O MET O 399 " pdb=" OH TYR O 445 " model vdw 2.353 3.040 nonbonded pdb=" N PRO M 52A" pdb=" O PRO M 52A" model vdw 2.378 2.496 ... (remaining 162775 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: 0.06 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'C' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'K' selection = chain 'P' } 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: 7.760 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.040 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- 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 18916 Z= 1.220 Angle : 1.855 13.590 25644 Z= 1.228 Chirality : 0.109 0.508 2708 Planarity : 0.010 0.055 3252 Dihedral : 10.037 85.218 6960 Min Nonbonded Distance : 2.353 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG A 326 TYR 0.055 0.009 TYR E 321 PHE 0.028 0.006 PHE L 98 TRP 0.060 0.013 TRP C 99 HIS 0.014 0.003 HIS H 100C Details of bonding type rmsd covalent geometry : bond 0.02316 (18868) covalent geometry : angle 1.84663 (25540) SS BOND : bond 0.00901 ( 40) SS BOND : angle 3.13955 ( 80) hydrogen bonds : bond 0.17232 ( 648) hydrogen bonds : angle 8.45131 ( 1584) link_BETA1-4 : bond 0.06925 ( 4) link_BETA1-4 : angle 5.02179 ( 12) link_NAG-ASN : bond 0.06197 ( 4) link_NAG-ASN : angle 2.09504 ( 12) *********************** 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 : 0.505 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: 0.4934 time to fit residues: 269.9038 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 : 0.542 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.151172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119737 restraints weight = 20595.026| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.98 r_work: 0.3296 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18916 Z= 0.189 Angle : 0.710 7.665 25644 Z= 0.385 Chirality : 0.048 0.155 2708 Planarity : 0.005 0.037 3252 Dihedral : 5.751 27.710 2728 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.78 % Favored : 97.04 % Rotamer: Outliers : 3.67 % Allowed : 11.41 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.16), residues: 2300 helix: None (None), residues: 0 sheet: 0.45 (0.17), residues: 876 loop : -1.01 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 54 TYR 0.017 0.002 TYR J 321 PHE 0.016 0.002 PHE A 118 TRP 0.017 0.002 TRP C 47 HIS 0.004 0.001 HIS M 95 Details of bonding type rmsd covalent geometry : bond 0.00397 (18868) covalent geometry : angle 0.70219 (25540) SS BOND : bond 0.00330 ( 40) SS BOND : angle 1.80850 ( 80) hydrogen bonds : bond 0.05230 ( 648) hydrogen bonds : angle 6.45056 ( 1584) link_BETA1-4 : bond 0.00610 ( 4) link_BETA1-4 : angle 2.26485 ( 12) link_NAG-ASN : bond 0.00039 ( 4) link_NAG-ASN : angle 0.72294 ( 12) *********************** 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 422 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 350 time to evaluate : 0.515 Fit side-chains REVERT: H 38 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7742 (ttp-170) REVERT: L 21 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6836 (mm) REVERT: A 125 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6416 (pm20) REVERT: A 218 ASN cc_start: 0.7417 (m-40) cc_final: 0.7187 (m-40) REVERT: A 284 LYS cc_start: 0.8350 (mttm) cc_final: 0.7717 (mttp) REVERT: A 360 ILE cc_start: 0.8220 (mt) cc_final: 0.7792 (tp) REVERT: A 390 SER cc_start: 0.8114 (p) cc_final: 0.7448 (t) REVERT: C 38 ARG cc_start: 0.7949 (ttp-170) cc_final: 0.7746 (ttp-170) REVERT: D 21 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6848 (mm) REVERT: E 125 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6392 (pm20) REVERT: E 218 ASN cc_start: 0.7417 (m-40) cc_final: 0.7190 (m-40) REVERT: E 284 LYS cc_start: 0.8348 (mttm) cc_final: 0.7720 (mttp) REVERT: E 360 ILE cc_start: 0.8213 (mt) cc_final: 0.7796 (tp) REVERT: E 390 SER cc_start: 0.8099 (p) cc_final: 0.7428 (t) REVERT: E 431 ASP cc_start: 0.5873 (t0) cc_final: 0.5517 (p0) REVERT: I 21 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6836 (mm) REVERT: J 125 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6429 (pm20) REVERT: J 218 ASN cc_start: 0.7390 (m-40) cc_final: 0.7169 (m-40) REVERT: J 284 LYS cc_start: 0.8348 (mttm) cc_final: 0.7716 (mttp) REVERT: J 360 ILE cc_start: 0.8205 (mt) cc_final: 0.7776 (tp) REVERT: J 390 SER cc_start: 0.8088 (p) cc_final: 0.7416 (t) REVERT: J 431 ASP cc_start: 0.5877 (t0) cc_final: 0.5521 (p0) REVERT: M 38 ARG cc_start: 0.7940 (ttp-170) cc_final: 0.7738 (ttp-170) REVERT: N 21 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6869 (mm) REVERT: O 125 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6401 (pm20) REVERT: O 218 ASN cc_start: 0.7393 (m-40) cc_final: 0.7171 (m-40) REVERT: O 284 LYS cc_start: 0.8365 (mttm) cc_final: 0.7734 (mttp) REVERT: O 360 ILE cc_start: 0.8204 (mt) cc_final: 0.7780 (tp) REVERT: O 390 SER cc_start: 0.8104 (p) cc_final: 0.7437 (t) REVERT: O 431 ASP cc_start: 0.5858 (t0) cc_final: 0.5517 (p0) outliers start: 72 outliers final: 24 residues processed: 372 average time/residue: 0.4867 time to fit residues: 205.7184 Evaluate side-chains 319 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 287 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 344 SER Chi-restraints excluded: chain A residue 442 THR 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 344 SER Chi-restraints excluded: chain E residue 442 THR 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 344 SER Chi-restraints excluded: chain J residue 442 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 