Starting phenix.real_space_refine on Tue Nov 19 02:59:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1c_41809/11_2024/8u1c_41809.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1c_41809/11_2024/8u1c_41809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1c_41809/11_2024/8u1c_41809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1c_41809/11_2024/8u1c_41809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1c_41809/11_2024/8u1c_41809.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1c_41809/11_2024/8u1c_41809.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 11632 2.51 5 N 3144 2.21 5 O 3464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18380 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2757 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 16, 'TRANS': 337} Chain breaks: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 10, 'TRANS': 115} Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Restraints were copied for chains: G, H, M, I, L, N, F, K, P, E, J, O Time building chain proxies: 11.07, per 1000 atoms: 0.60 Number of scatterers: 18380 At special positions: 0 Unit cell: (157.325, 157.325, 99.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3464 8.00 N 3144 7.00 C 11632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG K 1 " - " NAG K 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG B 1 " - " ASN A 283 " " NAG F 1 " - " ASN E 283 " " NAG K 1 " - " ASN J 283 " " NAG P 1 " - " ASN O 283 " Time building additional restraints: 5.79 Conformation dependent library (CDL) restraints added in 2.9 seconds 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 52 sheets defined 5.3% alpha, 46.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 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: 9.54 Time building geometry restraints manager: 6.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4568 1.32 - 1.46: 6292 1.46 - 1.60: 7788 1.60 - 1.74: 48 1.74 - 1.88: 172 Bond restraints: 18868 Sorted by residual: bond pdb=" CB ILE D 106 " pdb=" CG1 ILE D 106 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" CB ILE L 106 " pdb=" CG1 ILE L 106 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" CB ILE N 106 " pdb=" CG1 ILE N 106 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" CB ILE I 106 " pdb=" CG1 ILE I 106 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" NE ARG J 149 " pdb=" CZ ARG J 149 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.03e+01 ... (remaining 18863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 22448 2.72 - 5.44: 2692 5.44 - 8.15: 368 8.15 - 10.87: 24 10.87 - 13.59: 8 Bond angle restraints: 25540 Sorted by residual: angle pdb=" N ILE G 40 " pdb=" CA ILE G 40 " pdb=" C ILE G 40 " ideal model delta sigma weight residual 108.95 100.35 8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" N ILE H 40 " pdb=" CA ILE H 40 " pdb=" C ILE H 40 " ideal model delta sigma weight residual 108.95 100.35 8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" N ILE C 40 " pdb=" CA ILE C 40 " pdb=" C ILE C 40 " ideal model delta sigma weight residual 108.95 100.35 8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" N ILE M 40 " pdb=" CA ILE M 40 " pdb=" C ILE M 40 " ideal model delta sigma weight residual 108.95 100.35 8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" N PRO G 52A" pdb=" CA PRO G 52A" pdb=" C PRO G 52A" ideal model delta sigma weight residual 111.21 97.62 13.59 1.59e+00 3.96e-01 7.30e+01 ... (remaining 25535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 10752 17.04 - 34.09: 316 34.09 - 51.13: 56 51.13 - 68.17: 28 68.17 - 85.22: 16 Dihedral angle restraints: 11168 sinusoidal: 4524 harmonic: 6644 Sorted by residual: dihedral pdb=" N THR J 324 " pdb=" C THR J 324 " pdb=" CA THR J 324 " pdb=" CB THR J 324 " ideal model delta harmonic sigma weight residual 123.40 133.38 -9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" N THR E 324 " pdb=" C THR E 324 " pdb=" CA THR E 324 " pdb=" CB THR E 324 " ideal model delta harmonic sigma weight residual 123.40 133.38 -9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" N THR O 324 " pdb=" C THR O 324 " pdb=" CA THR O 324 " pdb=" CB THR O 324 " ideal model delta harmonic sigma weight residual 123.40 133.38 -9.98 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 11165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1896 0.102 - 0.203: 636 0.203 - 0.305: 124 0.305 - 0.407: 32 0.407 - 0.508: 20 Chirality restraints: 2708 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 2705 not shown) Planarity restraints: 3256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 99 " -0.060 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP M 99 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP M 99 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP M 99 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP M 99 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 99 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP M 99 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 99 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 99 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP M 99 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 99 " -0.060 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP H 99 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP H 99 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP H 99 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP H 99 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 99 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP H 99 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 99 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 