Starting phenix.real_space_refine on Sat Mar 7 11:29:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cdv_16596/03_2026/8cdv_16596.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cdv_16596/03_2026/8cdv_16596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cdv_16596/03_2026/8cdv_16596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cdv_16596/03_2026/8cdv_16596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cdv_16596/03_2026/8cdv_16596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cdv_16596/03_2026/8cdv_16596.map" } resolution = 4.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 1258 5.49 5 S 44 5.16 5 C 22451 2.51 5 N 8039 2.21 5 O 11801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43593 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 26755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1247, 26755 Classifications: {'RNA': 1247} Modifications used: {'rna2p_pur': 97, 'rna2p_pyr': 64, 'rna3p_pur': 614, 'rna3p_pyr': 472} Link IDs: {'rna2p': 161, 'rna3p': 1085} Chain breaks: 4 Chain: "B" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 242 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 9} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "C" Number of atoms: 3687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3687 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 17, 'TRANS': 439} Chain breaks: 1 Chain: "F" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1490 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 2 Chain: "G" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1170 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain: "H" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 727 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1036 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "J" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 776 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "K" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 489 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain breaks: 1 Chain: "L" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1052 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 128} Chain: "M" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 868 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "O" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 710 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "P" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 82} Chain: "Q" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 691 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "R" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 637 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain: "T" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 755 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "V" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 662 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Time building chain proxies: 8.69, per 1000 atoms: 0.20 Number of scatterers: 43593 At special positions: 0 Unit cell: (152.8, 220, 201.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 1258 15.00 O 11801 8.00 N 8039 7.00 C 22451 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 Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 987.4 milliseconds 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 21 sheets defined 48.7% alpha, 19.0% beta 342 base pairs and 689 stacking pairs defined. Time for finding SS restraints: 7.95 Creating SS restraints... Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 23 through 31 Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.982A pdb=" N TYR C 293 " --> pdb=" O ASP C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 371 through 379 Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 392 through 413 Processing helix chain 'C' and resid 442 through 467 Processing helix chain 'C' and resid 479 through 493 removed outlier: 3.519A pdb=" N THR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 504 removed outlier: 4.340A pdb=" N ILE C 504 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 517 removed outlier: 3.806A pdb=" N LEU C 509 " --> pdb=" O HIS C 505 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 533 Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 562 through 576 Processing helix chain 'C' and resid 582 through 616 Proline residue: C 594 - end of helix Processing helix chain 'F' and resid 7 through 16 removed outlier: 4.437A pdb=" N LEU F 11 " --> pdb=" O PRO F 7 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER F 12 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 62 Processing helix chain 'F' and resid 64 through 78 removed outlier: 3.822A pdb=" N LYS F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 92 Processing helix chain 'F' and resid 93 through 101 Processing helix chain 'F' and resid 106 through 116 Processing helix chain 'F' and resid 143 through 146 Processing helix chain 'F' and resid 148 through 154 Processing helix chain 'F' and resid 190 through 200 removed outlier: 3.649A pdb=" N ILE F 194 " --> pdb=" O ASN F 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 55 through 70 Processing helix chain 'G' and resid 108 through 119 Processing helix chain 'G' and resid 132 through 145 Processing helix chain 'G' and resid 149 through 158 Processing helix chain 'H' and resid 20 through 31 Processing helix chain 'H' and resid 35 through 55 removed outlier: 3.538A pdb=" N SER H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 69 Processing helix chain 'H' and resid 93 through 111 Processing helix chain 'H' and resid 115 through 128 Processing helix chain 'I' and resid 5 through 20 Processing helix chain 'I' and resid 30 through 43 Processing helix chain 'I' and resid 90 through 94 removed outlier: 3.555A pdb=" N VAL I 94 " --> pdb=" O SER I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 115 through 121 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 55 Proline residue: J 51 - end of helix Processing helix chain 'J' and resid 71 through 91 removed outlier: 3.580A pdb=" N GLU J 89 " --> pdb=" O ARG J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 101 Processing helix chain 'K' and resid 14 through 32 Processing helix chain 'K' and resid 80 through 89 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 24 Processing helix chain 'L' and resid 126 through 131 removed outlier: 3.683A pdb=" N GLY L 131 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 20 removed outlier: 3.647A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 44 through 48 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.797A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.649A pdb=" N THR O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 77 Processing helix chain 'P' and resid 78 through 89 removed outlier: 3.602A pdb=" N LYS P 87 " --> pdb=" O PHE P 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 25 Processing helix chain 'R' and resid 41 through 45 Processing helix chain 'R' and resid 63 through 67 Processing helix chain 'R' and resid 70 through 75 Processing helix chain 'S' and resid 5 through 41 removed outlier: 3.580A pdb=" N LYS S 9 " --> pdb=" O LYS S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 64 Processing helix chain 'S' and resid 68 through 85 Processing helix chain 'T' and resid 15 through 33 Processing helix chain 'T' and resid 68 through 82 Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 30 through 35 Processing helix chain 'U' and resid 36 through 38 No H-bonds generated for 'chain 'U' and resid 36 through 38' Processing helix chain 'U' and resid 46 through 51 Processing helix chain 'U' and resid 53 through 70 Processing helix chain 'V' and resid 50 through 53 Processing helix chain 'V' and resid 56 through 61 removed outlier: 4.007A pdb=" N SER V 60 " --> pdb=" O GLY V 56 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR V 61 " --> pdb=" O SER V 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 56 through 61' Processing helix chain 'V' and resid 61 through 80 removed outlier: 3.722A pdb=" N GLU V 78 " --> pdb=" O LYS V 74 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS V 79 " --> pdb=" O GLY V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 93 through 105 removed outlier: 4.765A pdb=" N ALA V 97 " --> pdb=" O SER V 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'C' and