344 SER 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 58 optimal weight: 0.0370 chunk 165 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 143 optimal weight: 0.2980 chunk 90 optimal weight: 3.9990 overall best weight: 1.4664 ------------------------------------------------------------------------------- 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 D 42 GLN D 90 HIS D 91 HIS I 42 GLN I 90 HIS I 91 HIS N 42 GLN N 90 HIS N 91 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.143602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112809 restraints weight = 21086.927| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.91 r_work: 0.3194 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 18916 Z= 0.264 Angle : 0.715 7.044 25644 Z= 0.385 Chirality : 0.049 0.147 2708 Planarity : 0.006 0.064 3252 Dihedral : 5.513 25.033 2724 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.91 % Favored : 95.91 % Rotamer: Outliers : 5.35 % Allowed : 13.80 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.41 (0.17), residues: 896 loop : -1.27 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 38 TYR 0.020 0.002 TYR D 32 PHE 0.017 0.003 PHE J 118 TRP 0.017 0.002 TRP C 99 HIS 0.006 0.002 HIS O 272 Details of bonding type rmsd covalent geometry : bond 0.00609 (18868) covalent geometry : angle 0.71166 (25540) SS BOND : bond 0.00633 ( 40) SS BOND : angle 1.29284 ( 80) hydrogen bonds : bond 0.05455 ( 648) hydrogen bonds : angle 6.00740 ( 1584) link_BETA1-4 : bond 0.00533 ( 4) link_BETA1-4 : angle 1.31964 ( 12) link_NAG-ASN : bond 0.00291 ( 4) link_NAG-ASN : angle 1.25783 ( 12) *********************** 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 413 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 308 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.7950 (m) cc_final: 0.7459 (t) REVERT: A 78 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7102 (tp30) REVERT: A 125 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6386 (pm20) REVERT: A 167 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: A 170 ILE cc_start: 0.8724 (mt) cc_final: 0.8449 (mp) REVERT: A 284 LYS cc_start: 0.8420 (mttm) cc_final: 0.7769 (mttp) REVERT: A 360 ILE cc_start: 0.8352 (mt) cc_final: 0.7991 (tp) REVERT: A 390 SER cc_start: 0.8210 (p) cc_final: 0.7516 (t) REVERT: A 403 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8125 (pttt) REVERT: A 438 HIS cc_start: 0.6332 (m-70) cc_final: 0.6087 (m-70) REVERT: D 74 THR cc_start: 0.7965 (m) cc_final: 0.7473 (t) REVERT: E 78 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7107 (tp30) REVERT: E 125 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6409 (pm20) REVERT: E 167 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: E 170 ILE cc_start: 0.8698 (mt) cc_final: 0.8423 (mp) REVERT: E 284 LYS cc_start: 0.8426 (mttm) cc_final: 0.7784 (mttp) REVERT: E 360 ILE cc_start: 0.8336 (mt) cc_final: 0.7983 (tp) REVERT: E 390 SER cc_start: 0.8206 (p) cc_final: 0.7509 (t) REVERT: E 403 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8114 (pttt) REVERT: E 438 HIS cc_start: 0.6342 (m-70) cc_final: 0.6099 (m-70) REVERT: I 74 THR cc_start: 0.7954 (m) cc_final: 0.7465 (t) REVERT: J 78 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7110 (tp30) REVERT: J 125 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6406 (pm20) REVERT: J 167 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: J 170 ILE cc_start: 0.8707 (mt) cc_final: 0.8430 (mp) REVERT: J 284 LYS cc_start: 0.8417 (mttm) cc_final: 0.7770 (mttp) REVERT: J 360 ILE cc_start: 0.8338 (mt) cc_final: 0.7979 (tp) REVERT: J 390 SER cc_start: 0.8212 (p) cc_final: 0.7516 (t) REVERT: J 403 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8112 (pttt) REVERT: J 438 HIS cc_start: 0.6339 (m-70) cc_final: 0.6094 (m-70) REVERT: N 74 THR cc_start: 0.7938 (m) cc_final: 0.7448 (t) REVERT: O 78 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7113 (tp30) REVERT: O 125 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6388 (pm20) REVERT: O 167 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: O 170 ILE cc_start: 0.8720 (mt) cc_final: 0.8446 (mp) REVERT: O 284 LYS cc_start: 0.8403 (mttm) cc_final: 0.7758 (mttp) REVERT: O 360 ILE cc_start: 0.8331 (mt) cc_final: 0.7985 (tp) REVERT: O 390 SER cc_start: 0.8215 (p) cc_final: 0.7520 (t) REVERT: O 403 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8123 (pttt) REVERT: O 438 HIS cc_start: 0.6326 (m-70) cc_final: 0.6081 (m-70) outliers start: 105 outliers final: 53 residues processed: 361 average time/residue: 0.4312 time to fit residues: 179.3486 Evaluate side-chains 348 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 283 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS 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 73 LYS Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 228 CYS 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 73 LYS Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 125 GLU Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 228 CYS Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 90 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 214 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN A 100 HIS C 81 GLN G 81 GLN M 81 GLN O 100 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.144690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114160 restraints weight = 21263.458| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.90 r_work: 0.3212 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18916 Z= 