99 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 99 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 99 " -0.060 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP C 99 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP C 99 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 99 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP C 99 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 99 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 99 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 99 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 99 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 99 " -0.034 2.00e-02 2.50e+03 ... (remaining 3253 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 236 2.59 - 3.17: 14876 3.17 - 3.75: 29120 3.75 - 4.32: 45236 4.32 - 4.90: 73432 Nonbonded interactions: 162900 Sorted by model distance: nonbonded pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " model vdw 2.013 3.760 nonbonded pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " model vdw 2.013 3.760 nonbonded pdb=" SG CYS G 22 " pdb=" SG CYS G 92 " model vdw 2.013 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " model vdw 2.013 3.760 nonbonded pdb=" SG CYS A 276 " pdb=" SG CYS A 290 " model vdw 2.017 3.760 ... (remaining 162895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: 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' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'L' selection = chain 'N' } 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: 31.100 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.600 Set scattering table: 0.000 Process input model: 49.340 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.950 ------------------------------------------------------------------------------- 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 18868 Z= 1.535 Angle : 1.847 13.590 25540 Z= 1.227 Chirality : 0.109 0.508 2708 Planarity : 0.010 0.055 3252 Dihedral : 10.037 85.218 6960 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.52 % Favored : 95.13 % Rotamer: Outliers : 0.20 % Allowed : 1.63 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.65 (0.17), residues: 892 loop : -0.38 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.013 TRP C 99 HIS 0.014 0.003 HIS H 100C PHE 0.028 0.006 PHE L 98 TYR 0.055 0.009 TYR E 321 ARG 0.009 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 480 time to evaluate : 2.053 Fit side-chains REVERT: J 417 LYS cc_start: 0.7185 (mmtt) cc_final: 0.6970 (mppt) outliers start: 4 outliers final: 4 residues processed: 484 average time/residue: 1.2764 time to fit residues: 696.5211 Evaluate side-chains 296 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 292 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain M residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 272 HIS E 133 HIS E 272 HIS J 133 HIS J 272 HIS O 133 HIS O 272 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18868 Z= 0.299 Angle : 0.715 9.111 25540 Z= 0.389 Chirality : 0.049 0.155 2708 Planarity : 0.005 0.035 3252 Dihedral : 5.980 27.878 2728 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.96 % Favored : 96.87 % Rotamer: Outliers : 4.48 % Allowed : 11.41 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2300 helix: None (None), residues: 0 sheet: 0.40 (0.17), residues: 884 loop : -1.05 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 47 HIS 0.004 0.001 HIS N 91 PHE 0.016 0.002 PHE D 83 TYR 0.017 0.002 TYR A 321 ARG 0.004 0.001 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 340 time to evaluate : 2.152 Fit side-chains REVERT: C 97 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7403 (tp30) REVERT: E 390 SER cc_start: 0.8882 (p) cc_final: 0.8680 (t) REVERT: G 97 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7406 (tp30) REVERT: J 390 SER cc_start: 0.8885 (p) cc_final: 0.8681 (t) REVERT: O 390 SER cc_start: 0.8891 (p) cc_final: 0.8690 (t) outliers start: 88 outliers final: 49 residues processed: 376 average time/residue: 1.1785 time to fit residues: 507.2880 Evaluate side-chains 324 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 275 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 124 ASN Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 336 CYS Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 359 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 73 LYS Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 124 ASN Chi-restraints excluded: chain O residue 125 GLU Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 336 CYS Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 166 optimal weight: 0.0370 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 GLN L 90 HIS L 91 HIS A 100 HIS ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 90 HIS D 91 HIS E 100 HIS ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN I 90 HIS I 91 HIS J 100 HIS N 42 GLN N 90 HIS N 91 HIS O 100 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 18868 Z= 0.380 Angle : 0.682 6.289 25540 Z= 0.369 Chirality : 0.049 0.162 2708 Planarity : 0.005 0.056 3252 Dihedral : 5.540 25.173 2724 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.43 % Favored : 95.39 % Rotamer: Outliers : 5.55 % Allowed : 14.15 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.47 (0.17), residues: 920 loop : -1.28 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 99 HIS 0.005 0.002 HIS O 272 PHE 0.016 0.002 PHE E 118 TYR 0.018 0.002 TYR L 32 ARG 0.004 0.001 ARG O 83 *********************** 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 425 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 316 time to evaluate : 2.105 Fit side-chains REVERT: