Starting phenix.real_space_refine on Mon Aug 10 05:00:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cdv_16596/08_2026/8cdv_16596.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cdv_16596/08_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_16596/08_2026/8cdv_16596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cdv_16596/08_2026/8cdv_16596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cdv_16596/08_2026/8cdv_16596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cdv_16596/08_2026/8cdv_16596.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8cdv_16596/08_2026/8cdv_16596.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cdv_16596/08_2026/8cdv_16596.cif" } 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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 7.69, per 1000 atoms: 0.18 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: 2.92 Conformation dependent library (CDL) restraints added in 794.8 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: 6.01 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: 15.48 Time building geometry restraints manager: 4.17 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=" CA SER P 15 " pdb=" CB SER P 15 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.13e-02 7.83e+03 1.27e+01 bond pdb=" C GLY G 90 " pdb=" O GLY G 90 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.35e-02 5.49e+03 9.67e+00 bond pdb=" CA SER F 18 " pdb=" CB SER F 18 " ideal model delta sigma weight residual 1.527 1.486 0.041 1.38e-02 5.25e+03 8.87e+00 ... (remaining 47048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 66654 3.39 - 6.79: 3004 6.79 - 10.18: 77 10.18 - 13.57: 12 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=" 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 angle pdb=" N THR I 4 " pdb=" CA THR I 4 " pdb=" CB THR I 4 " ideal model delta sigma weight residual 110.49 121.35 -10.86 1.69e+00 3.50e-01 4.13e+01 ... (remaining 69744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 24922 35.19 - 70.38: 3585 70.38 - 105.57: 507 105.57 - 140.76: 6 140.76 - 175.95: 16 Dihedral angle restraints: 29036 sinusoidal: 23006 harmonic: 6030 Sorted by residual: dihedral pdb=" C4' G A1153 " pdb=" C3' G A1153 " pdb=" C2' G A1153 " pdb=" C1' G A1153 " ideal model delta sinusoidal sigma weight residual 36.34 -47.85 84.20 1 3.10e+00 1.04e-01 8.98e+02 dihedral pdb=" C4' G A 900 " pdb=" C3' G A 900 " pdb=" C2' G A 900 " pdb=" C1' G A 900 " ideal model delta sinusoidal sigma weight residual 36.34 -46.22 82.57 1 3.10e+00 1.04e-01 8.70e+02 dihedral pdb=" C4' G A 180 " pdb=" C3' G A 180 " pdb=" C2' G A 180 " pdb=" C1' G A 180 " ideal model delta sinusoidal sigma weight residual 36.35 -45.47 81.81 1 3.10e+00 1.04e-01 8.57e+02 ... (remaining 29033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 6762 0.169 - 0.339: 933 0.339 - 0.508: 1106 0.508 - 0.678: 54 0.678 - 0.847: 6 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 2.17 3.02 -0.85 2.00e-01 2.50e+01 1.79e+01 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 2.17 -3.00 -0.83 2.00e-01 2.50e+01 1.70e+01 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 2.17 -2.99 -0.81 2.00e-01 2.50e+01 1.65e+01 ... (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: 3.850 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: 0.030 Extract box with map and model: 0.850 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 44.010 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 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= 0.496 Angle : 1.530 16.966 69749 Z= 0.755 Chirality : 0.186 0.847 8861 Planarity : 0.025 0.457 4164 Dihedral : 25.707 175.951 25136 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/Z covalent geometry : bond 0.00900 / 0.50 (47053) covalent geometry : angle 1.53005 / 0.75 (69749) hydrogen bonds : bond 0.17028 / 8.88 ( 1731) hydrogen bonds : angle 11.06224 / 4.48 ( 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 : 0.940 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: 0.2918 time to fit residues: 317.7800 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 : 1.088 ------------------------------------------------------------------------------- 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: 7.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN I 69 ASN J 66 ASN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN M 76 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 = 0.3924 r_free = 0.3924 target = 0.112279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.093979 restraints weight = 186689.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093582 restraints weight = 179291.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.094872 restraints weight = 111073.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.094764 restraints weight = 76887.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.094928 restraints weight = 65944.988| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 47053 Z= 0.274 Angle : 1.589 22.015 69749 Z= 0.628 Chirality : 0.134 1.648 8861 Planarity : 0.006 0.095 4164 Dihedral : 25.681 179.034 20906 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.61 % Favored : 98.10 % Rotamer: Outliers : 0.33 % Allowed : 3.62 % 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: 0.20 (0.18), residues: 2050 helix: 0.99 (0.16), residues: 935 sheet: -0.90 (0.26), residues: 336 loop : -0.29 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 9 TYR 0.021 0.002 TYR L 108 PHE 0.026 0.003 PHE U 18 TRP 0.011 0.002 TRP T 43 HIS 0.007 0.001 HIS J 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.27 (47053) covalent geometry : angle 1.58873 / 0.63 (69749) hydrogen bonds : bond 0.08489 / 4.52 ( 1731) hydrogen bonds : angle 4.19145 / 1.71 ( 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 501 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 495 time to evaluate : 0.931 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: C 50 GLU cc_start: 0.5333 (tt0) cc_final: 0.5096 (tt0) REVERT: C 312 TYR cc_start: 0.3659 (m-80) cc_final: 0.3439 (m-80) REVERT: C 407 ARG cc_start: 0.5503 (ttt180) cc_final: 0.4306 (mtm180) REVERT: C 458 THR cc_start: 0.6327 (m) cc_final: 0.5788 (m) REVERT: C 525 ILE cc_start: 0.6822 (mt) cc_final: 0.6596 (mt) REVERT: C 538 TYR cc_start: 0.4806 (m-80) cc_final: 0.4418 (m-10) REVERT: C 539 ASP cc_start: 0.4744 (t0) cc_final: 0.4108 (t0) REVERT: F 9 TRP cc_start: 0.3694 (m-10) cc_final: 0.3269 (m-10) REVERT: F 86 PHE cc_start: 0.5882 (t80) cc_final: 0.5505 (t80) REVERT: F 87 MET cc_start: 0.7743 (mmm) cc_final: 0.7198 (mmm) REVERT: F 125 ARG cc_start: 0.5646 (ttt180) cc_final: 0.5080 (mtt180) REVERT: F 146 ARG cc_start: 0.5327 (mtp180) cc_final: 0.4708 (ttp80) REVERT: F 147 ASN cc_start: 0.7374 (p0) cc_final: 0.6810 (p0) REVERT: G 132 THR cc_start: 0.8032 (m) cc_final: 0.7553 (p) REVERT: I 25 LEU cc_start: 0.7112 (pt) cc_final: 0.6865 (pt) REVERT: I 35 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7859 (tp30) REVERT: I 45 PHE cc_start: 0.7123 (m-80) cc_final: 0.6314 (m-80) REVERT: I 66 TYR cc_start: 0.5414 (m-80) cc_final: 0.4412 (m-10) REVERT: I 114 THR cc_start: 0.6527 (p) cc_final: 0.5837 (p) REVERT: L 50 VAL cc_start: 0.6394 (t) cc_final: 0.5971 (p) REVERT: L 55 PRO cc_start: 0.7390 (Cg_endo) cc_final: 0.6806 (Cg_exo) REVERT: L 76 VAL cc_start: 0.7358 (m) cc_final: 0.6817 (p) REVERT: L 77 THR cc_start: 0.7176 (m) cc_final: 0.6499 (p) REVERT: L 102 ASP cc_start: 0.4606 (p0) cc_final: 0.4136 (p0) REVERT: L 130 TYR cc_start: 0.7326 (m-80) cc_final: 0.7105 (m-80) REVERT: M 46 ARG cc_start: 0.5133 (mtt-85) cc_final: 0.4709 (tpp80) REVERT: O 7 ARG cc_start: 0.6463 (tpt170) cc_final: 0.6157 (tpp-160) REVERT: O 8 LYS cc_start: 0.6862 (mtmm) cc_final: 0.6365 (mmtp) REVERT: O 32 LEU cc_start: 0.7644 (mt) cc_final: 0.7342 (mt) REVERT: O 41 GLU cc_start: 0.6232 (tp30) cc_final: 0.5711 (tp30) REVERT: O 46 HIS cc_start: 0.6258 (m90) cc_final: 0.5951 (m90) REVERT: O 56 LEU cc_start: 0.8295 (tt) cc_final: 0.7913 (tp) REVERT: O 69 TYR cc_start: 0.7818 (t80) cc_final: 0.7386 (t80) REVERT: O 81 LEU cc_start: 0.6897 (tp) cc_final: 0.6353 (tp) REVERT: Q 18 LYS cc_start: 0.8513 (mttt) cc_final: 0.7837 (tptt) REVERT: R 49 ILE cc_start: 0.5395 (mt) cc_final: 0.5128 (mt) REVERT: S 25 LYS cc_start: 0.6740 (mtmt) cc_final: 0.6256 (mtpt) REVERT: S 57 ARG cc_start: 0.6837 (tpp-160) cc_final: 0.6569 (tpp-160) REVERT: S 71 THR cc_start: 0.7375 (m) cc_final: 0.5301 (m) REVERT: T 11 ARG cc_start: 0.5308 (ptp-170) cc_final: 0.4215 (ptp-170) REVERT: T 25 ARG cc_start: 0.7182 (ptp-170) cc_final: 0.6863 (ptp-170) REVERT: T 41 LYS cc_start: 0.6380 (mttt) cc_final: 0.6150 (tptt) REVERT: T 50 TYR cc_start: 0.5811 (p90) cc_final: 0.5445 (p90) REVERT: T 67 SER cc_start: 0.3660 (p) cc_final: 0.3458 (p) REVERT: U 17 TYR cc_start: 0.7261 (t80) cc_final: 0.6957 (t80) REVERT: U 56 TYR cc_start: 0.7587 (m-80) cc_final: 0.7183 (m-80) REVERT: U 60 LEU cc_start: 0.7363 (tp) cc_final: 0.7032 (tp) outliers start: 6 outliers final: 0 residues processed: 497 average time/residue: 0.2702 time to fit residues: 215.2791 Evaluate side-chains 362 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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: 7.9990 chunk 78 optimal weight: 8.9990 chunk 240 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 300 optimal weight: 0.7980 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN F 67 GLN F 112 GLN F 115 ASN G 135 ASN H 64 GLN I 57 GLN I 69 ASN P 72 ASN S 68 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.108537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.090468 restraints weight = 190962.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.090272 restraints weight = 171581.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091041 restraints weight = 108871.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.090856 restraints weight = 78164.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091018 restraints weight = 68455.097| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 47053 Z= 0.352 Angle : 1.482 21.280 69749 Z= 0.599 Chirality : 0.116 1.172 8861 Planarity : 0.007 0.076 4164 Dihedral : 25.799 178.492 20906 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.12 % Favored : 96.63 % Rotamer: Outliers : 0.39 % Allowed : 5.24 % Favored : 94.37 % 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: -0.45 (0.17), residues: 2050 helix: 0.32 (0.16), residues: 934 sheet: -0.63 (0.28), residues: 308 loop : -0.74 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 29 TYR 0.023 0.003 TYR C 371 PHE 0.042 0.004 PHE U 18 TRP 0.012 0.002 TRP F 9 HIS 0.014 0.003 HIS C 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.35 (47053) covalent geometry : angle 1.48162 / 0.60 (69749) hydrogen bonds : bond 0.09513 / 5.05 ( 1731) hydrogen bonds : angle 4.55141 / 1.84 ( 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 446 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 439 time to evaluate : 0.964 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: 0.7001 (t0) cc_final: 0.6719 (t0) REVERT: C 69 MET cc_start: 0.1380 (tmm) cc_final: 0.1121 (tmm) REVERT: C 407 ARG cc_start: 0.5512 (ttt180) cc_final: 0.4301 (mtm180) REVERT: C 518 ASP cc_start: 0.3238 (m-30) cc_final: 0.2617 (t0) REVERT: C 538 TYR cc_start: 0.5181 (m-80) cc_final: 0.4588 (m-80) REVERT: C 563 TYR cc_start: 0.4238 (t80) cc_final: 0.3717 (t80) REVERT: F 7 PRO cc_start: 0.6162 (Cg_exo) cc_final: 0.5115 (Cg_endo) REVERT: F 64 ASN cc_start: 0.7582 (m-40) cc_final: 0.7106 (m110) REVERT: F 67 GLN cc_start: 0.6317 (pt0) cc_final: 0.6016 (pt0) REVERT: F 111 ARG cc_start: 0.5900 (ttt-90) cc_final: 0.5518 (ttt-90) REVERT: F 112 GLN cc_start: 0.7393 (tm130) cc_final: 0.7123 (tm-30) REVERT: F 146 ARG cc_start: 0.5654 (mtp180) cc_final: 0.5182 (ttp80) REVERT: F 182 ARG cc_start: 0.5013 (tpt170) cc_final: 0.4727 (tpm170) REVERT: F 194 ILE cc_start: 0.8006 (mt) cc_final: 0.7799 (mp) REVERT: F 198 TYR cc_start: 0.7569 (m-10) cc_final: 0.7327 (m-10) REVERT: G 69 LYS cc_start: 0.5573 (mtmt) cc_final: 0.5172 (mmtp) REVERT: G 96 LEU cc_start: 0.6987 (mt) cc_final: 0.6731 (mt) REVERT: G 132 THR cc_start: 0.8067 (m) cc_final: 0.7625 (p) REVERT: H 98 THR cc_start: 0.4590 (OUTLIER) cc_final: 0.4348 (m) REVERT: I 35 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7799 (tp30) REVERT: I 45 PHE cc_start: 0.7268 (m-80) cc_final: 0.6894 (m-80) REVERT: I 66 TYR cc_start: 0.6027 (m-80) cc_final: 0.5591 (m-80) REVERT: I 98 LEU cc_start: 0.7871 (mt) cc_final: 0.7611 (mt) REVERT: L 32 LYS cc_start: 0.8238 (mtpp) cc_final: 0.7855 (mtpt) REVERT: L 75 GLU cc_start: 0.6317 (tt0) cc_final: 0.5486 (mp0) REVERT: O 41 GLU cc_start: 0.6745 (tp30) cc_final: 0.6389 (tp30) REVERT: O 45 THR cc_start: 0.8376 (p) cc_final: 0.7935 (p) REVERT: O 46 HIS cc_start: 0.6750 (m90) cc_final: 0.6498 (m90) REVERT: O 56 LEU cc_start: 0.8271 (tt) cc_final: 0.8034 (tp) REVERT: Q 18 LYS cc_start: 0.8607 (mttt) cc_final: 0.7683 (tptt) REVERT: Q 79 GLU cc_start: 0.6314 (tm-30) cc_final: 0.5555 (pt0) REVERT: R 49 ILE cc_start: 0.5034 (mt) cc_final: 0.4667 (mt) REVERT: S 75 TYR cc_start: 0.6788 (m-80) cc_final: 0.6493 (m-80) REVERT: T 5 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6210 (tm-30) REVERT: T 9 ILE cc_start: 0.5445 (mt) cc_final: 0.5147 (mt) REVERT: T 17 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7109 (mm-30) REVERT: T 25 ARG cc_start: 0.7339 (ptp-170) cc_final: 0.7007 (ptp-170) REVERT: T 41 LYS cc_start: 0.6308 (mttt) cc_final: 0.5986 (tptt) REVERT: T 50 TYR cc_start: 0.6621 (p90) cc_final: 0.5822 (p90) REVERT: U 16 CYS cc_start: 0.7615 (t) cc_final: 0.7215 (t) REVERT: V 67 MET cc_start: 0.4443 (ttm) cc_final: 0.3168 (tmm) outliers start: 7 outliers final: 1 residues processed: 441 average time/residue: 0.2928 time to fit residues: 207.2523 Evaluate side-chains 322 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 320 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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: 3.9990 chunk 206 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 541 GLN F 50 GLN F 115 ASN J 66 ASN M 32 GLN O 13 ASN O 65 ASN Q 52 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 57 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.110747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093673 restraints weight = 188938.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.092925 restraints weight = 177326.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.093733 restraints weight = 124776.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.093731 restraints weight = 86270.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093909 restraints weight = 82666.595| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 47053 Z= 0.227 Angle : 1.268 18.792 69749 Z= 0.510 Chirality : 0.102 1.238 8861 Planarity : 0.006 0.080 4164 Dihedral : 25.758 178.880 20906 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.63 % Favored : 97.12 % Rotamer: Outliers : 0.11 % Allowed : 3.73 % Favored : 96.16 % 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: -0.13 (0.18), residues: 2050 helix: 0.75 (0.16), residues: 928 sheet: -0.64 (0.27), residues: 332 loop : -0.71 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 36 TYR 0.029 0.002 TYR I 130 PHE 0.023 0.002 PHE F 86 TRP 0.017 0.002 TRP T 43 HIS 0.016 0.002 HIS R 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 (47053) covalent geometry : angle 1.26815 / 0.51 (69749) hydrogen bonds : bond 0.07801 / 4.14 ( 1731) hydrogen bonds : angle 4.19591 / 1.69 ( 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 415 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 413 time to evaluate : 0.913 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: C 19 TYR cc_start: 0.4025 (t80) cc_final: 0.3794 (t80) REVERT: C 32 ASN cc_start: 0.7048 (t0) cc_final: 0.6791 (t0) REVERT: C 69 MET cc_start: 0.1776 (tmm) cc_final: 0.1396 (tmm) REVERT: C 407 ARG cc_start: 0.5728 (ttt180) cc_final: 0.4333 (mtm180) REVERT: C 518 ASP cc_start: 0.3271 (m-30) cc_final: 0.2600 (t0) REVERT: C 535 GLN cc_start: 0.5784 (mt0) cc_final: 0.5220 (mm-40) REVERT: C 538 TYR cc_start: 0.5328 (m-80) cc_final: 0.4977 (m-10) REVERT: C 560 ILE cc_start: 0.6101 (mp) cc_final: 0.5875 (mt) REVERT: C 563 TYR cc_start: 0.3970 (t80) cc_final: 0.3633 (t80) REVERT: F 64 ASN cc_start: 0.7751 (m-40) cc_final: 0.6188 (m110) REVERT: G 132 THR cc_start: 0.8326 (m) cc_final: 0.7758 (p) REVERT: I 34 ARG cc_start: 0.7194 (ttm170) cc_final: 0.6444 (mtt180) REVERT: I 45 PHE cc_start: 0.7394 (m-80) cc_final: 0.6993 (m-80) REVERT: I 61 ARG cc_start: 0.4987 (mtp-110) cc_final: 0.4748 (mtp-110) REVERT: I 63 PHE cc_start: 0.6693 (m-10) cc_final: 0.6218 (m-10) REVERT: I 98 LEU cc_start: 0.7658 (mt) cc_final: 0.7196 (mt) REVERT: I 114 THR cc_start: 0.6504 (p) cc_final: 0.6150 (p) REVERT: L 32 LYS cc_start: 0.8459 (mtpp) cc_final: 0.8225 (mtpt) REVERT: L 55 PRO cc_start: 0.7245 (Cg_endo) cc_final: 0.7041 (Cg_exo) REVERT: L 75 GLU cc_start: 0.6049 (tt0) cc_final: 0.5273 (mp0) REVERT: L 76 VAL cc_start: 0.7237 (m) cc_final: 0.6841 (t) REVERT: O 41 GLU cc_start: 0.6850 (tp30) cc_final: 0.6531 (tp30) REVERT: O 46 HIS cc_start: 0.6643 (m90) cc_final: 