0.172 Angle : 0.617 5.552 25644 Z= 0.330 Chirality : 0.046 0.143 2708 Planarity : 0.005 0.035 3252 Dihedral : 5.343 25.425 2724 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.35 % Favored : 96.48 % Rotamer: Outliers : 5.65 % Allowed : 15.58 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.16), residues: 2300 helix: None (None), residues: 0 sheet: 0.30 (0.17), residues: 912 loop : -1.42 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 24 TYR 0.011 0.001 TYR I 32 PHE 0.012 0.002 PHE O 118 TRP 0.015 0.002 TRP M 100F HIS 0.004 0.001 HIS D 91 Details of bonding type rmsd covalent geometry : bond 0.00395 (18868) covalent geometry : angle 0.61374 (25540) SS BOND : bond 0.00332 ( 40) SS BOND : angle 1.13669 ( 80) hydrogen bonds : bond 0.04337 ( 648) hydrogen bonds : angle 5.81336 ( 1584) link_BETA1-4 : bond 0.00395 ( 4) link_BETA1-4 : angle 1.23436 ( 12) link_NAG-ASN : bond 0.00260 ( 4) link_NAG-ASN : angle 0.81464 ( 12) *********************** 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 384 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 273 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: L 93 THR cc_start: 0.8734 (p) cc_final: 0.8373 (m) REVERT: A 78 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7164 (tp30) REVERT: A 125 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6481 (pm20) REVERT: A 170 ILE cc_start: 0.8764 (mt) cc_final: 0.8497 (mp) REVERT: A 284 LYS cc_start: 0.8485 (mttm) cc_final: 0.7868 (mttp) REVERT: A 360 ILE cc_start: 0.8322 (mt) cc_final: 0.8051 (tp) REVERT: A 390 SER cc_start: 0.8245 (p) cc_final: 0.7609 (t) REVERT: A 403 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8108 (pttt) REVERT: C 97 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: D 93 THR cc_start: 0.8737 (p) cc_final: 0.8371 (m) REVERT: E 78 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7167 (tp30) REVERT: E 125 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6499 (pm20) REVERT: E 170 ILE cc_start: 0.8748 (mt) cc_final: 0.8481 (mp) REVERT: E 284 LYS cc_start: 0.8496 (mttm) cc_final: 0.7882 (mttp) REVERT: E 360 ILE cc_start: 0.8310 (mt) cc_final: 0.8043 (tp) REVERT: E 390 SER cc_start: 0.8255 (p) cc_final: 0.7623 (t) REVERT: E 403 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8104 (pttt) REVERT: G 97 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: I 93 THR cc_start: 0.8742 (p) cc_final: 0.8378 (m) REVERT: J 78 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7168 (tp30) REVERT: J 125 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6487 (pm20) REVERT: J 170 ILE cc_start: 0.8756 (mt) cc_final: 0.8489 (mp) REVERT: J 284 LYS cc_start: 0.8499 (mttm) cc_final: 0.7882 (mttp) REVERT: J 360 ILE cc_start: 0.8309 (mt) cc_final: 0.8038 (tp) REVERT: J 390 SER cc_start: 0.8253 (p) cc_final: 0.7621 (t) REVERT: J 403 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8103 (pttt) REVERT: M 97 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: N 93 THR cc_start: 0.8735 (p) cc_final: 0.8373 (m) REVERT: O 78 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7172 (tp30) REVERT: O 125 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6471 (pm20) REVERT: O 170 ILE cc_start: 0.8767 (mt) cc_final: 0.8499 (mp) REVERT: O 284 LYS cc_start: 0.8477 (mttm) cc_final: 0.7860 (mttp) REVERT: O 360 ILE cc_start: 0.8320 (mt) cc_final: 0.8043 (tp) REVERT: O 390 SER cc_start: 0.8254 (p) cc_final: 0.7622 (t) REVERT: O 403 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8108 (pttt) outliers start: 111 outliers final: 47 residues processed: 330 average time/residue: 0.3761 time to fit residues: 145.9782 Evaluate side-chains 329 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 371 THR 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 23 GLN Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 371 THR 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 23 GLN Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 228 CYS Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 371 THR Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 73 LYS Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 125 GLU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 228 CYS Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 371 THR 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 129 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 chunk 203 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.145495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114475 restraints weight = 21044.800| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.92 r_work: 0.3207 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18916 Z= 0.157 Angle : 0.583 5.819 25644 Z= 0.311 Chirality : 0.044 0.147 2708 Planarity : 0.004 0.035 3252 Dihedral : 5.150 24.646 2724 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.70 % Favored : 95.13 % Rotamer: Outliers : 4.53 % Allowed : 16.45 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.43 (0.17), residues: 880 loop : -1.31 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 24 TYR 0.010 0.001 TYR E 321 PHE 0.012 0.002 PHE A 118 TRP 0.013 0.002 TRP G 47 HIS 0.003 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00359 (18868) covalent geometry : angle 0.57964 (25540) SS BOND : bond 0.00287 ( 40) SS BOND : angle 1.09162 ( 80) hydrogen bonds : bond 0.04111 ( 648) hydrogen bonds : angle 5.61961 ( 1584) link_BETA1-4 : bond 0.00473 ( 4) link_BETA1-4 : angle 1.28284 ( 12) link_NAG-ASN : bond 0.00222 ( 4) link_NAG-ASN : angle 0.84092 ( 12) *********************** 