L 74 THR cc_start: 0.7580 (m) cc_final: 0.7328 (t) REVERT: A 291 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7786 (ttt180) REVERT: A 438 HIS cc_start: 0.6327 (m-70) cc_final: 0.6118 (m-70) REVERT: D 74 THR cc_start: 0.7585 (m) cc_final: 0.7332 (t) REVERT: E 291 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7783 (ttt180) REVERT: E 390 SER cc_start: 0.8936 (p) cc_final: 0.8726 (t) REVERT: E 438 HIS cc_start: 0.6355 (m-70) cc_final: 0.6147 (m-70) REVERT: I 74 THR cc_start: 0.7576 (m) cc_final: 0.7317 (t) REVERT: J 390 SER cc_start: 0.8937 (p) cc_final: 0.8730 (t) REVERT: J 438 HIS cc_start: 0.6353 (m-70) cc_final: 0.6150 (m-70) REVERT: N 74 THR cc_start: 0.7576 (m) cc_final: 0.7325 (t) REVERT: O 291 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7785 (ttt180) REVERT: O 390 SER cc_start: 0.8937 (p) cc_final: 0.8727 (t) REVERT: O 438 HIS cc_start: 0.6332 (m-70) cc_final: 0.6119 (m-70) outliers start: 109 outliers final: 50 residues processed: 367 average time/residue: 1.1268 time to fit residues: 474.0809 Evaluate side-chains 338 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 285 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS 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 150 ASN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain 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 150 ASN Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain 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 150 ASN Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 371 THR Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain 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 150 ASN Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 291 ARG Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 371 THR 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 204 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN L 42 GLN ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN D 42 GLN ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN I 42 GLN ** J 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN N 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18868 Z= 0.241 Angle : 0.599 5.562 25540 Z= 0.320 Chirality : 0.045 0.143 2708 Planarity : 0.004 0.035 3252 Dihedral : 5.288 25.452 2724 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.74 % Favored : 96.09 % Rotamer: Outliers : 5.35 % Allowed : 15.89 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 2300 helix: None (None), residues: 0 sheet: 0.36 (0.17), residues: 912 loop : -1.41 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 100F HIS 0.003 0.001 HIS L 91 PHE 0.011 0.002 PHE G 100E TYR 0.011 0.002 TYR I 32 ARG 0.003 0.000 ARG J 149 *********************** 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 394 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 289 time to evaluate : 2.043 Fit side-chains REVERT: L 69 THR cc_start: 0.8493 (p) cc_final: 0.8197 (m) REVERT: A 307 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: A 403 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7928 (pttt) REVERT: D 69 THR cc_start: 0.8495 (p) cc_final: 0.8204 (m) REVERT: E 307 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: E 403 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7932 (pttt) REVERT: I 69 THR cc_start: 0.8489 (p) cc_final: 0.8201 (m) REVERT: J 307 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: J 403 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7929 (pttt) REVERT: N 69 THR cc_start: 0.8495 (p) cc_final: 0.8201 (m) REVERT: O 307 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7133 (mm-30) REVERT: O 403 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7924 (pttt) outliers start: 105 outliers final: 33 residues processed: 352 average time/residue: 0.9708 time to fit residues: 398.8351 Evaluate side-chains 318 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 277 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 307 GLU Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 152 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18868 Z= 0.263 Angle : 0.584 5.876 25540 Z= 0.313 Chirality : 0.045 0.147 2708 Planarity : 0.004 0.035 3252 Dihedral : 5.217 24.595 2724 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.87 % Favored : 94.96 % Rotamer: Outliers : 4.79 % Allowed : 15.48 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.32 (0.17), residues: 912 loop : -1.31 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 100F HIS 0.003 0.001 HIS D 90 PHE 0.012 0.002 PHE J 118 TYR 0.010 0.001 TYR N 32 ARG 0.003 0.000 ARG D 24 *********************** 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 362 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 268 time to evaluate : 1.704 Fit side-chains REVERT: L 69 THR cc_start: 0.8520 (p) cc_final: 0.8249 (m) REVERT: A 307 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7158 (mm-30) REVERT: A 403 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7943 (pttt) REVERT: D 69 THR cc_start: 0.8522 (p) cc_final: 0.8246 (m) REVERT: E 307 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7153 (mm-30) REVERT: E 403 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7943 (pttt) REVERT: I 69 THR cc_start: 0.8510 (p) cc_final: 0.8249 (m) REVERT: J 307 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: J 403 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7944 (pttt) REVERT: N 69 THR cc_start: 0.8506 (p) cc_final: 0.8256 (m) REVERT: O 307 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: O 403 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7942 (pttt) outliers start: 94 outliers final: 48 residues processed: 320 average time/residue: 0.8917 