resid 249 through 250 removed outlier: 3.647A pdb=" N GLU C 355 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 257 through 260 removed outlier: 6.038A pdb=" N THR C 258 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 311 through 312 Processing sheet with id=AA5, first strand: chain 'C' and resid 422 through 427 removed outlier: 4.468A pdb=" N GLU C 422 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 472 through 474 Processing sheet with id=AA7, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=AA8, first strand: chain 'G' and resid 12 through 25 removed outlier: 5.311A pdb=" N GLU G 13 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY G 40 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU G 15 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL G 38 " --> pdb=" O LEU G 15 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 85 through 89 Processing sheet with id=AB1, first strand: chain 'I' and resid 24 through 28 removed outlier: 3.591A pdb=" N ASP I 48 " --> pdb=" O PHE I 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 76 through 79 Processing sheet with id=AB3, first strand: chain 'I' and resid 76 through 79 removed outlier: 5.424A pdb=" N VAL I 127 " --> pdb=" O SER I 107 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER I 107 " --> pdb=" O VAL I 127 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 6 through 12 removed outlier: 6.286A pdb=" N VAL J 29 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL J 67 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 71 through 75 Processing sheet with id=AB6, first strand: chain 'L' and resid 26 through 29 Processing sheet with id=AB7, first strand: chain 'L' and resid 42 through 53 removed outlier: 5.595A pdb=" N CYS L 47 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG L 69 " --> pdb=" O CYS L 47 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N TYR L 108 " --> pdb=" O GLU L 75 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR L 77 " --> pdb=" O TYR L 108 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE L 110 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TYR L 79 " --> pdb=" O ILE L 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 48 through 51 removed outlier: 6.401A pdb=" N ILE P 20 " --> pdb=" O VAL P 37 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR P 39 " --> pdb=" O TYR P 18 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR P 18 " --> pdb=" O THR P 39 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN P 41 " --> pdb=" O PRO P 16 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE P 17 " --> pdb=" O MET P 10 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 9 through 19 removed outlier: 16.739A pdb=" N VAL Q 9 " --> pdb=" O TYR Q 30 " (cutoff:3.500A) removed outlier: 13.694A pdb=" N TYR Q 30 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN Q 11 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU Q 28 " --> pdb=" O GLN Q 11 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR Q 24 " --> pdb=" O VAL Q 15 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASP Q 17 " --> pdb=" O THR Q 22 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR Q 22 " --> pdb=" O ASP Q 17 " (cutoff:3.500A) removed outlier: 15.949A pdb=" N LYS Q 73 " --> pdb=" O SER Q 43 " (cutoff:3.500A) removed outlier: 13.312A pdb=" N LYS Q 45 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N PHE Q 75 " --> pdb=" O LYS Q 45 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS Q 47 " --> pdb=" O PHE Q 75 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU Q 77 " --> pdb=" O LYS Q 47 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N HIS Q 49 " --> pdb=" O LEU Q 77 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLU Q 79 " --> pdb=" O HIS Q 49 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS Q 62 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL Q 80 " --> pdb=" O ILE Q 60 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE Q 60 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 31 through 33 Processing sheet with id=AC2, first strand: chain 'T' and resid 36 through 52 removed outlier: 6.975A pdb=" N THR T 38 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN T 66 " --> pdb=" O THR T 38 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR T 40 " --> pdb=" O ASN T 64 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN T 64 " --> pdb=" O THR T 40 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASP T 42 " --> pdb=" O ILE T 62 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE T 62 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY T 44 " --> pdb=" O TYR T 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR T 60 " --> pdb=" O GLY T 44 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG T 56 " --> pdb=" O LEU T 48 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG T 87 " --> pdb=" O ILE T 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 43 through 48 removed outlier: 6.887A pdb=" N ILE V 36 " --> pdb=" O ILE V 44 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TRP V 46 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL V 34 " --> pdb=" O TRP V 46 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER V 48 " --> pdb=" O THR V 32 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR V 32 " --> pdb=" O SER V 48 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 842 hydrogen bonds 1332 hydrogen bond angles 0 basepair planarities 342 basepair parallelities 689 stacking parallelities Total time for adding SS restraints: 15.90 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3953 1.28 - 1.42: 17935 1.42 - 1.56: 22571 1.56 - 1.70: 2510 1.70 - 1.84: 84 Bond restraints: 47053 Sorted by residual: bond pdb=" C LYS P 13 " pdb=" O LYS P 13 " ideal model delta sigma weight residual 1.235 1.143 0.092 1.26e-02 6.30e+03 5.36e+01 bond pdb=" C SER K 94 " pdb=" O SER K 94 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.26e-02 6.30e+03 3.50e+01 bond pdb=" O5' G A 764 " pdb=" C5' G A 764 " ideal model delta sigma weight residual 1.420 1.478 -0.058 1.50e-02 4.44e+03 1.50e+01 bond pdb=" O5' C A 668 " pdb=" C5' C A 668 " ideal model delta sigma weight residual 1.420 1.478 -0.058 1.50e-02 4.44e+03 1.47e+01 bond pdb=" O5' G A 736 " pdb=" C5' G A 736 " ideal model delta sigma weight residual 1.420 1.476 -0.056 1.50e-02 4.44e+03 1.40e+01 ... (remaining 47048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 67519 3.39 - 6.79: 2164 6.79 - 10.18: 55 10.18 - 13.57: 9 13.57 - 16.97: 2 Bond angle restraints: 69749 Sorted by residual: angle pdb=" CA LYS P 13 " pdb=" C LYS P 13 " pdb=" N LYS P 14 " ideal model delta sigma weight residual 116.84 129.59 -12.75 1.71e+00 3.42e-01 5.56e+01 angle pdb=" CB LYS S 81 " pdb=" CG LYS S 81 " pdb=" CD LYS S 81 " ideal model delta sigma weight residual 111.30 128.27 -16.97 2.30e+00 1.89e-01 5.44e+01 angle pdb=" CA SER K 94 " pdb=" C SER K 94 " pdb=" O SER K 94 " ideal model delta sigma weight residual 120.51 110.34 10.17 1.43e+00 4.89e-01 5.06e+01 angle pdb=" O3' G A1148 " pdb=" C3' G A1148 " pdb=" C2' G A1148 " ideal model delta sigma weight residual 109.50 119.27 -9.77 1.50e+00 4.44e-01 4.24e+01 angle pdb=" CA SER K 94 " pdb=" C SER K 94 " pdb=" N GLY K 95 " ideal model delta sigma weight residual 116.84 127.88 -11.04 1.71e+00 3.42e-01 4.17e+01 ... (remaining 69744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 26385 35.19 - 70.38: 3097 70.38 - 105.57: 489 105.57 - 140.76: 25 140.76 - 175.95: 24 Dihedral angle restraints: 30020 sinusoidal: 23990 harmonic: 6030 Sorted by residual: dihedral pdb=" CA ASP G 5 " pdb=" C ASP G 5 " pdb=" N PRO G 6 " pdb=" CA PRO G 6 " ideal model delta harmonic sigma weight residual -180.00 -126.42 -53.58 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA LYS R 28 " pdb=" C LYS R 28 " pdb=" N GLN R 29 " pdb=" CA GLN R 29 " ideal model delta harmonic sigma weight residual -180.00 -130.21 -49.79 0 5.00e+00 4.00e-02 9.92e+01 dihedral pdb=" C4' G A 641 " pdb=" C3' G A 641 " pdb=" C2' G A 641 " pdb=" C1' G A 641 " ideal model delta sinusoidal sigma weight residual -35.00 33.54 -68.54 1 8.00e+00 1.56e-02 9.51e+01 ... (remaining 30017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 6102 0.122 - 0.244: 2597 0.244 - 0.366: 148 0.366 - 0.488: 7 0.488 - 0.610: 7 Chirality restraints: 8861 Sorted by residual: chirality pdb=" P A B -1 " pdb=" OP1 A