0.6439 (m90) REVERT: O 53 ARG cc_start: 0.7586 (mtp85) cc_final: 0.6674 (tpt170) REVERT: O 56 LEU cc_start: 0.8160 (tt) cc_final: 0.7956 (tp) REVERT: O 81 LEU cc_start: 0.6679 (tp) cc_final: 0.6463 (tp) REVERT: Q 18 LYS cc_start: 0.8761 (mttt) cc_final: 0.7767 (tptt) REVERT: Q 79 GLU cc_start: 0.6201 (tm-30) cc_final: 0.5517 (pt0) REVERT: R 49 ILE cc_start: 0.5110 (mt) cc_final: 0.4765 (mt) REVERT: S 75 TYR cc_start: 0.7066 (m-80) cc_final: 0.6713 (m-80) REVERT: T 46 ARG cc_start: 0.6665 (mtp85) cc_final: 0.6456 (mtp85) REVERT: U 16 CYS cc_start: 0.7448 (t) cc_final: 0.7071 (t) REVERT: U 64 ILE cc_start: 0.7605 (mm) cc_final: 0.7272 (mm) REVERT: V 24 HIS cc_start: 0.6115 (m-70) cc_final: 0.5616 (m90) REVERT: V 37 THR cc_start: 0.5899 (p) cc_final: 0.5680 (p) outliers start: 2 outliers final: 1 residues processed: 414 average time/residue: 0.2675 time to fit residues: 178.2269 Evaluate side-chains 325 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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: 7.9990 chunk 86 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 475 HIS ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN F 115 ASN G 54 GLN G 142 GLN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.109167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091294 restraints weight = 189727.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.091179 restraints weight = 167179.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.091930 restraints weight = 114628.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091737 restraints weight = 90412.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091918 restraints weight = 75496.167| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 47053 Z= 0.281 Angle : 1.328 18.684 69749 Z= 0.535 Chirality : 0.101 0.979 8861 Planarity : 0.007 0.101 4164 Dihedral : 25.754 179.588 20906 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.05 % Favored : 95.71 % Rotamer: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.82 % 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: 0.42 (0.16), residues: 920 sheet: -0.87 (0.26), residues: 330 loop : -0.88 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 106 TYR 0.038 0.002 TYR I 130 PHE 0.030 0.003 PHE C 463 TRP 0.010 0.002 TRP F 9 HIS 0.015 0.002 HIS C 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.28 (47053) covalent geometry : angle 1.32820 / 0.54 (69749) hydrogen bonds : bond 0.08632 / 4.59 ( 1731) hydrogen bonds : angle 4.42038 / 1.78 ( 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 403 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 400 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TYR cc_start: 0.3904 (t80) cc_final: 0.3577 (t80) REVERT: C 32 ASN cc_start: 0.7119 (t0) cc_final: 0.6915 (t0) REVERT: C 69 MET cc_start: 0.1865 (tmm) cc_final: 0.1504 (tmm) REVERT: C 320 MET cc_start: 0.5601 (tpt) cc_final: 0.5225 (tpt) REVERT: C 407 ARG cc_start: 0.5558 (ttt180) cc_final: 0.3989 (mtm180) REVERT: C 518 ASP cc_start: 0.3186 (m-30) cc_final: 0.2412 (t0) REVERT: C 538 TYR cc_start: 0.5445 (m-80) cc_final: 0.4227 (m-10) REVERT: C 560 ILE cc_start: 0.6345 (mp) cc_final: 0.5985 (mt) REVERT: C 563 TYR cc_start: 0.4352 (t80) cc_final: 0.3791 (t80) REVERT: C 596 ILE cc_start: 0.3669 (tp) cc_final: 0.3413 (tp) REVERT: F 150 ILE cc_start: 0.6981 (pt) cc_final: 0.6766 (pt) REVERT: G 33 PHE cc_start: 0.5639 (m-80) cc_final: 0.5295 (m-80) REVERT: G 36 LEU cc_start: 0.6417 (tp) cc_final: 0.6215 (tp) REVERT: G 41 ASP cc_start: 0.8107 (m-30) cc_final: 0.7879 (m-30) REVERT: G 96 LEU cc_start: 0.6940 (mt) cc_final: 0.6735 (mt) REVERT: G 127 SER cc_start: 0.6953 (t) cc_final: 0.6511 (p) REVERT: G 132 THR cc_start: 0.8155 (m) cc_final: 0.7619 (p) REVERT: H 119 ARG cc_start: 0.3816 (tpp-160) cc_final: 0.3515 (mtp85) REVERT: I 45 PHE cc_start: 0.7196 (m-80) cc_final: 0.6973 (m-80) REVERT: I 63 PHE cc_start: 0.6567 (m-10) cc_final: 0.6087 (m-10) REVERT: I 66 TYR cc_start: 0.5942 (m-80) cc_final: 0.5370 (m-10) REVERT: J 98 LEU cc_start: 0.6441 (mm) cc_final: 0.5875 (tp) REVERT: L 55 PRO cc_start: 0.7253 (Cg_endo) cc_final: 0.6991 (Cg_exo) REVERT: L 75 GLU cc_start: 0.6129 (tt0) cc_final: 0.5203 (mp0) REVERT: L 76 VAL cc_start: 0.6938 (m) cc_final: 0.6737 (t) REVERT: L 95 ILE cc_start: 0.7722 (pt) cc_final: 0.7497 (pt) REVERT: O 32 LEU cc_start: 0.7648 (mt) cc_final: 0.7377 (mt) REVERT: O 41 GLU cc_start: 0.6698 (tp30) cc_final: 0.6384 (tp30) REVERT: O 46 HIS cc_start: 0.6675 (m90) cc_final: 0.6472 (m90) REVERT: O 56 LEU cc_start: 0.8305 (tt) cc_final: 0.8033 (tp) REVERT: O 81 LEU cc_start: 0.6901 (tp) cc_final: 0.6479 (tp) REVERT: Q 18 LYS cc_start: 0.8845 (mttt) cc_final: 0.7638 (tptt) REVERT: R 9 PRO cc_start: 0.5169 (Cg_endo) cc_final: 0.4742 (Cg_exo) REVERT: R 49 ILE cc_start: 0.4964 (mt) cc_final: 0.4550 (mt) REVERT: S 75 TYR cc_start: 0.7033 (m-80) cc_final: 0.6512 (m-80) REVERT: T 5 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6319 (tm-30) REVERT: T 41 LYS cc_start: 0.6284 (mttt) cc_final: 0.5932 (tppt) REVERT: U 16 CYS cc_start: 0.7713 (t) cc_final: 0.7281 (t) REVERT: V 107 LEU cc_start: 0.7153 (mm) cc_final: 0.6927 (mt) outliers start: 3 outliers final: 0 residues processed: 401 average time/residue: 0.2799 time to fit residues: 181.5376 Evaluate side-chains 308 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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: 0.8980 chunk 312 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 148 optimal weight: 0.0060 chunk 307 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 67 GLN F 109 GLN F 112 GLN F 115 ASN J 38 HIS ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 ASN ** R 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 57 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.111032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.093267 restraints weight = 189333.