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 381 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 292 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 56 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7630 (p) REVERT: L 69 THR cc_start: 0.8242 (p) cc_final: 0.7711 (m) REVERT: A 78 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7388 (tp30) REVERT: A 125 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6841 (pm20) REVERT: A 170 ILE cc_start: 0.8879 (mt) cc_final: 0.8646 (mp) REVERT: A 284 LYS cc_start: 0.8586 (mttm) cc_final: 0.7983 (mttp) REVERT: A 390 SER cc_start: 0.8566 (p) cc_final: 0.8099 (t) REVERT: A 403 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8168 (pttt) REVERT: D 56 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7632 (p) REVERT: D 69 THR cc_start: 0.8243 (p) cc_final: 0.7714 (m) REVERT: E 78 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7394 (tp30) REVERT: E 125 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6855 (pm20) REVERT: E 170 ILE cc_start: 0.8856 (mt) cc_final: 0.8629 (mp) REVERT: E 284 LYS cc_start: 0.8595 (mttm) cc_final: 0.7996 (mttp) REVERT: E 390 SER cc_start: 0.8563 (p) cc_final: 0.8097 (t) REVERT: E 403 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8168 (pttt) REVERT: I 56 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7629 (p) REVERT: I 69 THR cc_start: 0.8245 (p) cc_final: 0.7708 (m) REVERT: J 78 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7392 (tp30) REVERT: J 125 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6845 (pm20) REVERT: J 170 ILE cc_start: 0.8864 (mt) cc_final: 0.8638 (mp) REVERT: J 284 LYS cc_start: 0.8600 (mttm) cc_final: 0.8002 (mttp) REVERT: J 390 SER cc_start: 0.8564 (p) cc_final: 0.8096 (t) REVERT: J 403 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8164 (pttt) REVERT: N 56 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7630 (p) REVERT: N 69 THR cc_start: 0.8243 (p) cc_final: 0.7712 (m) REVERT: O 78 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7385 (tp30) REVERT: O 125 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: O 170 ILE cc_start: 0.8877 (mt) cc_final: 0.8642 (mp) REVERT: O 284 LYS cc_start: 0.8589 (mttm) cc_final: 0.7996 (mttp) REVERT: O 390 SER cc_start: 0.8567 (p) cc_final: 0.8100 (t) REVERT: O 403 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8168 (pttt) outliers start: 89 outliers final: 44 residues processed: 332 average time/residue: 0.4250 time to fit residues: 162.9229 Evaluate side-chains 330 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 274 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 23 GLN 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 201 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS 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 17 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 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 5 VAL Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 23 GLN 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 201 LEU Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 228 CYS 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 17 SER Chi-restraints excluded: chain M residue 23 GLN 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 201 LEU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 228 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 220 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 0.0570 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN J 100 HIS ** J 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.145972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114199 restraints weight = 20685.483| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.89 r_work: 0.3224 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18916 Z= 0.178 Angle : 0.588 6.141 25644 Z= 0.312 Chirality : 0.045 0.145 2708 Planarity : 0.005 0.038 3252 Dihedral : 5.159 24.073 2724 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.91 % Favored : 94.96 % Rotamer: Outliers : 4.99 % Allowed : 16.40 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.33 (0.18), residues: 892 loop : -1.27 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 24 TYR 0.010 0.001 TYR A 321 PHE 0.012 0.002 PHE O 118 TRP 0.015 0.002 TRP G 100F HIS 0.004 0.001 HIS N 91 Details of bonding type rmsd covalent geometry : bond 0.00412 (18868) covalent geometry : angle 0.58555 (25540) SS BOND : bond 0.00309 ( 40) SS BOND : angle 1.00305 ( 80) hydrogen bonds : bond 0.04073 ( 648) hydrogen bonds : angle 5.60829 ( 1584) link_BETA1-4 : bond 0.00451 ( 4) link_BETA1-4 : angle 1.27595 ( 12) link_NAG-ASN : bond 0.00348 ( 4) link_NAG-ASN : angle 0.91805 ( 12) *********************** 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 378 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 280 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 56 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7715 (p) REVERT: L 69 THR cc_start: 0.8321 (p) cc_final: 0.7818 (m) REVERT: A 78 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7526 (tp30) REVERT: A 125 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7086 (pm20) REVERT: A 170 ILE cc_start: 0.8936 (mt) cc_final: 0.8733 (mp) REVERT: A 284 LYS cc_start: 0.8653 (mttm) cc_final: 0.8124 (mttp) REVERT: A 390 SER cc_start: 0.8636 (p) cc_final: 0.8187 (t) REVERT: A 403 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8185 (pttt) REVERT: D 56 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7712 (p) REVERT: D 69 THR cc_start: 0.8321 (p) cc_final: 0.7830 (m) REVERT: E 78 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7528 (tp30) REVERT: E 125 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7069 (pm20) REVERT: E 284 LYS cc_start: 0.8677 (mttm) cc_final: 0.8125 (mttp) REVERT: E 390 SER cc_start: 0.8640 (p) cc_final: 0.8193 (t) REVERT: E 403 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8172 (pttt) REVERT: G 72 ASP cc_start: 0.8255 (t70) cc_final: 0.7909 (t70) REVERT: I 56 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7714 (p) REVERT: I 69 THR cc_start: 0.8331 (p) cc_final: 0.7834 (m) REVERT: J 78 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7534 (tp30) REVERT: J 125 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: J 170 ILE cc_start: 0.8922 (mt) cc_final: 0.8722 (mp) REVERT: J 284 LYS cc_start: 0.8668 (mttm) cc_final: 0.8115 (mttp) REVERT: J 390 SER cc_start: 0.8635 (p) cc_final: 0.8182 (t) REVERT: J 403 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8181 (pttt) REVERT: M 72 ASP cc_start: 0.8270 (t70) cc_final: 0.7915 (t70) REVERT: N 56 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7717 (p) REVERT: N 69 THR cc_start: 0.8324 (p) cc_final: 0.7820 (m) REVERT: O 78 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7528 (tp30) REVERT: O 125 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7090 (pm20) REVERT: O 170 ILE cc_start: 0.8941 (mt) cc_final: 0.8736 (mp) REVERT: O 284 LYS cc_start: 0.8660 (mttm) cc_final: 0.8119 (mttp) REVERT: O 390 SER cc_start: 0.8629 (p) cc_final: 0.8180 (t) REVERT: O 403 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8177 (pttt) outliers start: 98 outliers final: 57 residues processed: 328 average time/residue: 0.3814 time to fit residues: 146.3123 Evaluate side-chains 341 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 272 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 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 201 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS 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 17 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 17 SER 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 125 GLU 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 228 CYS 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 17 SER 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 201 LEU Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 228 CYS Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 195 optimal weight: 0.1980 chunk 55 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.143747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111739 restraints weight = 20874.582| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.92 r_work: 0.3186 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18916 Z= 0.222 Angle : 0.619 6.195 25644 Z= 0.329 Chirality : 0.046 0.144 2708 Planarity : 0.005 0.048 3252 Dihedral : 5.285 23.925 2724 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.48 % Favored : 94.39 % Rotamer: Outliers : 4.68 % Allowed : 17.26 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.23 (0.17), residues: 912 loop : -1.28 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 58 TYR 0.010 0.002 TYR J 321 PHE 0.014 0.002 PHE O 118 TRP 0.022 0.002 TRP H 100F HIS 0.005 0.001 HIS N 91 Details of bonding type rmsd covalent geometry : bond 0.00520 (18868) covalent geometry : angle 0.61648 (25540) SS BOND : bond 0.00437 ( 40) SS BOND : angle 1.04091 ( 80) hydrogen bonds : bond 0.04337 ( 648) hydrogen bonds : angle 5.67632 ( 1584) link_BETA1-4 : bond 0.00423 ( 4) link_BETA1-4 : angle 1.32494 ( 12) link_NAG-ASN : bond 0.00491 ( 4) link_NAG-ASN : angle 1.05471 ( 12) *********************** 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 366 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 274 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 56 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7816 (p) REVERT: L 69 THR cc_start: 0.8318 (p) cc_final: 0.7817 (m) REVERT: A 78 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7556 (tp30) REVERT: A 125 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: A 284 LYS cc_start: 0.8651 (mttm) cc_final: 0.8106 (mttp) REVERT: A 390 SER cc_start: 0.8674 (p) cc_final: 0.8188 (t) REVERT: A 403 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8210 (pttt) REVERT: A 418 LYS cc_start: 0.8370 (mtmm) cc_final: 0.8161 (mttm) REVERT: D 56 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7818 (p) REVERT: D 69 THR cc_start: 0.8321 (p) cc_final: 0.7820 (m) REVERT: E 78 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7555 (tp30) REVERT: E 125 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: E 284 LYS cc_start: 0.8628 (mttm) cc_final: 0.8089 (mttp) REVERT: E 390 SER cc_start: 0.8678 (p) cc_final: 0.8195 (t) REVERT: E 403 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8203 (pttt) REVERT: E 418 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8159 (mttm) REVERT: I 56 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7811 (p) REVERT: I 69 THR cc_start: 0.8332 (p) cc_final: 0.7829 (m) REVERT: J 78 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7552 (tp30) REVERT: J 125 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7189 (pm20) REVERT: J 284 LYS cc_start: 0.8625 (mttm) cc_final: 0.8088 (mttp) REVERT: J 390 SER cc_start: 0.8665 (p) cc_final: 0.8174 (t) REVERT: J 403 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8208 (pttt) REVERT: N 56 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7810 (p) REVERT: N 69 THR cc_start: 0.8325 (p) cc_final: 