B -1 " pdb=" OP2 A B -1 " pdb=" O5' A B -1 " both_signs ideal model delta sigma weight residual True 2.41 3.02 -0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" P C A 815 " pdb=" OP1 C A 815 " pdb=" OP2 C A 815 " pdb=" O5' C A 815 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" P G A 8 " pdb=" OP1 G A 8 " pdb=" OP2 G A 8 " pdb=" O5' G A 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.57 2.00e-01 2.50e+01 8.26e+00 ... (remaining 8858 not shown) Planarity restraints: 4164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 89 " 1.019 9.50e-02 1.11e+02 4.57e-01 1.27e+02 pdb=" NE ARG K 89 " -0.068 2.00e-02 2.50e+03 pdb=" CZ ARG K 89 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG K 89 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 89 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 39 " -0.925 9.50e-02 1.11e+02 4.15e-01 1.12e+02 pdb=" NE ARG Q 39 " 0.073 2.00e-02 2.50e+03 pdb=" CZ ARG Q 39 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 39 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 78 " -0.918 9.50e-02 1.11e+02 4.12e-01 1.07e+02 pdb=" NE ARG R 78 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG R 78 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG R 78 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG R 78 " -0.012 2.00e-02 2.50e+03 ... (remaining 4161 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 4 1.93 - 2.67: 2293 2.67 - 3.41: 62382 3.41 - 4.16: 147745 4.16 - 4.90: 206452 Nonbonded interactions: 418876 Sorted by model distance: nonbonded pdb=" O2' G A 641 " pdb=" OP1 U A 642 " model vdw 1.187 3.040 nonbonded pdb=" C5' A B 6 " pdb=" N3 A B 6 " model vdw 1.659 3.520 nonbonded pdb=" O5' A B 6 " pdb=" N3 A B 6 " model vdw 1.808 3.120 nonbonded pdb=" O2' U A1198 " pdb=" OP1 G A1199 " model vdw 1.920 3.040 nonbonded pdb=" OP1 U A 64 " pdb=" O2' U A 393 " model vdw 1.972 3.040 ... (remaining 418871 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 5.920 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: 0.050 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 49.030 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 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 : 0.009 0.092 47053 Z= 0.597 Angle : 1.435 16.966 69749 Z= 0.900 Chirality : 0.114 0.610 8861 Planarity : 0.025 0.457 4164 Dihedral : 24.687 175.951 26120 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.93 % Allowed : 3.02 % Favored : 96.05 % Rotamer: Outliers : 3.68 % Allowed : 5.24 % Favored : 91.09 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.16), residues: 2050 helix: -1.21 (0.14), residues: 916 sheet: -1.55 (0.24), residues: 364 loop : -0.87 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.004 ARG J 18 TYR 0.096 0.008 TYR U 17 PHE 0.052 0.007 PHE C 463 TRP 0.034 0.005 TRP P 59 HIS 0.042 0.004 HIS S 20 Details of bonding type rmsd covalent geometry : bond 0.00934 (47053) covalent geometry : angle 1.43529 (69749) hydrogen bonds : bond 0.17028 ( 1731) hydrogen bonds : angle 11.06224 ( 3858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 656 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 PHE cc_start: 0.5327 (t80) cc_final: 0.5067 (t80) REVERT: C 267 LEU cc_start: 0.6066 (mt) cc_final: 0.5599 (mp) REVERT: C 367 GLU cc_start: 0.5685 (tp30) cc_final: 0.5464 (mp0) REVERT: C 407 ARG cc_start: 0.4453 (ttt180) cc_final: 0.3880 (mtm180) REVERT: C 472 TYR cc_start: 0.3319 (m-80) cc_final: 0.3106 (m-80) REVERT: C 525 ILE cc_start: 0.6422 (mt) cc_final: 0.6060 (mt) REVERT: C 535 GLN cc_start: 0.5041 (mt0) cc_final: 0.4492 (mm-40) REVERT: C 538 TYR cc_start: 0.5257 (m-80) cc_final: 0.4683 (m-10) REVERT: C 541 GLN cc_start: 0.4968 (mt0) cc_final: 0.4450 (mt0) REVERT: C 604 GLU cc_start: 0.5524 (tt0) cc_final: 0.4960 (mm-30) REVERT: F 24 LYS cc_start: 0.6273 (pttm) cc_final: 0.5901 (mttm) REVERT: F 66 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.5828 (tpp-160) REVERT: F 90 LEU cc_start: 0.7827 (mt) cc_final: 0.7439 (mp) REVERT: F 91 ASP cc_start: 0.7431 (t70) cc_final: 0.7205 (t0) REVERT: F 142 ARG cc_start: 0.6685 (ptt180) cc_final: 0.6170 (ptp-170) REVERT: F 164 TYR cc_start: 0.6819 (p90) cc_final: 0.6428 (p90) REVERT: F 179 LEU cc_start: 0.7700 (mt) cc_final: 0.7448 (pp) REVERT: F 191 GLU cc_start: 0.7900 (pm20) cc_final: 0.7533 (pm20) REVERT: G 64 VAL cc_start: 0.4542 (t) cc_final: 0.4207 (p) REVERT: G 69 LYS cc_start: 0.6664 (mptt) cc_final: 0.6446 (mttt) REVERT: G 70 ASN cc_start: 0.6833 (m-40) cc_final: 0.6630 (p0) REVERT: G 96 LEU cc_start: 0.7618 (mt) cc_final: 0.7329 (mt) REVERT: G 105 VAL cc_start: 0.7561 (t) cc_final: 0.7294 (t) REVERT: G 132 THR cc_start: 0.7021 (m) cc_final: 0.6714 (p) REVERT: G 141 LEU cc_start: 0.7083 (mt) cc_final: 0.6637 (mt) REVERT: G 152 ASP cc_start: 0.4062 (m-30) cc_final: 0.3426 (p0) REVERT: G 157 ARG cc_start: 0.4864 (OUTLIER) cc_final: 0.4521 (mtt-85) REVERT: H 114 LYS cc_start: 0.6989 (mttt) cc_final: 0.6555 (tttm) REVERT: I 25 LEU cc_start: 0.7438 (pt) cc_final: 0.7235 (pt) REVERT: I 35 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8402 (tp30) REVERT: I 51 PHE cc_start: 0.8349 (m-80) cc_final: 0.8069 (m-10) REVERT: I 66 TYR cc_start: 0.5691 (m-80) cc_final: 0.5468 (m-80) REVERT: I 99 ASN cc_start: 0.7767 (t0) cc_final: 0.7553 (t0) REVERT: J 12 ARG cc_start: 0.4947 (OUTLIER) cc_final: 0.4717 (ttm170) REVERT: J 25 GLU cc_start: 0.3613 (OUTLIER) cc_final: 0.3398 (pp20) REVERT: K 87 LEU cc_start: 0.3307 (mt) cc_final: 0.3054 (mp) REVERT: K 89 ARG cc_start: 0.3006 (OUTLIER) cc_final: 0.2739 (mtt90) REVERT: L 21 SER cc_start: 0.5208 (m) cc_final: 0.4947 (t) REVERT: L 47 CYS cc_start: 0.7130 (m) cc_final: 0.6278 (t) REVERT: L 50 VAL cc_start: 0.6833 (t) cc_final: 0.5662 (p) REVERT: L 54 THR cc_start: 0.7077 (p) cc_final: 0.6426 (t) REVERT: L 67 ARG cc_start: 0.5379 (tpt170) cc_final: 0.4966 (ttt-90) REVERT: L 75 GLU cc_start: 0.7424 (tt0) cc_final: 0.6718 (pm20) REVERT: L 77 THR cc_start: 0.7814 (m) cc_final: 0.6689 (p) REVERT: L 103 LEU cc_start: 0.6827 (mt) cc_final: 0.6615 (tp) REVERT: L 111 VAL cc_start: 0.7145 (t) cc_final: 0.6902 (p) REVERT: L 136 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6145 (tttt) REVERT: M 97 VAL cc_start: 0.1882 (OUTLIER) cc_final: 0.1610 (m) REVERT: O 6 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: O 7 ARG cc_start: 0.7345 (tpt170) cc_final: 0.6355 (tpt170) REVERT: O 20 SER cc_start: 0.6680 (p) cc_final: 0.6433 (t) REVERT: O 69 TYR cc_start: 0.8090 (t80) cc_final: 0.7547 (t80) REVERT: O 72 ASN cc_start: 0.8294 (m110) cc_final: 0.8087 (m-40) REVERT: O 74 ASP cc_start: 0.3522 (t0) cc_final: 0.3277 (t0) REVERT: O 82 ILE cc_start: 0.8460 (pt) cc_final: 0.8153 (tt) REVERT: P 54 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8003 (mm-30) REVERT: P 77 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7550 (tp40) REVERT: Q 5 ASN cc_start: 0.8401 (m-40) cc_final: 0.8197 (m110) REVERT: Q 17 ASP cc_start: 0.6433 (p0) cc_final: 0.6120 (t0) REVERT: Q 24 THR cc_start: 0.6333 (m) cc_final: 0.5816 (p) REVERT: Q 63 ILE cc_start: 0.8178 (pt) cc_final: 0.7941 (pt) REVERT: R 16 MET cc_start: 0.2413 (tpp) cc_final: -0.0059 (tmm) REVERT: R 62 ILE cc_start: 0.6475 (mm) cc_final: 0.6162 (mp) REVERT: R 81 LYS cc_start: 0.2042 (OUTLIER) cc_final: 0.1774 (mmtp) REVERT: S 25 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7122 (tttt) REVERT: S 29 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7399 (mmp-170) REVERT: S 66 LEU cc_start: 0.6403 (tp) cc_final: 0.6180 (tp) REVERT: T 5 GLU cc_start: 0.7494 (tt0) cc_final: 0.7165 (tm-30) REVERT: T 26 PHE cc_start: 0.7152 (m-80) cc_final: 0.6799 (m-10) REVERT: T 41 LYS cc_start: 0.7142 (mttt) cc_final: 0.6908 (tptt) REVERT: T 52 ILE cc_start: 0.7731 (mt) cc_final: 0.7421 (tp) REVERT: T 87 ARG cc_start: 0.4207 (OUTLIER) cc_final: 0.3725 (ttm-80) REVERT: T 93 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7515 (mm-30) REVERT: U 27 ASP cc_start: 0.5584 (t70) cc_final: 0.5190 (t70) REVERT: U 33 LEU cc_start: 0.6158 (tp) cc_final: 0.5881 (tt) REVERT: U 60 LEU cc_start: 0.7948 (tp) cc_final: 0.7622 (tp) REVERT: U 61 THR cc_start: 0.7586 (m) cc_final: 0.7254 (m) REVERT: U 64 ILE cc_start: 0.8346 (mt) cc_final: 0.8032 (mp) REVERT: U 65 LYS cc_start: 0.8317 (mttt) cc_final: 0.8113 (mttt) REVERT: V 27 SER cc_start: 0.7421 (t) cc_final: 0.7146 (m) outliers start: 66 outliers final: 12 residues processed: 696 average time/residue: 0.2923 time to fit residues: 316.6049 Evaluate side-chains 421 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 397 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 HIS C 535 GLN F 64 ASN F 67 GLN F 112 GLN F 115 ASN H 56 ASN H 106 ASN H 122 ASN I 22 HIS I 57 GLN I 69 ASN J 66 ASN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 ASN O 18 HIS O 72 ASN O 83 ASN R 47 HIS R 57 HIS T 33 ASN T 61 GLN V 42 ASN V 66 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.111978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.094899 restraints weight = 185720.