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092386 restraints weight = 147861.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.092607 restraints weight = 116947.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.092893 restraints weight = 90200.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.093038 restraints weight = 79356.615| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 47053 Z= 0.208 Angle : 1.203 17.315 69749 Z= 0.485 Chirality : 0.095 0.885 8861 Planarity : 0.006 0.098 4164 Dihedral : 25.761 178.918 20906 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.27 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -0.30 (0.18), residues: 2050 helix: 0.64 (0.17), residues: 916 sheet: -0.74 (0.26), residues: 325 loop : -0.81 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 106 TYR 0.023 0.002 TYR L 65 PHE 0.025 0.002 PHE C 451 TRP 0.008 0.001 TRP V 46 HIS 0.011 0.002 HIS O 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.21 (47053) covalent geometry : angle 1.20260 / 0.48 (69749) hydrogen bonds : bond 0.07562 / 4.01 ( 1731) hydrogen bonds : angle 4.21831 / 1.70 ( 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 398 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TYR cc_start: 0.4043 (t80) cc_final: 0.3632 (t80) REVERT: C 69 MET cc_start: 0.1849 (tmm) cc_final: 0.1500 (tmm) REVERT: C 399 MET cc_start: 0.1445 (tpp) cc_final: 0.1112 (tpp) REVERT: C 407 ARG cc_start: 0.5236 (ttt180) cc_final: 0.3933 (mtm180) REVERT: C 495 TYR cc_start: 0.2551 (m-80) cc_final: 0.2005 (m-80) REVERT: C 533 MET cc_start: 0.3030 (ptm) cc_final: 0.2658 (ptm) REVERT: C 534 LYS cc_start: 0.4838 (pptt) cc_final: 0.4570 (pptt) REVERT: C 560 ILE cc_start: 0.6421 (mp) cc_final: 0.6119 (mt) REVERT: C 563 TYR cc_start: 0.4040 (t80) cc_final: 0.3768 (t80) REVERT: C 596 ILE cc_start: 0.3735 (tp) cc_final: 0.3369 (tp) REVERT: F 51 LEU cc_start: 0.7571 (tt) cc_final: 0.7136 (tp) REVERT: F 64 ASN cc_start: 0.7720 (m110) cc_final: 0.7292 (m-40) REVERT: F 72 PHE cc_start: 0.7938 (t80) cc_final: 0.7717 (t80) REVERT: F 101 LEU cc_start: 0.7832 (mt) cc_final: 0.7540 (mt) REVERT: F 112 GLN cc_start: 0.6783 (tm130) cc_final: 0.5679 (tt0) REVERT: G 33 PHE cc_start: 0.5615 (m-80) cc_final: 0.5266 (m-80) REVERT: G 36 LEU cc_start: 0.6412 (tp) cc_final: 0.6191 (tp) REVERT: G 112 ARG cc_start: 0.5099 (mtp180) cc_final: 0.4565 (mtp85) REVERT: G 127 SER cc_start: 0.7126 (t) cc_final: 0.6678 (p) REVERT: G 128 LEU cc_start: 0.8517 (mt) cc_final: 0.8278 (mt) REVERT: G 130 SER cc_start: 0.6258 (t) cc_final: 0.5922 (t) REVERT: G 132 THR cc_start: 0.8297 (m) cc_final: 0.7683 (p) REVERT: I 21 ARG cc_start: 0.6612 (mtt-85) cc_final: 0.6153 (mtm180) REVERT: I 45 PHE cc_start: 0.7232 (m-80) cc_final: 0.6848 (m-80) REVERT: I 66 TYR cc_start: 0.5911 (m-80) cc_final: 0.5302 (m-10) REVERT: J 98 LEU cc_start: 0.6354 (mm) cc_final: 0.5747 (tp) REVERT: L 75 GLU cc_start: 0.6360 (tt0) cc_final: 0.5450 (mp0) REVERT: O 41 GLU cc_start: 0.6695 (tp30) cc_final: 0.6377 (tp30) REVERT: O 46 HIS cc_start: 0.6803 (m90) cc_final: 0.6578 (m90) REVERT: O 53 ARG cc_start: 0.7886 (mtp85) cc_final: 0.6767 (tpt170) REVERT: O 56 LEU cc_start: 0.8314 (tt) cc_final: 0.7991 (tp) REVERT: O 62 LYS cc_start: 0.7417 (ttmt) cc_final: 0.7184 (ttpt) REVERT: P 4 LYS cc_start: 0.5291 (tptm) cc_final: 0.4958 (tptp) REVERT: Q 18 LYS cc_start: 0.8855 (mttt) cc_final: 0.7597 (tptt) REVERT: Q 39 ARG cc_start: 0.6001 (mtt90) cc_final: 0.5732 (mtt90) REVERT: Q 64 MET cc_start: 0.4629 (ttt) cc_final: 0.4398 (ttt) REVERT: R 9 PRO cc_start: 0.5311 (Cg_endo) cc_final: 0.4878 (Cg_exo) REVERT: R 49 ILE cc_start: 0.4792 (mt) cc_final: 0.4417 (mt) REVERT: S 74 ARG cc_start: 0.5991 (ttp80) cc_final: 0.5417 (ttp-170) REVERT: S 75 TYR cc_start: 0.6971 (m-80) cc_final: 0.6514 (m-80) REVERT: T 5 GLU cc_start: 0.7745 (tm-30) cc_final: 0.6652 (tm-30) REVERT: T 25 ARG cc_start: 0.7495 (ptt180) cc_final: 0.7169 (ptt180) REVERT: T 41 LYS cc_start: 0.6256 (mttt) cc_final: 0.5935 (tppt) REVERT: T 46 ARG cc_start: 0.6975 (mtp85) cc_final: 0.5787 (mtp85) REVERT: T 50 TYR cc_start: 0.6768 (p90) cc_final: 0.6561 (p90) REVERT: U 16 CYS cc_start: 0.7533 (t) cc_final: 0.6640 (t) REVERT: V 37 THR cc_start: 0.5976 (p) cc_final: 0.5678 (p) REVERT: V 63 PHE cc_start: 0.6391 (t80) cc_final: 0.6136 (t80) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.2870 time to fit residues: 183.6930 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 : 0.959 ------------------------------------------------------------------------------- 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: 9.9990 chunk 60 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 356 HIS C 462 HIS F 64 ASN F 109 GLN F 115 ASN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN O 65 ASN U 57 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.109557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.090816 restraints weight = 188973.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.090706 restraints weight = 157065.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091190 restraints weight = 102296.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.091309 restraints weight = 80509.