0.7823 (m) REVERT: O 78 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7556 (tp30) REVERT: O 125 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: O 284 LYS cc_start: 0.8611 (mttm) cc_final: 0.8074 (mttp) REVERT: O 390 SER cc_start: 0.8671 (p) cc_final: 0.8182 (t) REVERT: O 403 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8202 (pttt) REVERT: O 418 LYS cc_start: 0.8380 (mtmm) cc_final: 0.8174 (mttm) outliers start: 92 outliers final: 64 residues processed: 326 average time/residue: 0.4274 time to fit residues: 161.8520 Evaluate side-chains 338 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 262 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 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 L residue 94 SER 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 201 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 243 SER 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 17 SER 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 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 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 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 17 SER 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 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 125 GLU 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 228 CYS 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 17 SER 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 N residue 94 SER 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 201 LEU Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 228 CYS 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 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 128 optimal weight: 8.9990 chunk 82 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 188 optimal weight: 0.0770 chunk 92 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.147945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116468 restraints weight = 20548.434| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.88 r_work: 0.3249 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18916 Z= 0.125 Angle : 0.556 6.856 25644 Z= 0.294 Chirality : 0.044 0.146 2708 Planarity : 0.004 0.036 3252 Dihedral : 4.981 23.767 2724 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.70 % Favored : 96.13 % Rotamer: Outliers : 4.02 % Allowed : 17.67 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.26 (0.17), residues: 904 loop : -1.24 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 24 TYR 0.010 0.001 TYR J 321 PHE 0.012 0.001 PHE M 100E TRP 0.027 0.002 TRP C 100F HIS 0.002 0.001 HIS J 353 Details of bonding type rmsd covalent geometry : bond 0.00282 (18868) covalent geometry : angle 0.55492 (25540) SS BOND : bond 0.00255 ( 40) SS BOND : angle 0.78560 ( 80) hydrogen bonds : bond 0.03670 ( 648) hydrogen bonds : angle 5.47469 ( 1584) link_BETA1-4 : bond 0.00436 ( 4) link_BETA1-4 : angle 1.24131 ( 12) link_NAG-ASN : bond 0.00057 ( 4) link_NAG-ASN : angle 0.71325 ( 12) *********************** 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 368 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 289 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 56 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7809 (p) REVERT: L 69 THR cc_start: 0.8263 (p) cc_final: 0.7821 (m) REVERT: A 78 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7535 (tp30) REVERT: A 125 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7096 (pm20) REVERT: A 284 LYS cc_start: 0.8595 (mttm) cc_final: 0.8071 (mttp) REVERT: A 359 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7050 (ttmt) REVERT: A 390 SER cc_start: 0.8627 (p) cc_final: 0.8166 (t) REVERT: A 403 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8125 (pttt) REVERT: D 56 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7805 (p) REVERT: D 69 THR cc_start: 0.8282 (p) cc_final: 0.7835 (m) REVERT: E 78 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7527 (tp30) REVERT: E 125 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: E 284 LYS cc_start: 0.8604 (mttm) cc_final: 0.8073 (mttp) REVERT: E 359 LYS cc_start: 0.8285 (ttpp) cc_final: 0.7049 (ttmt) REVERT: E 390 SER cc_start: 0.8621 (p) cc_final: 0.8160 (t) REVERT: E 403 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8122 (pttt) REVERT: G 72 ASP cc_start: 0.8139 (t70) cc_final: 0.7848 (t70) REVERT: I 56 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7809 (p) REVERT: I 69 THR cc_start: 0.8288 (p) cc_final: 0.7838 (m) REVERT: J 78 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7534 (tp30) REVERT: J 125 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: J 284 LYS cc_start: 0.8587 (mttm) cc_final: 0.8058 (mttp) REVERT: J 359 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7048 (ttmt) REVERT: J 390 SER cc_start: 0.8618 (p) cc_final: 0.8154 (t) REVERT: J 403 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8127 (pttt) REVERT: M 72 ASP cc_start: 0.8134 (t70) cc_final: 0.7847 (t70) REVERT: N 56 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7805 (p) REVERT: N 69 THR cc_start: 0.8273 (p) cc_final: 0.7837 (m) REVERT: O 78 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7536 (tp30) REVERT: O 125 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7083 (pm20) REVERT: O 284 LYS cc_start: 0.8570 (mttm) cc_final: 0.8042 (mttp) REVERT: O 359 LYS cc_start: 0.8295 (ttpp) cc_final: 0.7053 (ttmt) REVERT: O 390 SER cc_start: 0.8611 (p) cc_final: 0.8152 (t) REVERT: O 403 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8118 (pttt) outliers