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.094421 restraints weight = 159997.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.095208 restraints weight = 114376.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.095074 restraints weight = 82259.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.095214 restraints weight = 76392.910| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 47053 Z= 0.212 Angle : 0.825 10.457 69749 Z= 0.432 Chirality : 0.048 0.329 8861 Planarity : 0.006 0.119 4164 Dihedral : 25.114 178.562 21890 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.46 % Favored : 98.24 % Rotamer: Outliers : 0.28 % Allowed : 3.68 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2050 helix: 1.03 (0.16), residues: 935 sheet: -0.82 (0.26), residues: 329 loop : -0.28 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 89 TYR 0.018 0.002 TYR L 108 PHE 0.029 0.003 PHE U 18 TRP 0.009 0.002 TRP T 43 HIS 0.008 0.001 HIS J 68 Details of bonding type rmsd covalent geometry : bond 0.00384 (47053) covalent geometry : angle 0.82458 (69749) hydrogen bonds : bond 0.07908 ( 1731) hydrogen bonds : angle 4.12415 ( 3858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 508 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 GLU cc_start: 0.5434 (tt0) cc_final: 0.5126 (tt0) REVERT: C 407 ARG cc_start: 0.5555 (ttt180) cc_final: 0.4419 (mtm180) REVERT: C 458 THR cc_start: 0.6091 (m) cc_final: 0.5484 (m) REVERT: C 538 TYR cc_start: 0.4807 (m-80) cc_final: 0.4508 (m-10) REVERT: C 539 ASP cc_start: 0.4763 (t0) cc_final: 0.4048 (t0) REVERT: F 9 TRP cc_start: 0.3196 (m-10) cc_final: 0.2850 (m-10) REVERT: F 15 LEU cc_start: 0.6932 (mm) cc_final: 0.6705 (mm) REVERT: F 86 PHE cc_start: 0.5933 (t80) cc_final: 0.5477 (t80) REVERT: F 87 MET cc_start: 0.7743 (mmm) cc_final: 0.7142 (mmm) REVERT: F 91 ASP cc_start: 0.5480 (t70) cc_final: 0.5187 (t0) REVERT: F 125 ARG cc_start: 0.5590 (ttt180) cc_final: 0.4998 (mtt180) REVERT: F 127 ASP cc_start: 0.7219 (p0) cc_final: 0.6938 (p0) REVERT: F 146 ARG cc_start: 0.5352 (mtp180) cc_final: 0.4751 (ttp80) REVERT: F 147 ASN cc_start: 0.7320 (p0) cc_final: 0.6672 (p0) REVERT: F 164 TYR cc_start: 0.4713 (p90) cc_final: 0.4401 (p90) REVERT: F 167 PHE cc_start: 0.6710 (t80) cc_final: 0.5893 (t80) REVERT: G 132 THR cc_start: 0.8069 (m) cc_final: 0.7757 (p) REVERT: I 25 LEU cc_start: 0.7085 (pt) cc_final: 0.6859 (pt) REVERT: I 35 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7819 (tp30) REVERT: I 45 PHE cc_start: 0.7152 (m-80) cc_final: 0.6380 (m-80) REVERT: I 66 TYR cc_start: 0.5261 (m-80) cc_final: 0.4331 (m-10) REVERT: I 80 ILE cc_start: 0.6152 (mm) cc_final: 0.5422 (mm) REVERT: I 114 THR cc_start: 0.6518 (p) cc_final: 0.5846 (p) REVERT: L 3 THR cc_start: 0.6927 (m) cc_final: 0.6706 (m) REVERT: L 50 VAL cc_start: 0.6350 (t) cc_final: 0.5968 (p) REVERT: L 55 PRO cc_start: 0.7331 (Cg_endo) cc_final: 0.6815 (Cg_exo) REVERT: L 76 VAL cc_start: 0.7364 (m) cc_final: 0.6918 (p) REVERT: L 77 THR cc_start: 0.7268 (m) cc_final: 0.6300 (p) REVERT: L 102 ASP cc_start: 0.4520 (p0) cc_final: 0.4072 (p0) REVERT: L 130 TYR cc_start: 0.7429 (m-80) cc_final: 0.7214 (m-80) REVERT: M 46 ARG cc_start: 0.5173 (mtt-85) cc_final: 0.4635 (tpp80) REVERT: O 7 ARG cc_start: 0.6451 (tpt170) cc_final: 0.6208 (tpp-160) REVERT: O 8 LYS cc_start: 0.6853 (mtmm) cc_final: 0.6417 (mmtp) REVERT: O 32 LEU cc_start: 0.7656 (mt) cc_final: 0.7397 (mt) REVERT: O 41 GLU cc_start: 0.6260 (tp30) cc_final: 0.5813 (tp30) REVERT: O 46 HIS cc_start: 0.6237 (m90) cc_final: 0.5939 (m90) REVERT: O 56 LEU cc_start: 0.8300 (tt) cc_final: 0.7884 (tp) REVERT: O 69 TYR cc_start: 0.7857 (t80) cc_final: 0.7336 (t80) REVERT: O 81 LEU cc_start: 0.7014 (tp) cc_final: 0.6515 (tp) REVERT: P 19 ARG cc_start: 0.5465 (mmm-85) cc_final: 0.5262 (mtp180) REVERT: R 49 ILE cc_start: 0.5468 (mt) cc_final: 0.5189 (mt) REVERT: S 25 LYS cc_start: 0.6755 (mtmt) cc_final: 0.6224 (mtpt) REVERT: S 39 VAL cc_start: 0.7550 (p) cc_final: 0.7291 (p) REVERT: S 57 ARG cc_start: 0.6871 (tpp-160) cc_final: 0.6597 (tpp-160) REVERT: T 9 ILE cc_start: 0.5206 (mt) cc_final: 0.4940 (mt) REVERT: T 11 ARG cc_start: 0.5328 (ptp-170) cc_final: 0.4271 (ptp-170) REVERT: T 25 ARG cc_start: 0.7209 (ptp-170) cc_final: 0.6918 (ptp-170) REVERT: T 41 LYS cc_start: 0.6398 (mttt) cc_final: 0.6153 (tptt) REVERT: T 50 TYR cc_start: 0.5813 (p90) cc_final: 0.5432 (p90) REVERT: U 17 TYR cc_start: 0.7305 (t80) cc_final: 0.7021 (t80) REVERT: U 56 TYR cc_start: 0.7426 (m-80) cc_final: 0.6922 (m-80) REVERT: U 60 LEU cc_start: 0.7375 (tp) cc_final: 0.7028 (tp) REVERT: V 27 SER cc_start: 0.6661 (t) cc_final: 0.6318 (m) outliers start: 5 outliers final: 0 residues processed: 509 average time/residue: 0.2669 time to fit residues: 217.8813 Evaluate side-chains 358 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 309 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 240 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 288 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 264 optimal weight: 0.0370 chunk 300 optimal weight: 3.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN F 64 ASN F 67 GLN F 112 GLN F 115 ASN H 64 GLN H 122 ASN I 57 GLN I 69 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.111075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.092512 restraints weight = 184736.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.091794 restraints weight = 165026.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.092394 restraints weight = 113206.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092541 restraints weight = 94966.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.092632 restraints weight = 84108.678| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 47053 Z= 0.187 Angle : 0.715 9.983 69749 Z= 0.376 Chirality : 0.042 0.293 8861 Planarity : 0.006 0.048 4164 Dihedral : 24.935 179.208 21890 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.15 % Favored : 97.61 % Rotamer: Outliers : 0.28 % Allowed : 3.12 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.18), residues: 2050 helix: 1.19 (0.16), residues: 931 sheet: -0.39 (0.27), residues: 318 loop : -0.35 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 111 TYR 0.024 0.002 TYR C 371 PHE 0.032 0.003 PHE U 18 TRP 0.007 0.002 TRP C 589 HIS 0.018 0.002 HIS C 599 Details of bonding type rmsd covalent geometry : bond 0.00358 (47053) covalent geometry : angle 0.71513 (69749) hydrogen bonds : bond 0.06932 ( 1731) hydrogen bonds : angle 3.95426 ( 3858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 432 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 407 ARG cc_start: 0.5374 (ttt180) cc_final: 0.4093 (mtm180) REVERT: C 538 TYR cc_start: 0.4907 (m-80) cc_final: 0.4286 (m-80) REVERT: F 51 LEU cc_start: 0.7852 (tt) cc_final: 0.7651 (tp) REVERT: F 58 ARG cc_start: 0.4865 (ttp80) cc_final: 0.4359 (ttp80) REVERT: F 60 MET cc_start: 0.7104 (ttt) cc_final: 0.6738 (ttt) REVERT: F 64 ASN cc_start: 0.6878 (m-40) cc_final: 0.6659 (m110) REVERT: F 87 MET cc_start: 0.7433 (mmm) cc_final: 0.7215 (mmm) REVERT: F 112 GLN cc_start: 0.7339 (tm130) cc_final: 0.7047 (tm-30) REVERT: F 125 ARG cc_start: 0.5420 (ttt180) cc_final: 0.5133 (mtt180) REVERT: F 146 ARG cc_start: 0.5274 (mtp180) cc_final: 0.4978 (ttp80) REVERT: F 147 ASN cc_start: 0.7752 (p0) cc_final: 0.7526 (p0) REVERT: F 198 TYR cc_start: 0.7529 (m-10) cc_final: 0.7285 (m-10) REVERT: G 132 THR cc_start: 0.8134 (m) cc_final: 0.7776 (p) REVERT: G 141 LEU cc_start: 0.6227 (mt) cc_final: 0.6016 (mt) REVERT: I 45 PHE cc_start: 0.7295 (m-80) cc_final: 0.6411 (m-80) REVERT: I 62 VAL cc_start: 0.7794 (p) cc_final: 0.7387 (p) REVERT: I 66 TYR cc_start: 0.5504 (m-80) cc_final: 0.4968 (m-80) REVERT: I 69 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7409 (t0) REVERT: I 98 LEU cc_start: 0.7843 (mt) cc_final: 0.7573 (mt) REVERT: I 103 ILE cc_start: 0.8382 (pt) cc_final: 0.8138 (mp) REVERT: I 114 THR cc_start: 0.6617 (p) cc_final: 0.6031 (p) REVERT: L 21 SER cc_start: 0.5010 (m) cc_final: 0.4606 (t) REVERT: L 25 ASN cc_start: 0.7576 (m-40) cc_final: 0.7222 (m-40) REVERT: L 32 LYS cc_start: 0.7948 (mtpp) cc_final: 0.7705 (tttt) REVERT: L 77 THR cc_start: 0.7178 (m) cc_final: 0.6492 (p) REVERT: O 32 LEU cc_start: 0.7919 (mt) cc_final: 0.7663 (mt) REVERT: O 41 GLU cc_start: 0.6581 (tp30) cc_final: 0.6275 (tp30) REVERT: O 45 THR cc_start: 0.8384 (p) cc_final: 0.8001 (p) REVERT: O 46 HIS cc_start: 0.6509 (m90) cc_final: 0.6297 (m90) REVERT: O 81 LEU cc_start: 0.7314 (tp) cc_final: 0.6719 (tp) REVERT: Q 18 LYS cc_start: 0.8572 (mttt) cc_final: 0.7632 (tptt) REVERT: Q 36 TYR cc_start: 0.6378 (m-80) cc_final: 0.6101 (m-80) REVERT: Q 79 GLU cc_start: 0.5677 (tm-30) cc_final: 0.5259 (pt0) REVERT: S 39 VAL cc_start: 0.7665 (p) cc_final: 0.7437 (p) REVERT: S 71 THR cc_start: 0.7545 (m) cc_final: 0.5210 (m) REVERT: S 75 TYR cc_start: 0.7227 (m-10) cc_final: 0.6943 (m-80) REVERT: T 5 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6181 (tm-30) REVERT: T 25 ARG cc_start: 0.7299 (ptp-170) cc_final: 0.7030 (ptp-170) REVERT: T 41 LYS cc_start: 0.6396 (mttt) cc_final: 0.6050 (tptt) REVERT: T 50 TYR cc_start: 0.6008 (p90) cc_final: 0.5573 (p90) REVERT: V 67 MET cc_start: 0.4656 (ttm) cc_final: 0.3713 (tmm) REVERT: V 89 LYS cc_start: 0.6519 (mtpt) cc_final: 0.6104 (mptt) REVERT: V 108 GLU cc_start: 0.5563 (pm20) cc_final: 0.5304 (mm-30) outliers start: 5 outliers final: 1 residues processed: 432 average time/residue: 0.2602 time to fit residues: 181.3036 Evaluate side-chains 338 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 336 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 277 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 HIS C 541 GLN C 569 HIS F 50 GLN F 67 GLN F 82 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN G 43 ASN G 142 GLN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.107521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.089509 restraints weight = 188988.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088853 restraints weight = 173528.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.089668 restraints weight = 124833.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.089484 restraints weight = 83786.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.089619 restraints weight = 77793.975| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.135 47053 Z= 0.334 Angle : 0.912 12.251 69749 Z= 0.465 Chirality : 0.050 0.332 8861 Planarity : 0.007 0.086 4164 Dihedral : 25.130 177.092 21890 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Rotamer: Outliers : 0.11 % Allowed : 5.68 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2050 helix: 0.25 (0.16), residues: 934 sheet: -0.59 (0.27), residues: 327 loop : -0.80 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG T 46 TYR 0.034 0.003 TYR I 130 PHE 0.037 0.004 PHE R 74 TRP 0.011 0.003 TRP R 34 HIS 0.017 0.003 HIS G 83 Details of bonding type rmsd covalent geometry : bond 0.00655 (47053) covalent geometry : angle 0.91236 (69749) hydrogen bonds : bond 0.09063 ( 1731) hydrogen bonds : angle 4.55607 ( 3858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 401 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 ASN cc_start: 0.7111 (t0) cc_final: 0.6798 (t0) REVERT: C 69 MET cc_start: 0.1603 (tmm) cc_final: 0.1339 (tmm) REVERT: C 269 ASP cc_start: 0.2793 (p0) cc_final: 0.2355 (t0) REVERT: C 286 HIS cc_start: 0.0511 (m-70) cc_final: -0.0064 (m-70) REVERT: C 407 ARG cc_start: 0.5541 (ttt180) cc_final: 0.4159 (mtm180) REVERT: C 493 PHE cc_start: 0.1560 (m-80) cc_final: 0.1256 (m-80) REVERT: C 518 ASP cc_start: 0.3254 (m-30) cc_final: 0.2539 (t0) REVERT: C 529 MET cc_start: 0.2083 (mtt) cc_final: 0.1782 (mtt) REVERT: C 535 GLN cc_start: 0.5605 (mt0) cc_final: 0.4886 (mm-40) REVERT: C 538 TYR cc_start: 0.5352 (m-80) cc_final: 0.4823 (m-10) REVERT: F 64 ASN cc_start: 0.7330 (m-40) cc_final: 0.6964 (m110) REVERT: F 67 GLN cc_start: 0.6109 (pt0) cc_final: 0.5877 (pt0) REVERT: F 112 GLN cc_start: 0.7031 (pp30) cc_final: 0.6815 (tm-30) REVERT: F 125 ARG cc_start: 0.5547 (ttt180) cc_final: 0.5180 (mtt180) REVERT: F 134 LYS cc_start: 0.6847 (mtmt) cc_final: 0.6437 (tppt) REVERT: F 153 GLU cc_start: 0.6637 (pt0) cc_final: 0.6414 (tm-30) REVERT: G 96 LEU cc_start: 0.7063 (mt) cc_final: 0.6764 (mt) REVERT: G 127 SER cc_start: 0.6688 (t) cc_final: 0.6400 (p) REVERT: G 132 THR cc_start: 0.8037 (m) cc_final: 0.7467 (p) REVERT: H 116 MET cc_start: 0.5858 (tpt) cc_final: 0.5541 (tpp) REVERT: H 117 GLU cc_start: 0.6343 (pm20) cc_final: 0.5991 (pm20) REVERT: I 21 ARG cc_start: 0.6784 (mtt-85) cc_final: 0.6170 (mtm180) REVERT: I 45 PHE cc_start: 0.7202 (m-80) cc_final: 0.6931 (m-80) REVERT: I 63 PHE cc_start: 0.6717 (m-10) cc_final: 0.6245 (m-10) REVERT: I 98 LEU cc_start: 0.7644 (mt) cc_final: 0.7284 (mt) REVERT: J 98 LEU cc_start: 0.6252 (mm) cc_final: 0.5991 (tp) REVERT: L 77 THR cc_start: 0.7079 (m) cc_final: 0.6082 (p) REVERT: O 10 GLN cc_start: 0.7452 (tm-30) cc_final: 0.7227 (tm-30) REVERT: O 31 ILE cc_start: 0.7312 (tt) cc_final: 0.7052 (tt) REVERT: O 32 LEU cc_start: 0.7700 (mt) cc_final: 0.7450 (mt) REVERT: O 41 GLU cc_start: 0.6671 (tp30) cc_final: 0.6389 (tp30) REVERT: O 45 THR cc_start: 0.8457 (p) cc_final: 0.8088 (p) REVERT: O 46 HIS cc_start: 0.6807 (m90) cc_final: 0.6526 (m90) REVERT: O 56 LEU cc_start: 0.8529 (tp) cc_final: 0.8303 (tp) REVERT: O 81 LEU cc_start: 0.7005 (tp) cc_final: 0.6616 (tp) REVERT: Q 18 LYS cc_start: 0.8763 (mttt) cc_final: 0.7717 (tptp) REVERT: Q 39 ARG cc_start: 0.7441 (mtp85) cc_final: 0.7136 (mtp85) REVERT: R 49 ILE cc_start: 0.4955 (mt) cc_final: 0.4627 (mt) REVERT: R 79 THR cc_start: 0.4292 (m) cc_final: 0.4039 (m) REVERT: S 75 TYR cc_start: 0.7141 (m-10) cc_final: 0.6789 (m-80) REVERT: T 41 LYS cc_start: 0.6276 (mttt) cc_final: 0.5933 (tptt) REVERT: T 56 ARG cc_start: 0.7287 (mmm-85) cc_final: 0.7052 (mmm160) REVERT: U 16 CYS cc_start: 0.7494 (t) cc_final: 0.6960 (t) REVERT: U 64 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.6721 (mp) REVERT: V 63 PHE cc_start: 0.6305 (t80) cc_final: 0.5998 (t80) REVERT: V 89 LYS cc_start: 0.6489 (mtpt) cc_final: 0.6232 (mptt) outliers start: 2 outliers final: 0 residues processed: 402 average time/residue: 0.2589 time to fit residues: 166.3176 Evaluate side-chains 302 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 297 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 239 optimal weight: 0.5980 chunk 180 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 HIS ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS M 32 GLN M 101 ASN O 13 ASN P 88 GLN Q 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.109064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091499 restraints weight = 188044.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.091417 restraints weight = 159169.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091898 restraints weight = 112971.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091823 restraints weight = 81575.