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.091524 restraints weight = 69192.257| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 47053 Z= 0.262 Angle : 1.274 16.944 69749 Z= 0.513 Chirality : 0.096 0.910 8861 Planarity : 0.007 0.148 4164 Dihedral : 25.736 179.498 20906 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.49 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: 0.41 (0.16), residues: 903 sheet: -0.64 (0.27), residues: 315 loop : -0.96 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 119 TYR 0.026 0.002 TYR F 47 PHE 0.023 0.003 PHE U 18 TRP 0.009 0.002 TRP F 9 HIS 0.009 0.002 HIS G 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.26 (47053) covalent geometry : angle 1.27357 / 0.51 (69749) hydrogen bonds : bond 0.08260 / 4.39 ( 1731) hydrogen bonds : angle 4.41970 / 1.78 ( 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 364 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 MET cc_start: 0.1857 (tmm) cc_final: 0.0995 (tmm) REVERT: C 345 MET cc_start: 0.1924 (ttm) cc_final: 0.0525 (mpp) REVERT: C 399 MET cc_start: 0.1501 (tpp) cc_final: 0.1167 (tpp) REVERT: C 407 ARG cc_start: 0.5467 (ttt180) cc_final: 0.3762 (mtm180) REVERT: C 560 ILE cc_start: 0.6361 (mp) cc_final: 0.6011 (mt) REVERT: F 64 ASN cc_start: 0.7445 (m-40) cc_final: 0.6889 (m-40) REVERT: F 67 GLN cc_start: 0.6334 (pt0) cc_final: 0.6088 (pt0) REVERT: F 112 GLN cc_start: 0.6839 (pp30) cc_final: 0.6341 (tt0) REVERT: F 194 ILE cc_start: 0.7806 (mp) cc_final: 0.7537 (mp) REVERT: G 33 PHE cc_start: 0.5534 (m-80) cc_final: 0.5251 (m-80) REVERT: G 127 SER cc_start: 0.7012 (t) cc_final: 0.6555 (p) REVERT: G 130 SER cc_start: 0.6396 (t) cc_final: 0.5990 (t) REVERT: G 132 THR cc_start: 0.8248 (m) cc_final: 0.7662 (p) REVERT: I 63 PHE cc_start: 0.6121 (m-10) cc_final: 0.5714 (t80) REVERT: I 66 TYR cc_start: 0.6069 (m-80) cc_final: 0.5246 (m-10) REVERT: L 75 GLU cc_start: 0.6361 (tt0) cc_final: 0.5487 (mp0) REVERT: O 10 GLN cc_start: 0.7220 (tm-30) cc_final: 0.6950 (tm-30) REVERT: O 11 LEU cc_start: 0.6864 (mt) cc_final: 0.6572 (mt) REVERT: O 19 GLU cc_start: 0.7147 (mp0) cc_final: 0.6301 (mt-10) REVERT: O 41 GLU cc_start: 0.6709 (tp30) cc_final: 0.6425 (tp30) REVERT: O 46 HIS cc_start: 0.6743 (m90) cc_final: 0.6387 (m90) REVERT: O 56 LEU cc_start: 0.8363 (tt) cc_final: 0.8129 (tp) REVERT: O 62 LYS cc_start: 0.7171 (ttmt) cc_final: 0.6931 (ttmt) REVERT: P 4 LYS cc_start: 0.5637 (tptm) cc_final: 0.5304 (tptp) REVERT: P 58 LYS cc_start: 0.7660 (tttt) cc_final: 0.7453 (tptt) REVERT: Q 18 LYS cc_start: 0.8852 (mttt) cc_final: 0.7578 (tptt) REVERT: Q 64 MET cc_start: 0.4769 (ttt) cc_final: 0.4541 (ttt) REVERT: Q 79 GLU cc_start: 0.7283 (tp30) cc_final: 0.6689 (pt0) REVERT: R 49 ILE cc_start: 0.4421 (mt) cc_final: 0.4076 (mt) REVERT: S 75 TYR cc_start: 0.7012 (m-80) cc_final: 0.6564 (m-80) REVERT: T 5 GLU cc_start: 0.7791 (tm-30) cc_final: 0.6704 (tm-30) REVERT: T 25 ARG cc_start: 0.7414 (ptt180) cc_final: 0.7012 (ptt180) REVERT: T 41 LYS cc_start: 0.6296 (mttt) cc_final: 0.5859 (tppt) REVERT: T 50 TYR cc_start: 0.6627 (p90) cc_final: 0.6406 (p90) REVERT: U 16 CYS cc_start: 0.7379 (t) cc_final: 0.6974 (t) REVERT: U 70 MET cc_start: 0.6410 (mmt) cc_final: 0.6161 (mmt) REVERT: U 72 LEU cc_start: 0.5757 (tp) cc_final: 0.5549 (tp) REVERT: V 63 PHE cc_start: 0.6463 (t80) cc_final: 0.6123 (t80) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2778 time to fit residues: 165.3840 Evaluate side-chains 302 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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: 10.0000 chunk 55 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 306 optimal weight: 9.9990 chunk 309 optimal weight: 0.9980 chunk 268 optimal weight: 0.9990 chunk 313 optimal weight: 0.7980 chunk 294 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 311 optimal weight: 0.0470 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 ASN C 356 HIS F 67 GLN F 115 ASN G 45 HIS ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN O 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.112991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.094449 restraints weight = 188000.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.094171 restraints weight = 146003.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.094553 restraints weight = 104403.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.094672 restraints weight = 86569.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.094899 restraints weight = 74752.262| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 47053 Z= 0.169 Angle : 1.135 18.734 69749 Z= 0.458 Chirality : 0.090 1.029 8861 Planarity : 0.006 0.137 4164 Dihedral : 25.699 179.303 20906 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.83 % Favored : 96.98 % Rotamer: Outliers : 0.06 % Allowed : 1.17 % Favored : 98.77 % 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: -0.11 (0.18), residues: 2050 helix: 0.79 (0.17), residues: 910 sheet: -0.42 (0.27), residues: 310 loop : -0.82 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG H 119 TYR 0.022 0.002 TYR I 130 PHE 0.020 0.002 PHE R 41 TRP 0.012 0.001 TRP F 9 HIS 0.008 0.001 HIS I 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (47053) covalent geometry : angle 1.13475 / 0.46 (69749) hydrogen bonds : bond 0.07166 / 3.79 ( 1731) hydrogen bonds : angle 4.06743 / 1.63 ( 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: 1 poor density : 389 time to evaluate : 1.351 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: 0.4232 (t80) cc_final: 0.3731 (t80) REVERT: C 69 MET cc_start: 0.1671 (tmm) cc_final: 0.0848 (tmm) REVERT: C 399 MET cc_start: 0.1515 (tpp) cc_final: 0.1159 (tpp) REVERT: C 407 ARG cc_start: 0.5172 (ttt180) cc_final: 0.3711 (mtm180) REVERT: C 560 ILE cc_start: 0.6293 (mp) cc_final: 0.6074 (mt) REVERT: C 563 TYR cc_start: 0.4031 (t80) cc_final: 0.3796 (t80) REVERT: F 112 GLN cc_start: 0.6861 (pp30) cc_final: 0.6363 (tt0) REVERT: G 33 PHE cc_start: 0.5502 (m-80) cc_final: 0.5226 (m-80) REVERT: G 127 SER cc_start: 0.7043 (t) cc_final: 0.6608 (p) REVERT: G 130 SER cc_start: 0.6304 (t) cc_final: 0.5921 (t) REVERT: G 132 THR cc_start: 0.8319 (m) cc_final: 0.7701 (p) REVERT: I 21 ARG cc_start: 0.6476 (mtt-85) cc_final: 0.6034 (mtm180) REVERT: I 34 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6460 (mtt180) REVERT: I 45 PHE cc_start: 0.7162 (m-80) cc_final: 0.6694 (m-80) REVERT: I 66 TYR cc_start: 0.6117 (m-80) cc_final: 0.5550 (m-10) REVERT: J 103 LEU cc_start: 0.5512 (mt) cc_final: 0.4169 (tp) REVERT: L 75 GLU cc_start: 0.5943 (tt0) cc_final: 0.5367 (pm20) REVERT: M 11 ARG cc_start: 0.2940 (mpp80) cc_final: 0.2693 (mtt180) REVERT: O 19 GLU cc_start: 0.6978 (mp0) cc_final: 0.6284 (mt-10) REVERT: O 41 GLU cc_start: 0.6702 (tp30) cc_final: 0.6303 (tp30) REVERT: O 46 HIS cc_start: 0.6653 (m90) cc_final: 0.6326 (m90) REVERT: O 53 ARG cc_start: 0.7866 (mtp85) cc_final: 0.6665 (tpt170) REVERT: O 56 LEU cc_start: 0.8309 (tt) cc_final: 0.7923 (tp) REVERT: O 81 LEU cc_start: 0.6909 (tp) cc_final: 0.6621 (tp) REVERT: P 4 LYS cc_start: 0.5332 (tptm) cc_final: 0.5058 (tptp) REVERT: P 58 LYS cc_start: 0.7611 (tttt) cc_final: 0.7390 (tptt) REVERT: Q 18 LYS cc_start: 0.8830 (mttt) cc_final: 0.7614 (tptt) REVERT: Q 79 GLU cc_start: 0.7126 (tp30) cc_final: 0.6596 (pt0) REVERT: R 49 ILE cc_start: 0.4369 (mt) cc_final: 0.4048 (mt) REVERT: S 74 ARG cc_start: 0.6020 (ttp80) cc_final: 0.5656 (ttp-170) REVERT: S 75 TYR cc_start: 0.7101 (m-80) cc_final: 0.6674 (m-80) REVERT: T 5 GLU cc_start: 0.7889 (tm-30) cc_final: 0.6763 (tm-30) REVERT: T 25 ARG cc_start: 0.7519 (ptt180) cc_final: 0.7173 (ptt90) REVERT: T 41 LYS cc_start: 0.6301 (mttt) cc_final: 0.5867 (tppt) REVERT: T 78 LEU cc_start: 0.7734 (pp) cc_final: 0.7355 (tp) REVERT: U 16 CYS cc_start: 0.7278 (t) cc_final: 0.7015 (t) REVERT: U 56 TYR cc_start: 0.7183 (m-80) cc_final: 0.6887 (m-80) REVERT: U 70 MET cc_start: 0.6210 (mmt) cc_final: 0.5788 (mmt) REVERT: V 63 PHE cc_start: 0.6338 (t80) cc_final: 0.5893 (t80) REVERT: V 107 LEU cc_start: 0.7230 (mm) cc_final: 0.6987 (mt) outliers start: 1 outliers final: 0 residues processed: 389 average time/residue: 0.2827 time to fit residues: 178.8768 Evaluate side-chains 311 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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: 0.6980 chunk 234 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 229 optimal weight: 9.9990 chunk 323 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 285 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 555 HIS F 67 GLN F 115 ASN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN O 65 ASN O 72 ASN U 57 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.112391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.092906 restraints weight = 186976.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093236 restraints weight = 123555.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.093736 restraints weight = 87283.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093796 restraints weight = 64750.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.093929 restraints weight = 61084.439| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 47053 Z= 0.186 Angle : 1.135 18.284 69749 Z= 0.458 Chirality : 0.089 1.093 8861 Planarity : 0.006 0.087 4164 Dihedral : 25.588 179.909 20906 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.27 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.18), residues: 2050 helix: 0.76 (0.17), residues: 914 sheet: -0.38 (0.27), residues: 310 loop : -0.79 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG H 119 TYR 0.024 0.002 TYR C 538 PHE 0.017 0.002 PHE F 86 TRP 0.010 0.001 TRP V 46 HIS 0.008 0.001 HIS I 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (47053) covalent geometry : angle 1.13485 / 0.46 (69749) hydrogen bonds : bond 0.07255 / 3.86 ( 1731) hydrogen bonds : angle 4.14834 / 1.67 ( 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 376 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TYR cc_start: 0.4253 (t80) cc_final: 0.3791 (t80) REVERT: C 69 MET cc_start: 0.1439 (tmm) cc_final: 0.0803 (tmm) REVERT: C 399 MET cc_start: 0.1298 (tpp) cc_final: 0.0956 (tpp) REVERT: C 407 ARG cc_start: 0.4868 (ttt180) cc_final: 0.3738 (mtm180) REVERT: C 560 ILE cc_start: 0.6156 (mp) cc_final: 0.5876 (mt) REVERT: F 64 ASN cc_start: 0.7290 (m-40) cc_final: 0.6935 (m110) REVERT: F 112 GLN cc_start: 0.6803 (pp30) cc_final: 0.6173 (tt0) REVERT: G 33 PHE cc_start: 0.5517 (m-80) cc_final: 0.5289 (m-80) REVERT: G 36 LEU cc_start: 0.6480 (tp) cc_final: 0.6209 (tp) REVERT: G 54 GLN cc_start: 0.5150 (tp-100) cc_final: 0.4907 (mt0) REVERT: G 96 LEU cc_start: 0.6653 (mt) cc_final: 0.6360 (mt) REVERT: G 127 SER cc_start: 0.6947 (t) cc_final: 0.6504 (p) REVERT: G 130 SER cc_start: 0.6180 (t) cc_final: 0.5862 (t) REVERT: G 132 THR cc_start: 0.8270 (m) cc_final: 0.7682 (p) REVERT: I 66 TYR cc_start: 0.6070 (m-80) cc_final: 0.5512 (m-10) REVERT: J 103 LEU cc_start: 0.5665 (mt) cc_final: 0.4276 (tp) REVERT: L 75 GLU cc_start: 0.5882 (tt0) cc_final: 0.5523 (mp0) REVERT: O 11 LEU cc_start: 0.6709 (mt) cc_final: 0.6493 (mt) REVERT: O 19 GLU cc_start: 0.6892 (mp0) cc_final: 0.6299 (mt-10) REVERT: O 33 THR cc_start: 0.8005 (p) cc_final: 0.7725 (p) REVERT: O 41 GLU cc_start: 0.6740 (tp30) cc_final: 0.6231 (tp30) REVERT: O 44 ARG cc_start: 0.7028 (mtt180) cc_final: 0.6064 (mtt180) REVERT: O 46 HIS cc_start: 0.6737 (m90) cc_final: 0.6324 (m90) REVERT: O 56 LEU cc_start: 0.8345 (tt) cc_final: 0.8073 (tp) REVERT: P 4 LYS cc_start: 0.5169 (tptm) cc_final: 0.4849 (tptp) REVERT: P 50 LYS cc_start: 0.6682 (mptt) cc_final: 0.6386 (mptt) REVERT: P 58 LYS cc_start: 0.7577 (tttt) cc_final: 0.7358 (tptt) REVERT: Q 18 LYS cc_start: 0.8744 (mttt) cc_final: 0.7514 (tptt) REVERT: Q 19 MET cc_start: 0.7473 (mtm) cc_final: 0.7218 (ptp) REVERT: Q 64 