start: 79 outliers final: 55 residues processed: 330 average time/residue: 0.4642 time to fit residues: 174.2016 Evaluate side-chains 345 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 278 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL 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 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 201 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 THR 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 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 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 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 371 THR 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 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 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 201 LEU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 228 CYS Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 352 VAL Chi-restraints excluded: chain J residue 371 THR 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 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 80 THR Chi-restraints excluded: chain O residue 125 GLU Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 228 CYS Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 403 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 184 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 227 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.142913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.110764 restraints weight = 20877.370| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.93 r_work: 0.3173 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 18916 Z= 0.249 Angle : 0.633 6.214 25644 Z= 0.334 Chirality : 0.047 0.143 2708 Planarity : 0.005 0.049 3252 Dihedral : 5.262 23.453 2724 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.26 % Favored : 93.61 % Rotamer: Outliers : 3.97 % Allowed : 17.97 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.18 (0.17), residues: 972 loop : -1.33 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 24 TYR 0.010 0.002 TYR O 321 PHE 0.014 0.002 PHE G 100E TRP 0.033 0.003 TRP G 100F HIS 0.005 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00590 (18868) covalent geometry : angle 0.63004 (25540) SS BOND : bond 0.00386 ( 40) SS BOND : angle 1.17805 ( 80) hydrogen bonds : bond 0.04414 ( 648) hydrogen bonds : angle 5.68561 ( 1584) link_BETA1-4 : bond 0.00491 ( 4) link_BETA1-4 : angle 1.34442 ( 12) link_NAG-ASN : bond 0.00547 ( 4) link_NAG-ASN : angle 1.17042 ( 12) *********************** 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 348 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 270 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 56 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7860 (p) REVERT: L 69 THR cc_start: 0.8350 (p) cc_final: 0.7888 (m) REVERT: A 78 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7582 (tp30) REVERT: A 125 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7264 (pm20) REVERT: A 207 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8151 (mm-30) REVERT: A 284 LYS cc_start: 0.8613 (mttm) cc_final: 0.8088 (mttp) REVERT: A 390 SER cc_start: 0.8664 (p) cc_final: 0.8189 (t) REVERT: A 403 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8218 (pttt) REVERT: D 56 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7875 (p) REVERT: D 69 THR cc_start: 0.8354 (p) cc_final: 0.7892 (m) REVERT: E 78 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7579 (tp30) REVERT: E 125 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7237 (pm20) REVERT: E 207 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8133 (mm-30) REVERT: E 284 LYS cc_start: 0.8630 (mttm) cc_final: 0.8101 (mttp) REVERT: E 390 SER cc_start: 0.8662 (p) cc_final: 0.8189 (t) REVERT: E 403 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8172 (pttt) REVERT: I 56 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7864 (p) REVERT: I 69 THR cc_start: 0.8370 (p) cc_final: 0.7927 (m) REVERT: J 78 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7594 (tp30) REVERT: J 125 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: J 207 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8143 (mm-30) REVERT: J 284 LYS cc_start: 0.8625 (mttm) cc_final: 0.8098 (mttp) REVERT: J 390 SER cc_start: 0.8662 (p) cc_final: 0.8186 (t) REVERT: J 403 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8206 (pttt) REVERT: O 78 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7590 (tp30) REVERT: O 125 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: O 207 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8146 (mm-30) REVERT: O 284 LYS cc_start: 0.8612 (mttm) cc_final: 0.8086 (mttp) REVERT: O 390 SER cc_start: 0.8657 (p) cc_final: 0.8178 (t) REVERT: O 403 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8213 (pttt) outliers start: 78 outliers final: 56 residues processed: 312 average time/residue: 0.4519 time to fit residues: 162.3122 Evaluate side-chains 325 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 258 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 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 125 GLU 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 228 CYS Chi-restraints excluded: chain A residue 243 SER 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 17 SER 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 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 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 228 CYS 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 