time to fit residues: 338.2959 Evaluate side-chains 309 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 253 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 307 GLU 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 17 SER Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 307 GLU 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 17 SER Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 307 GLU 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 17 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 307 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 102 optimal weight: 0.0970 chunk 18 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 18868 Z= 0.401 Angle : 0.641 5.864 25540 Z= 0.341 Chirality : 0.047 0.170 2708 Planarity : 0.005 0.052 3252 Dihedral : 5.366 24.237 2724 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 5.09 % Allowed : 16.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.20 (0.17), residues: 924 loop : -1.33 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 100F HIS 0.006 0.002 HIS N 91 PHE 0.013 0.002 PHE J 118 TYR 0.013 0.002 TYR L 32 ARG 0.003 0.000 ARG M 58 *********************** 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 340 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 240 time to evaluate : 1.933 Fit side-chains REVERT: L 69 THR cc_start: 0.8540 (p) cc_final: 0.8291 (m) REVERT: A 403 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7988 (pttt) REVERT: D 69 THR cc_start: 0.8536 (p) cc_final: 0.8289 (m) REVERT: E 403 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7988 (pttt) REVERT: I 69 THR cc_start: 0.8516 (p) cc_final: 0.8283 (m) REVERT: J 403 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7981 (pttt) REVERT: N 69 THR cc_start: 0.8517 (p) cc_final: 0.8286 (m) REVERT: O 359 LYS cc_start: 0.8458 (ttpp) cc_final: 0.7734 (tttp) REVERT: O 403 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7984 (pttt) outliers start: 100 outliers final: 60 residues processed: 297 average time/residue: 1.0653 time to fit residues: 365.1224 Evaluate side-chains 300 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 236 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 324 THR 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 17 SER Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 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 17 SER Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 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 17 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 371 THR 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 212 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 185 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18868 Z= 0.236 Angle : 0.576 6.419 25540 Z= 0.309 Chirality : 0.045 0.146 2708 Planarity : 0.004 0.036 3252 Dihedral : 5.177 24.235 2724 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.96 % Rotamer: Outliers : 4.28 % Allowed : 17.46 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.10 (0.18), residues: 892 loop : -1.25 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 100F HIS 0.003 0.001 HIS J 353 PHE 0.013 0.002 PHE M 100E TYR 0.010 0.001 TYR O 321 ARG 0.003 0.000 ARG D 24 *********************** 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 319 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 235 time to evaluate : 2.338 Fit side-chains REVERT: L 69 THR cc_start: 0.8486 (p) cc_final: 0.8258 (m) REVERT: A 403 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7941 (pttt) REVERT: D 69 THR cc_start: 0.8490 (p) cc_final: 0.8257 (m) REVERT: E 403 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7936 (pttt) REVERT: J 359 LYS cc_start: 0.8393 (ttpp) cc_final: 0.7667 (tttp) REVERT: J 403 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7938 (pttt) REVERT: O 359 LYS cc_start: 0.8356 (ttpp) cc_final: 0.7665 (tttp) REVERT: O 403 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7942 (pttt) outliers start: 84 outliers final: 54 residues processed: 279 average time/residue: 0.8415 time to fit residues: 274.6028 Evaluate side-chains 276 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 324 THR 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 D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 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 I residue 33 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 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 N residue 33 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 371 THR 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 135 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 328 ASN J 328 ASN O 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18868 Z= 0.273 Angle : 0.583 6.620 25540 Z= 0.311 Chirality : 0.045 0.145 2708 Planarity : 0.005 0.040 3252 Dihedral : 5.151 23.804 2724 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 3.97 % Allowed : 17.31 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.12 (0.17), residues: 932 loop : -1.31 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 100F HIS 0.003 0.001 HIS L 91 PHE 0.013 0.002 PHE M 100E TYR 0.010 0.001 TYR A 321 ARG 0.002 0.000 ARG O 83 *********************** 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 305 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 227 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 69 THR cc_start: 0.8469 (p) cc_final: 0.8259 (m) REVERT: A 359 LYS cc_start: 0.8458 (ttpp) cc_final: 0.7505 (ttmt) REVERT: A 403 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7934 (pttt) REVERT: D 69 THR cc_start: 0.8475 (p) cc_final: 0.8259 (m) REVERT: E 359 LYS cc_start: 0.8459 (ttpp) cc_final: 