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091933 restraints weight = 75235.517| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 47053 Z= 0.215 Angle : 0.746 8.708 69749 Z= 0.387 Chirality : 0.043 0.289 8861 Planarity : 0.006 0.059 4164 Dihedral : 25.026 177.553 21890 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Rotamer: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.18), residues: 2050 helix: 0.48 (0.16), residues: 919 sheet: -0.71 (0.27), residues: 313 loop : -0.86 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 106 TYR 0.035 0.002 TYR I 130 PHE 0.032 0.003 PHE R 74 TRP 0.022 0.002 TRP V 46 HIS 0.023 0.003 HIS R 14 Details of bonding type rmsd covalent geometry : bond 0.00416 (47053) covalent geometry : angle 0.74583 (69749) hydrogen bonds : bond 0.07469 ( 1731) hydrogen bonds : angle 4.36172 ( 3858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 394 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TYR cc_start: 0.3949 (t80) cc_final: 0.3627 (t80) REVERT: C 32 ASN cc_start: 0.6994 (t0) cc_final: 0.6737 (t0) REVERT: C 407 ARG cc_start: 0.5671 (ttt180) cc_final: 0.4088 (mtm180) REVERT: C 493 PHE cc_start: 0.1485 (m-80) cc_final: 0.1240 (m-80) REVERT: C 495 TYR cc_start: 0.2576 (m-80) cc_final: 0.1269 (t80) REVERT: C 518 ASP cc_start: 0.3144 (m-30) cc_final: 0.2428 (t0) REVERT: C 535 GLN cc_start: 0.5622 (mt0) cc_final: 0.5151 (mm-40) REVERT: C 538 TYR cc_start: 0.5113 (m-80) cc_final: 0.4688 (m-10) REVERT: C 560 ILE cc_start: 0.6379 (mp) cc_final: 0.6150 (mp) REVERT: C 563 TYR cc_start: 0.4120 (t80) cc_final: 0.3710 (t80) REVERT: F 60 MET cc_start: 0.7245 (ttt) cc_final: 0.7023 (ttt) REVERT: F 93 ARG cc_start: 0.6705 (ttm-80) cc_final: 0.6377 (ttm170) REVERT: G 127 SER cc_start: 0.6753 (t) cc_final: 0.6400 (p) REVERT: G 130 SER cc_start: 0.6457 (t) cc_final: 0.5904 (t) REVERT: G 132 THR cc_start: 0.8182 (m) cc_final: 0.7585 (p) REVERT: I 34 ARG cc_start: 0.7063 (ttm170) cc_final: 0.6572 (mtt90) REVERT: I 45 PHE cc_start: 0.7338 (m-80) cc_final: 0.7044 (m-80) REVERT: I 51 PHE cc_start: 0.6895 (m-80) cc_final: 0.6412 (m-80) REVERT: I 66 TYR cc_start: 0.6048 (m-80) cc_final: 0.5557 (m-10) REVERT: I 98 LEU cc_start: 0.7685 (mt) cc_final: 0.7283 (mt) REVERT: K 87 LEU cc_start: 0.4801 (mp) cc_final: 0.4571 (pp) REVERT: L 55 PRO cc_start: 0.6803 (Cg_endo) cc_final: 0.6305 (Cg_exo) REVERT: L 77 THR cc_start: 0.7407 (m) cc_final: 0.6845 (p) REVERT: M 11 ARG cc_start: 0.3116 (mpp80) cc_final: 0.2889 (mtt180) REVERT: O 19 GLU cc_start: 0.7071 (mp0) cc_final: 0.6060 (tt0) REVERT: O 41 GLU cc_start: 0.6790 (tp30) cc_final: 0.6251 (tp30) REVERT: O 53 ARG cc_start: 0.7701 (mtp85) cc_final: 0.6757 (tpt170) REVERT: Q 18 LYS cc_start: 0.8845 (mttt) cc_final: 0.7797 (tptp) REVERT: R 49 ILE cc_start: 0.5139 (mt) cc_final: 0.4747 (mt) REVERT: R 79 THR cc_start: 0.4174 (m) cc_final: 0.3936 (m) REVERT: T 78 LEU cc_start: 0.7831 (tp) cc_final: 0.7385 (pp) REVERT: U 16 CYS cc_start: 0.7349 (t) cc_final: 0.6720 (t) REVERT: V 24 HIS cc_start: 0.5966 (m-70) cc_final: 0.5726 (m170) REVERT: V 89 LYS cc_start: 0.6477 (mtpt) cc_final: 0.6128 (mptt) REVERT: V 107 LEU cc_start: 0.7166 (mm) cc_final: 0.6902 (mt) outliers start: 2 outliers final: 0 residues processed: 394 average time/residue: 0.2531 time to fit residues: 160.8403 Evaluate side-chains 316 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 214 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 307 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 GLN F 112 GLN F 115 ASN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.107751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090002 restraints weight = 187918.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.089702 restraints weight = 159216.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.090523 restraints weight = 106597.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.090437 restraints weight = 73500.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.090586 restraints weight = 63439.206| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 47053 Z= 0.267 Angle : 0.823 10.966 69749 Z= 0.420 Chirality : 0.046 0.334 8861 Planarity : 0.007 0.109 4164 Dihedral : 25.071 179.237 21890 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.39 % Favored : 95.37 % Rotamer: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.17), residues: 2050 helix: 0.13 (0.16), residues: 916 sheet: -0.75 (0.27), residues: 312 loop : -1.14 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 71 TYR 0.034 0.003 TYR S 75 PHE 0.029 0.003 PHE C 556 TRP 0.013 0.002 TRP R 34 HIS 0.014 0.002 HIS G 45 Details of bonding type rmsd covalent geometry : bond 0.00520 (47053) covalent geometry : angle 0.82303 (69749) hydrogen bonds : bond 0.08349 ( 1731) hydrogen bonds : angle 4.60931 ( 3858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TYR cc_start: 0.3803 (t80) cc_final: 0.3342 (t80) REVERT: C 269 ASP cc_start: 0.3157 (p0) cc_final: 0.2200 (t0) REVERT: C 345 MET cc_start: 0.1553 (mpp) cc_final: 0.1046 (tpp) REVERT: C 407 ARG cc_start: 0.5719 (ttt180) cc_final: 0.3835 (mtm180) REVERT: C 495 TYR cc_start: 0.3054 (m-80) cc_final: 0.2335 (m-80) REVERT: C 518 ASP cc_start: 0.3122 (m-30) cc_final: 0.2897 (t0) REVERT: C 533 MET cc_start: 0.3032 (ptm) cc_final: 0.2633 (ptm) REVERT: C 538 TYR cc_start: 0.5383 (m-80) cc_final: 0.4706 (m-10) REVERT: C 560 ILE cc_start: 0.6191 (mp) cc_final: 0.5894 (mp) REVERT: C 563 TYR cc_start: 0.4296 (t80) cc_final: 0.3919 (t80) REVERT: F 64 ASN cc_start: 0.7419 (m-40) cc_final: 0.7204 (m-40) REVERT: F 93 ARG cc_start: 0.6531 (ttm-80) cc_final: 0.6061 (ttm170) REVERT: F 112 GLN cc_start: 0.6719 (tm130) cc_final: 0.5587 (tt0) REVERT: G 33 PHE cc_start: 0.6115 (m-80) cc_final: 0.5555 (m-80) REVERT: G 127 SER cc_start: 0.6897 (t) cc_final: 0.6526 (p) REVERT: G 130 SER cc_start: 0.6474 (t) cc_final: 0.6095 (t) REVERT: G 132 THR cc_start: 0.8170 (m) cc_final: 0.7506 (p) REVERT: I 61 ARG cc_start: 0.5455 (mtp-110) cc_final: 0.5171 (mtp-110) REVERT: I 63 PHE cc_start: 0.6593 (m-10) cc_final: 0.6356 (m-10) REVERT: I 66 TYR cc_start: 0.6291 (m-80) cc_final: 0.5597 (m-10) REVERT: J 98 LEU cc_start: 0.6507 (tp) cc_final: 0.6035 (tp) REVERT: L 55 PRO cc_start: 0.6878 (Cg_endo) cc_final: 0.6325 (Cg_exo) REVERT: L 77 THR cc_start: 0.6967 (m) cc_final: 0.6571 (p) REVERT: L 95 ILE cc_start: 0.7703 (pt) cc_final: 0.7466 (pt) REVERT: O 19 GLU cc_start: 0.7038 (mp0) cc_final: 0.5986 (tt0) REVERT: O 41 GLU cc_start: 0.6909 (tp30) cc_final: 0.6698 (tp30) REVERT: P 58 LYS cc_start: 0.7633 (tttt) cc_final: 0.7232 (tptp) REVERT: Q 18 LYS cc_start: 0.8821 (mttt) cc_final: 0.7750 (tptp) REVERT: R 49 ILE cc_start: 0.4683 (mt) cc_final: 0.4292 (mt) REVERT: S 75 TYR cc_start: 0.6946 (m-80) cc_final: 0.6247 (m-80) REVERT: T 78 LEU cc_start: 0.7701 (tp) cc_final: 0.7281 (pp) REVERT: U 16 CYS cc_start: 0.7548 (t) cc_final: 0.6941 (t) REVERT: U 64 ILE cc_start: 0.7367 (mp) cc_final: 0.7150 (mp) REVERT: V 26 ARG cc_start: 0.6856 (tpt90) cc_final: 0.6501 (mmm160) REVERT: V 46 TRP cc_start: 0.0631 (p90) cc_final: -0.0079 (p90) REVERT: V 63 PHE cc_start: 0.6375 (t80) cc_final: 0.6117 (t80) REVERT: V 89 LYS cc_start: 0.6512 (mtpt) cc_final: 0.5915 (mptt) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.2553 time to fit residues: 156.2781 Evaluate side-chains 305 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 291 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 236 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN C 356 HIS C 462 HIS C 555 HIS F 50 GLN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN G 45 HIS J 32 ASN J 38 HIS ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 HIS ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.109284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.091664 restraints weight = 186305.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.090915 restraints weight = 168778.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.092065 restraints weight = 118660.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091856 restraints weight = 83317.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.092102 restraints weight = 76679.212| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 47053 Z= 0.190 Angle : 0.718 11.206 69749 Z= 0.371 Chirality : 0.042 0.324 8861 Planarity : 0.006 0.066 4164 Dihedral : 24.965 179.445 21890 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.32 % Favored : 96.44 % Rotamer: Outliers : 0.11 % Allowed : 1.84 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2050 helix: 0.37 (0.16), residues: 916 sheet: -0.60 (0.27), residues: 319 loop : -1.07 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 441 TYR 0.031 0.002 TYR S 75 PHE 0.026 0.003 PHE R 74 TRP 0.025 0.002 TRP T 43 HIS 0.010 0.002 HIS C 475 Details of bonding type rmsd covalent geometry : bond 0.00369 (47053) covalent geometry : angle 0.71812 (69749) hydrogen bonds : bond 0.07241 ( 1731) hydrogen bonds : angle 4.39098 ( 3858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 384 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TYR cc_start: 0.3910 (t80) cc_final: 0.3408 (t80) REVERT: C 399 MET cc_start: 0.1738 (tpp) cc_final: 0.1060 (tpp) REVERT: C 407 ARG cc_start: 0.5441 (ttt180) cc_final: 0.3716 (mtm180) REVERT: C 495 TYR cc_start: 0.3131 (m-80) cc_final: 0.2516 (m-80) REVERT: C 518 ASP cc_start: 0.3148 (m-30) cc_final: 0.2893 (t0) REVERT: C 538 TYR cc_start: 0.5489 (m-80) cc_final: 0.4927 (m-10) REVERT: C 560 ILE cc_start: 0.6382 (mp) cc_final: 0.6125 (mp) REVERT: C 563 TYR