17 SER 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 125 GLU 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 228 CYS 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 403 LYS 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 8 optimal weight: 2.9990 chunk 176 optimal weight: 0.0980 chunk 144 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.112480 restraints weight = 20777.352| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.86 r_work: 0.3193 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18916 Z= 0.205 Angle : 0.613 6.750 25644 Z= 0.323 Chirality : 0.046 0.144 2708 Planarity : 0.005 0.043 3252 Dihedral : 5.206 23.931 2724 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.87 % Favored : 94.96 % Rotamer: Outliers : 4.38 % Allowed : 17.67 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.20 (0.17), residues: 952 loop : -1.38 (0.15), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 24 TYR 0.010 0.002 TYR J 321 PHE 0.014 0.002 PHE A 118 TRP 0.034 0.002 TRP M 100F HIS 0.004 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00484 (18868) covalent geometry : angle 0.61019 (25540) SS BOND : bond 0.00335 ( 40) SS BOND : angle 1.05326 ( 80) hydrogen bonds : bond 0.04139 ( 648) hydrogen bonds : angle 5.67202 ( 1584) link_BETA1-4 : bond 0.00448 ( 4) link_BETA1-4 : angle 1.28739 ( 12) link_NAG-ASN : bond 0.00399 ( 4) link_NAG-ASN : angle 0.98961 ( 12) ********************** 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 338 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 252 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7575 (tp30) REVERT: A 125 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: A 207 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8114 (mm-30) REVERT: A 284 LYS cc_start: 0.8627 (mttm) cc_final: 0.8092 (mttp) REVERT: A 390 SER cc_start: 0.8677 (p) cc_final: 0.8202 (t) REVERT: A 403 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8170 (pttt) REVERT: E 78 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7570 (tp30) REVERT: E 125 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7222 (pm20) REVERT: E 207 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8091 (mm-30) REVERT: E 284 LYS cc_start: 0.8643 (mttm) cc_final: 0.8105 (mttp) REVERT: E 390 SER cc_start: 0.8683 (p) cc_final: 0.8207 (t) REVERT: E 403 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8136 (pttt) REVERT: J 78 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7581 (tp30) REVERT: J 125 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7248 (pm20) REVERT: J 207 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8107 (mm-30) REVERT: J 284 LYS cc_start: 0.8638 (mttm) cc_final: 0.8102 (mttp) REVERT: J 390 SER cc_start: 0.8672 (p) cc_final: 0.8189 (t) REVERT: J 403 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8173 (pttt) REVERT: O 78 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7569 (tp30) REVERT: O 125 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: O 284 LYS cc_start: 0.8621 (mttm) cc_final: 0.8089 (mttp) REVERT: O 390 SER cc_start: 0.8673 (p) cc_final: 0.8191 (t) REVERT: O 403 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8168 (pttt) outliers start: 86 outliers final: 60 residues processed: 300 average time/residue: 0.4747 time to fit residues: 163.1102 Evaluate side-chains 308 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 240 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 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 125 GLU 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 228 CYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 SER 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 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 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 371 THR 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 17 SER Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 228 CYS Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 352 VAL 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 17 SER 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 125 GLU 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 228 CYS Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 191 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN J 328 ASN O 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113066 restraints weight = 20749.015| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.88 r_work: 0.3204 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18916 Z= 0.178 Angle : 0.597 6.880 25644 Z= 0.315 Chirality : 0.045 0.144 2708 Planarity : 0.005 0.041 3252 Dihedral : 5.117 21.656 2724 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.91 % Favored : 93.91 % Rotamer: Outliers : 4.02 % Allowed : 18.08 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.20 (0.17), residues: 952 loop : -1.37 (0.15), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 24 TYR 0.010 0.001 TYR O 321 PHE 0.014 0.002 PHE G 100E TRP 0.041 0.002 TRP M 100F HIS 0.003 0.001 HIS N 91 Details of bonding type rmsd covalent geometry : bond 0.00418 (18868) covalent geometry : angle 0.59469 (25540) SS BOND : bond 0.00322 ( 40) SS BOND : angle 0.98587 ( 80) hydrogen bonds : bond 0.03997 ( 648) hydrogen bonds : angle 5.60903 ( 1584) link_BETA1-4 : bond 0.00425 ( 4) link_BETA1-4 : angle 1.25551 ( 12) link_NAG-ASN : bond 0.00339 ( 4) link_NAG-ASN : angle 0.91440 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5544.65 seconds wall clock time: 95 minutes 31.42 seconds (5731.42 seconds total)