0.7506 (ttmt) REVERT: J 359 LYS cc_start: 0.8367 (ttpp) cc_final: 0.7646 (tttp) REVERT: J 403 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7936 (pttt) REVERT: O 359 LYS cc_start: 0.8316 (ttpp) cc_final: 0.7638 (tttp) REVERT: O 403 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7939 (pttt) outliers start: 78 outliers final: 51 residues processed: 275 average time/residue: 1.1985 time to fit residues: 381.9029 Evaluate side-chains 275 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 221 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ARG 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 243 SER Chi-restraints excluded: chain A residue 324 THR 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 58 ARG Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ARG 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 243 SER Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 371 THR Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 58 ARG 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 243 SER Chi-restraints excluded: chain O residue 324 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.5980 chunk 210 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 62 optimal weight: 0.0770 chunk 185 optimal weight: 0.0170 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18868 Z= 0.231 Angle : 0.562 7.139 25540 Z= 0.299 Chirality : 0.044 0.145 2708 Planarity : 0.004 0.036 3252 Dihedral : 5.040 23.397 2724 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.17 % Favored : 94.65 % Rotamer: Outliers : 3.26 % Allowed : 17.41 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.14 (0.17), residues: 932 loop : -1.29 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 100F HIS 0.003 0.001 HIS I 91 PHE 0.013 0.002 PHE C 100E TYR 0.010 0.001 TYR A 321 ARG 0.003 0.000 ARG N 24 *********************** 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 290 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7887 (pttt) REVERT: E 403 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7914 (pttt) REVERT: J 359 LYS cc_start: 0.8400 (ttpp) cc_final: 0.7652 (tttp) REVERT: J 403 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7914 (pttt) REVERT: O 359 LYS cc_start: 0.8364 (ttpp) cc_final: 0.7671 (tttp) REVERT: O 403 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7912 (pttt) outliers start: 64 outliers final: 41 residues processed: 262 average time/residue: 1.1263 time to fit residues: 340.1447 Evaluate side-chains 252 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ARG 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 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 58 ARG Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR 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 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 58 ARG 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 243 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 58 ARG 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 243 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.1980 chunk 132 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18868 Z= 0.234 Angle : 0.562 7.244 25540 Z= 0.299 Chirality : 0.044 0.145 2708 Planarity : 0.004 0.037 3252 Dihedral : 5.015 23.155 2724 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.65 % Favored : 94.17 % Rotamer: Outliers : 2.65 % Allowed : 18.13 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.09 (0.17), residues: 952 loop : -1.31 (0.15), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 100F HIS 0.003 0.001 HIS D 91 PHE 0.013 0.002 PHE C 100E TYR 0.010 0.001 TYR A 321 ARG 0.003 0.000 ARG I 24 ********************** 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 263 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7872 (pttt) REVERT: E 403 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7882 (pttt) REVERT: J 403 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7894 (pttt) REVERT: O 359 LYS cc_start: 0.8275 (ttpp) cc_final: 0.7597 (tttp) REVERT: O 403 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7877 (pttt) outliers start: 52 outliers final: 42 residues processed: 244 average time/residue: 1.2589 time to fit residues: 353.8596 Evaluate side-chains 247 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 201 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ARG 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 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 58 ARG 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 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 58 ARG 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 243 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 58 ARG 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 243 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.143283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111353 restraints weight = 21088.192| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.91 r_work: 0.3183 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18868 Z= 0.360 Angle : 0.614 7.126 25540 Z= 0.326 Chirality : 0.046 0.142 2708 Planarity : 0.005 0.046 3252 Dihedral : 5.234 23.323 2724 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.74 % Favored : 94.09 % Rotamer: Outliers : 2.80 % Allowed : 17.92 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.13 (0.17), residues: 980 loop : -1.39 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 100F HIS 0.005 0.001 HIS L 91 PHE 0.015 0.002 PHE C 100E TYR 0.010 0.002 TYR A 321 ARG 0.003 0.000 ARG J 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7232.15 seconds wall clock time: 156 minutes 8.52 seconds (9368.52 seconds total)