cc_start: 0.4158 (t80) cc_final: 0.3843 (t80) REVERT: G 33 PHE cc_start: 0.6091 (m-80) cc_final: 0.5582 (m-80) REVERT: G 127 SER cc_start: 0.6870 (t) cc_final: 0.6516 (p) REVERT: G 130 SER cc_start: 0.6523 (t) cc_final: 0.6069 (t) REVERT: G 132 THR cc_start: 0.8204 (m) cc_final: 0.7578 (p) REVERT: I 66 TYR cc_start: 0.6021 (m-80) cc_final: 0.5464 (m-10) REVERT: J 98 LEU cc_start: 0.6511 (tp) cc_final: 0.6162 (tp) REVERT: O 8 LYS cc_start: 0.7133 (mtmm) cc_final: 0.6743 (mmtt) REVERT: O 12 ILE cc_start: 0.5953 (pt) cc_final: 0.5736 (pt) REVERT: O 19 GLU cc_start: 0.6868 (mp0) cc_final: 0.6080 (tt0) REVERT: O 41 GLU cc_start: 0.6883 (tp30) cc_final: 0.6466 (tp30) REVERT: O 44 ARG cc_start: 0.6941 (mtt180) cc_final: 0.6716 (mtt180) REVERT: O 53 ARG cc_start: 0.7782 (mtp85) cc_final: 0.6710 (tpt170) REVERT: O 81 LEU cc_start: 0.7018 (tp) cc_final: 0.6598 (tp) REVERT: O 82 ILE cc_start: 0.6473 (tt) cc_final: 0.6262 (tt) REVERT: P 4 LYS cc_start: 0.5548 (tptm) cc_final: 0.5214 (tptp) REVERT: P 67 SER cc_start: 0.8780 (m) cc_final: 0.8575 (m) REVERT: Q 13 ARG cc_start: 0.5177 (ttp80) cc_final: 0.4643 (mtm110) REVERT: Q 18 LYS cc_start: 0.8871 (mttt) cc_final: 0.7767 (tptp) REVERT: R 49 ILE cc_start: 0.4629 (mt) cc_final: 0.4230 (mt) REVERT: S 75 TYR cc_start: 0.7108 (m-80) cc_final: 0.6414 (m-80) REVERT: T 5 GLU cc_start: 0.7869 (tm-30) cc_final: 0.6716 (tm-30) REVERT: U 16 CYS cc_start: 0.7412 (t) cc_final: 0.6881 (t) REVERT: U 64 ILE cc_start: 0.7503 (mp) cc_final: 0.7298 (mp) REVERT: V 46 TRP cc_start: 0.0539 (p90) cc_final: -0.0124 (p90) REVERT: V 63 PHE cc_start: 0.6379 (t80) cc_final: 0.6147 (t80) REVERT: V 89 LYS cc_start: 0.6600 (mtpt) cc_final: 0.6192 (mptt) REVERT: V 107 LEU cc_start: 0.7306 (mm) cc_final: 0.7079 (mt) outliers start: 2 outliers final: 0 residues processed: 384 average time/residue: 0.2476 time to fit residues: 154.6250 Evaluate side-chains 317 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 103 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 306 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 chunk 268 optimal weight: 0.9980 chunk 313 optimal weight: 0.6980 chunk 294 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 311 optimal weight: 0.0870 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN J 66 ASN M 100 GLN ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.111091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.093799 restraints weight = 185973.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.093586 restraints weight = 147722.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.094461 restraints weight = 107590.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094208 restraints weight = 79973.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094448 restraints weight = 75331.770| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.6393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 47053 Z= 0.147 Angle : 0.652 9.937 69749 Z= 0.338 Chirality : 0.039 0.353 8861 Planarity : 0.005 0.050 4164 Dihedral : 24.824 178.652 21890 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.07 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2050 helix: 0.70 (0.16), residues: 918 sheet: -0.71 (0.27), residues: 315 loop : -0.83 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 561 TYR 0.032 0.002 TYR L 65 PHE 0.033 0.002 PHE C 556 TRP 0.010 0.001 TRP P 59 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00282 (47053) covalent geometry : angle 0.65157 (69749) hydrogen bonds : bond 0.06538 ( 1731) hydrogen bonds : angle 4.13670 ( 3858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TYR cc_start: 0.4011 (t80) cc_final: 0.3509 (t80) REVERT: C 69 MET cc_start: 0.1719 (tmm) cc_final: 0.1341 (tmm) REVERT: C 320 MET cc_start: 0.4527 (tpt) cc_final: 0.3274 (mmm) REVERT: C 399 MET cc_start: 0.1657 (tpp) cc_final: 0.1376 (tpp) REVERT: C 407 ARG cc_start: 0.5217 (ttt180) cc_final: 0.3778 (mtm180) REVERT: C 495 TYR cc_start: 0.3348 (m-80) cc_final: 0.2750 (m-80) REVERT: C 518 ASP cc_start: 0.3096 (m-30) cc_final: 0.2894 (t0) REVERT: C 533 MET cc_start: 0.3012 (ptm) cc_final: 0.2553 (ptm) REVERT: C 538 TYR cc_start: 0.5162 (m-80) cc_final: 0.4851 (m-10) REVERT: C 563 TYR cc_start: 0.4094 (t80) cc_final: 0.3868 (t80) REVERT: F 127 ASP cc_start: 0.7340 (p0) cc_final: 0.6372 (m-30) REVERT: F 142 ARG cc_start: 0.4844 (ptt-90) cc_final: 0.4085 (ptp90) REVERT: G 112 ARG cc_start: 0.5181 (ttt180) cc_final: 0.4956 (mtp85) REVERT: G 127 SER cc_start: 0.6872 (t) cc_final: 0.6462 (p) REVERT: G 130 SER cc_start: 0.6459 (t) cc_final: 0.6134 (t) REVERT: G 132 THR cc_start: 0.8174 (m) cc_final: 0.7578 (p) REVERT: I 52 VAL cc_start: 0.8030 (t) cc_final: 0.7803 (t) REVERT: I 66 TYR cc_start: 0.5904 (m-80) cc_final: 0.5436 (m-10) REVERT: K 87 LEU cc_start: 0.4504 (mp) cc_final: 0.4290 (pp) REVERT: L 17 GLU cc_start: 0.5624 (tt0) cc_final: 0.5404 (tp30) REVERT: O 10 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6674 (mt0) REVERT: O 11 LEU cc_start: 0.6990 (mt) cc_final: 0.6337 (mt) REVERT: O 19 GLU cc_start: 0.6842 (mp0) cc_final: 0.6022 (tt0) REVERT: O 33 THR cc_start: 0.7957 (p) cc_final: 0.7756 (p) REVERT: O 41 GLU cc_start: 0.6835 (tp30) cc_final: 0.6448 (tp30) REVERT: O 44 ARG cc_start: 0.7050 (mtt180) cc_final: 0.6744 (mtt180) REVERT: O 53 ARG cc_start: 0.7773 (mtp85) cc_final: 0.6622 (tpt170) REVERT: O 81 LEU cc_start: 0.6964 (tp) cc_final: 0.6696 (tp) REVERT: P 50 LYS cc_start: 0.6870 (mptt) cc_final: 0.6524 (mptt) REVERT: P 67 SER cc_start: 0.8827 (m) cc_final: 0.8545 (m) REVERT: Q 13 ARG cc_start: 0.5088 (ttp80) cc_final: 0.4808 (mtm110) REVERT: Q 18 LYS cc_start: 0.8998 (mttt) cc_final: 0.7691 (tptp) REVERT: R 4 SER cc_start: 0.4082 (m) cc_final: 0.3815 (t) REVERT: R 49 ILE cc_start: 0.4578 (mt) cc_final: 0.4245 (mt) REVERT: S 75 TYR cc_start: 0.7116 (m-80) cc_final: 0.6486 (m-80) REVERT: T 5 GLU cc_start: 0.8006 (tm-30) cc_final: 0.6790 (tm-30) REVERT: T 46 ARG cc_start: 0.6687 (mtp-110) cc_final: 0.6476 (mtp-110) REVERT: T 78 LEU cc_start: 0.7490 (tp) cc_final: 0.6976 (pp) REVERT: U 16 CYS cc_start: 0.7346 (t) cc_final: 0.6820 (t) REVERT: U 64 ILE cc_start: 0.7502 (mp) cc_final: 0.7262 (mp) REVERT: V 46 TRP cc_start: 0.0675 (p90) cc_final: -0.0182 (p90) REVERT: V 107 LEU cc_start: 0.7337 (mm) cc_final: 0.7045 (mt) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.2425 time to fit residues: 154.9703 Evaluate side-chains 317 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 303 optimal weight: 4.9990 chunk 234 optimal weight: 8.9990 chunk 254 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 chunk 312 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 323 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 132 optimal weight: 0.0970 chunk 285 optimal weight: 9.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN F 115 ASN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 ASN M 100 GLN ** O 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.109561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.091822 restraints weight = 186000.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091946 restraints weight = 139037.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.092099 restraints weight = 102495.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.092164 restraints weight = 81453.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.092310 restraints weight = 64944.012| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 47053 Z= 0.206 Angle : 0.723 11.356 69749 Z= 0.371 Chirality : 0.041 0.348 8861 Planarity : 0.006 0.072 4164 Dihedral : 24.855 177.899 21890 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.15 % Favored : 95.66 % Rotamer: Outliers : 0.06 % Allowed : 1.06 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.18), residues: 2050 helix: 0.49 (0.16), residues: 916 sheet: -0.71 (0.27), residues: 316 loop : -1.04 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 561 TYR 0.026 0.002 TYR S 75 PHE 0.026 0.002 PHE I 51 TRP 0.016 0.002 TRP R 34 HIS 0.010 0.002 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00403 (47053) covalent geometry : angle 0.72284 (69749) hydrogen bonds : bond 0.07381 ( 1731) hydrogen bonds : angle 4.34085 ( 3858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 MET cc_start: 0.1785 (tmm) cc_final: 0.1440 (tmm) REVERT: C 399 MET cc_start: 0.1553 (tpp) cc_final: 0.1155 (tpp) REVERT: C 407 ARG cc_start: 0.5170 (ttt180) cc_final: 0.3767 (mtm180) REVERT: C 518 ASP cc_start: 0.2993 (m-30) cc_final: 0.2636 (t0) REVERT: C 533 MET cc_start: 0.3016 (ptm) cc_final: 0.2607 (ptm) REVERT: F 77 LYS cc_start: 0.6748 (mtmt) cc_final: 0.5547 (tmmt) REVERT: F 91 ASP cc_start: 0.5873 (t70) cc_final: 0.5572 (t0) REVERT: G 33 PHE cc_start: 0.5999 (m-80) cc_final: 0.5493 (m-80) REVERT: G 127 SER cc_start: 0.6832 (t) cc_final: 0.6422 (p) REVERT: G 130 SER cc_start: 0.6635 (t) cc_final: 0.6241 (t) REVERT: G 132 THR cc_start: 0.8207 (m) cc_final: 0.7616 (p) REVERT: I 63 PHE cc_start: 0.6033 (m-10) cc_final: 0.5716 (t80) REVERT: I 66 TYR cc_start: 0.6039 (m-80) cc_final: 0.5544 (m-10) REVERT: J 103 LEU cc_start: 0.6332 (mt) cc_final: 0.4996 (tt) REVERT: M 11 ARG cc_start: 0.3230 (mpp80) cc_final: 0.2919 (mtt90) REVERT: O 10 GLN cc_start: 0.7144 (tm-30) cc_final: 0.6688 (mt0) REVERT: O 11 LEU cc_start: 0.7031 (mt) cc_final: 0.6382 (mt) REVERT: O 12 ILE cc_start: 0.5769 (pt) cc_final: 0.5551 (pt) REVERT: O 19 GLU cc_start: 0.6905 (mp0) cc_final: 0.6103 (tt0) REVERT: O 41 GLU cc_start: 0.6713 (tp30) cc_final: 0.6206 (tp30) REVERT: O 44 ARG cc_start: 0.6999 (mtt180) cc_final: 0.5912 (mtt180) REVERT: Q 13 ARG cc_start: 0.5199 (ttp80) cc_final: 0.4845 (mtm110) REVERT: Q 18 LYS cc_start: 0.8923 (mttt) cc_final: 0.7660 (tptp) REVERT: Q 54 GLN cc_start: 0.7666 (mp10) cc_final: 0.7339 (mp10) REVERT: R 34 TRP cc_start: -0.0007 (m-90) cc_final: -0.0466 (m-90) REVERT: R 49 ILE cc_start: 0.4557 (mt) cc_final: 0.4215 (mt) REVERT: S 75 TYR cc_start: 0.7223 (m-80) cc_final: 0.6575 (m-80) REVERT: T 5 GLU cc_start: 0.7965 (tm-30) cc_final: 0.6776 (tm-30) REVERT: T 7 MET cc_start: 0.5731 (tmm) cc_final: 0.5399 (tmm) REVERT: T 25 ARG cc_start: 0.7093 (ptt180) cc_final: 0.6578 (ptt90) REVERT: T 78 LEU cc_start: 0.7491 (tp) cc_final: 0.7046 (pp) REVERT: U 16 CYS cc_start: 0.7469 (t) cc_final: 0.6860 (t) REVERT: V 46 TRP cc_start: 0.0748 (p90) cc_final: 0.0040 (p90) REVERT: V 107 LEU cc_start: 0.7394 (mm) cc_final: 0.7162 (mt) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.2526 time to fit residues: 156.4282 Evaluate side-chains 306 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 240 optimal weight: 0.4980 chunk 203 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 315 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN G 54 GLN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN ** O 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.111725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.094322 restraints weight = 187364.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.093739 restraints weight = 167857.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.094784 restraints weight = 120919.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094619 restraints weight = 83290.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.094734 restraints weight = 82330.249| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 47053 Z= 0.133 Angle : 0.633 11.924 69749 Z= 0.328 Chirality : 0.038 0.333 8861 Planarity : 0.005 0.074 4164 Dihedral : 24.731 179.204 21890 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.78 % Favored : 96.98 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 2050 helix: 0.73 (0.16), residues: 920 sheet: -0.48 (0.27), residues: 314 loop : -0.88 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 80 TYR 0.032 0.002 TYR O 78 PHE 0.040 0.002 PHE C 556 TRP 0.011 0.001 TRP F 9 HIS 0.008 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00260 (47053) covalent geometry : angle 0.63314 (69749) hydrogen bonds : bond 0.06361 ( 1731) hydrogen bonds : angle 4.09446 ( 3858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 394 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TYR cc_start: 0.3984 (t80) cc_final: 0.3488 (t80) REVERT: C 69 MET cc_start: 0.1705 (tmm) cc_final: 0.1371 (tmm) REVERT: C 320 MET cc_start: 0.4265 (tpt) cc_final: 0.3045 (mmm) REVERT: C 399 MET cc_start: 0.1741 (tpp) cc_final: 0.1379 (tpp) REVERT: C 407 ARG cc_start: 0.5073 (ttt180) cc_final: 0.3809 (mtm180) REVERT: C 518 ASP cc_start: 0.3132 (m-30) cc_final: 0.2872 (t0) REVERT: C 537 LYS cc_start: 0.6443 (pttp) cc_final: 0.5116 (mttp) REVERT: C 563 TYR cc_start: 0.4126 (t80) cc_final: 0.3919 (t80) REVERT: F 64 ASN cc_start: 0.7026 (m-40) cc_final: 0.6822 (m-40) REVERT: F 77 LYS cc_start: 0.6643 (mtmt) cc_final: 0.5477 (tmmt) REVERT: F 127 ASP cc_start: 0.7374 (p0) cc_final: 0.6533 (m-30) REVERT: G 112 ARG cc_start: 0.5226 (ttt180) cc_final: 0.5009 (mtp85) REVERT: G 127 SER cc_start: 0.6859 (t) cc_final: 0.6404 (p) REVERT: G 130 SER cc_start: 0.6619 (t) cc_final: 0.6230 (t) REVERT: G 132 THR cc_start: 0.8235 (m) cc_final: 0.7658 (p) REVERT: I 52 VAL cc_start: 0.7997 (t) cc_final: 0.7616 (t) REVERT: I 66 TYR cc_start: 0.6048 (m-80) cc_final: 0.5538 (m-10) REVERT: J 7 TYR cc_start: 0.5145 (t80) cc_final: 0.4894 (t80) REVERT: J 80 ARG cc_start: 0.4248 (tmt170) cc_final: 0.3900 (ttt90) REVERT: J 103 LEU cc_start: 0.6576 (mt) cc_final: 0.5242 (tp) REVERT: M 11 ARG cc_start: 0.3278 (mpp80) cc_final: 0.2935 (mtt180) REVERT: O 10 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6659 (mt0) REVERT: O 11 LEU cc_start: 0.6974 (mt) cc_final: 0.6327 (mt) REVERT: O 19 GLU cc_start: 0.6904 (mp0) cc_final: 0.6121 (tt0) REVERT: O 41 GLU cc_start: 0.6724 (tp30) cc_final: 0.5978 (tp30) REVERT: O 44 ARG cc_start: 0.7039 (mtt180) cc_final: 0.5978 (mtt180) REVERT: O 53 ARG cc_start: 0.7721 (mtp85) cc_final: 0.6591 (tpt170) REVERT: Q 13 ARG cc_start: 0.5110 (ttp80) cc_final: 0.4828 (mtm110) REVERT: Q 18 LYS cc_start: 0.8909 (mttt) cc_final: 0.7527 (tptp) REVERT: Q 19 MET cc_start: 0.7566 (ptp) cc_final: 0.7251 (ptp) REVERT: Q 22 THR cc_start: 0.7366 (m) cc_final: 0.7104 (m) REVERT: Q 54 GLN cc_start: 0.7627 (mp10) cc_final: 0.7275 (mp10) REVERT: R 4 SER cc_start: 0.4306 (m) cc_final: 0.3952 (t) REVERT: R 34 TRP cc_start: -0.0288 (m-90) cc_final: -0.0659 (m-90) REVERT: R 49 ILE cc_start: 0.4691 (mt) cc_final: 0.4386 (mt) REVERT: S 57 ARG cc_start: 0.6787 (tpp-160) cc_final: 0.6254 (tpp-160) REVERT: S 75 TYR cc_start: 0.7336 (m-80) cc_final: 0.6718 (m-80) REVERT: T 5 GLU cc_start: 0.8192 (tm-30) cc_final: 0.6924 (tm-30) REVERT: T 78 LEU cc_start: 0.7496 (tp) cc_final: 0.6965 (pp) REVERT: U 16 CYS cc_start: 0.7313 (t) cc_final: 0.6935 (t) REVERT: U 31 VAL cc_start: 0.5808 (t) cc_final: 0.5501 (m) REVERT: V 107 LEU cc_start: 0.7378 (mm) cc_final: 0.7080 (mt) outliers start: 1 outliers final: 1 residues processed: 395 average time/residue: 0.2449 time to fit residues: 157.7370 Evaluate side-chains 309 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 137 optimal weight: 20.0000 chunk 240 optimal weight: 3.9990 chunk 306 optimal weight: 7.9990 chunk 291 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 211 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 115 ASN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN O 72 ASN P 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.110473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.091819 restraints weight = 187652.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091588 restraints weight = 147175.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091888 restraints weight = 103895.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.092247 restraints weight = 85232.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.092329 restraints weight = 79038.683| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.6958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 47053 Z= 0.186 Angle : 0.682 10.882 69749 Z= 0.350 Chirality : 0.039 0.341 8861 Planarity : 0.005 0.055 4164 Dihedral : 24.735 178.307 21890 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.56 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.18), residues: 2050 helix: 0.59 (0.16), residues: 920 sheet: -0.59 (0.26), residues: 320 loop : -0.95 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 561 TYR 0.026 0.002 TYR S 75 PHE 0.023 0.002 PHE R 74 TRP 0.015 0.002 TRP R 34 HIS 0.009 0.002 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00361 (47053) covalent geometry : angle 0.68171 (69749) hydrogen bonds : bond 0.06846 ( 1731) hydrogen bonds : angle 4.25214 ( 3858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5824.59 seconds wall clock time: 102 minutes 54.10 seconds (6174.10 seconds total)