MET cc_start: 0.5160 (ttt) cc_final: 0.4912 (ttt) REVERT: Q 79 GLU cc_start: 0.7233 (tp30) cc_final: 0.6774 (pt0) REVERT: R 34 TRP cc_start: -0.0225 (m-90) cc_final: -0.0532 (m-90) REVERT: R 49 ILE cc_start: 0.4248 (mt) cc_final: 0.3949 (mt) REVERT: S 74 ARG cc_start: 0.6142 (ttp80) cc_final: 0.5846 (ttp-170) REVERT: T 5 GLU cc_start: 0.7880 (tm-30) cc_final: 0.6724 (tm-30) REVERT: T 41 LYS cc_start: 0.6293 (mttt) cc_final: 0.5825 (tppt) REVERT: T 46 ARG cc_start: 0.7543 (mtm180) cc_final: 0.6803 (mtp85) REVERT: T 50 TYR cc_start: 0.6446 (p90) cc_final: 0.6237 (p90) REVERT: U 16 CYS cc_start: 0.7677 (t) cc_final: 0.7177 (t) REVERT: U 70 MET cc_start: 0.6507 (mmt) cc_final: 0.6092 (mmt) REVERT: V 63 PHE cc_start: 0.6335 (t80) cc_final: 0.6094 (t80) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.2650 time to fit residues: 164.7635 Evaluate side-chains 304 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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: 0.8980 chunk 53 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 147 optimal weight: 0.0020 chunk 134 optimal weight: 0.6980 chunk 315 optimal weight: 0.7980 chunk 293 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 284 optimal weight: 5.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 ASN C 462 HIS C 484 GLN C 510 GLN F 59 HIS F 67 GLN F 115 ASN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.115336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.097583 restraints weight = 186866.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.097457 restraints weight = 158946.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098158 restraints weight = 100933.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.098304 restraints weight = 82309.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.098397 restraints weight = 72736.344| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.7398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 47053 Z= 0.154 Angle : 1.072 18.445 69749 Z= 0.433 Chirality : 0.085 1.164 8861 Planarity : 0.005 0.109 4164 Dihedral : 25.513 179.391 20906 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.44 % Favored : 97.37 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2050 helix: 1.02 (0.17), residues: 915 sheet: -0.32 (0.26), residues: 321 loop : -0.71 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 80 TYR 0.029 0.002 TYR L 65 PHE 0.015 0.002 PHE C 39 TRP 0.017 0.001 TRP F 9 HIS 0.008 0.001 HIS I 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (47053) covalent geometry : angle 1.07247 / 0.43 (69749) hydrogen bonds : bond 0.06829 / 3.61 ( 1731) hydrogen bonds : angle 3.93721 / 1.59 ( 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 392 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 391 time to evaluate : 0.967 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: 0.4060 (t80) cc_final: 0.3729 (t80) REVERT: C 69 MET cc_start: 0.1358 (tmm) cc_final: 0.0773 (tmm) REVERT: C 399 MET cc_start: 0.1449 (tpp) cc_final: 0.0994 (tpp) REVERT: C 407 ARG cc_start: 0.5002 (ttt180) cc_final: 0.3998 (mtm180) REVERT: C 537 LYS cc_start: 0.7151 (pttm) cc_final: 0.5962 (mmtt) REVERT: C 553 TYR cc_start: 0.4349 (t80) cc_final: 0.4082 (t80) REVERT: C 560 ILE cc_start: 0.6091 (mp) cc_final: 0.5837 (mt) REVERT: F 64 ASN cc_start: 0.7064 (m-40) cc_final: 0.6693 (m-40) REVERT: F 112 GLN cc_start: 0.6654 (pp30) cc_final: 0.6267 (tt0) REVERT: F 127 ASP cc_start: 0.7039 (p0) cc_final: 0.6373 (m-30) REVERT: G 33 PHE cc_start: 0.5603 (m-80) cc_final: 0.5366 (m-80) REVERT: G 36 LEU cc_start: 0.6641 (tp) cc_final: 0.6374 (tp) REVERT: G 42 LYS cc_start: 0.8318 (tttt) cc_final: 0.7093 (ptpt) REVERT: G 54 GLN cc_start: 0.5213 (tp-100) cc_final: 0.4986 (mt0) REVERT: G 96 LEU cc_start: 0.6459 (mt) cc_final: 0.6157 (mt) REVERT: G 132 THR cc_start: 0.8353 (m) cc_final: 0.7879 (p) REVERT: G 151 GLU cc_start: 0.6104 (pp20) cc_final: 0.5894 (pp20) REVERT: I 35 GLU cc_start: 0.7551 (tm-30) cc_final: 0.6975 (tm-30) REVERT: I 36 ILE cc_start: 0.7560 (mt) cc_final: 0.7281 (mt) REVERT: I 45 PHE cc_start: 0.7312 (m-80) cc_final: 0.6639 (m-80) REVERT: I 66 TYR cc_start: 0.5939 (m-80) cc_final: 0.5344 (m-10) REVERT: L 75 GLU cc_start: 0.5933 (tt0) cc_final: 0.5578 (pm20) REVERT: L 77 THR cc_start: 0.7158 (m) cc_final: 0.6625 (p) REVERT: L 87 LEU cc_start: 0.8495 (mm) cc_final: 0.7777 (tp) REVERT: O 12 ILE cc_start: 0.5909 (pt) cc_final: 0.5271 (mt) REVERT: O 19 GLU cc_start: 0.6899 (mp0) cc_final: 0.6295 (mt-10) REVERT: O 33 THR cc_start: 0.7889 (p) cc_final: 0.7624 (p) REVERT: O 46 HIS cc_start: 0.6547 (m90) cc_final: 0.6162 (m90) REVERT: O 53 ARG cc_start: 0.7762 (mtp85) cc_final: 0.6514 (tpt170) REVERT: O 56 LEU cc_start: 0.8195 (tt) cc_final: 0.7818 (tp) REVERT: P 4 LYS cc_start: 0.5427 (tptm) cc_final: 0.5049 (tptp) REVERT: P 50 LYS cc_start: 0.6821 (mptt) cc_final: 0.6593 (mptt) REVERT: P 67 SER cc_start: 0.8597 (m) cc_final: 0.8383 (m) REVERT: Q 18 LYS cc_start: 0.8728 (mttt) cc_final: 0.7483 (tptt) REVERT: Q 22 THR cc_start: 0.7386 (m) cc_final: 0.7119 (m) REVERT: Q 64 MET cc_start: 0.5395 (ttt) cc_final: 0.5188 (ttt) REVERT: Q 79 GLU cc_start: 0.7189 (tp30) cc_final: 0.6605 (pt0) REVERT: R 9 PRO cc_start: 0.5413 (Cg_endo) cc_final: 0.4807 (Cg_exo) REVERT: R 49 ILE cc_start: 0.4642 (mt) cc_final: 0.4377 (mt) REVERT: T 5 GLU cc_start: 0.8002 (tm-30) cc_final: 0.6833 (tm-30) REVERT: T 41 LYS cc_start: 0.6304 (mttt) cc_final: 0.5842 (tppt) REVERT: T 46 ARG cc_start: 0.7480 (mtm180) cc_final: 0.6019 (mtp85) REVERT: T 78 LEU cc_start: 0.7666 (pp) cc_final: 0.7346 (tp) REVERT: U 16 CYS cc_start: 0.7517 (t) cc_final: 0.6923 (t) REVERT: U 70 MET cc_start: 0.6170 (mmt) cc_final: 0.5489 (mmm) REVERT: V 107 LEU cc_start: 0.7285 (mm) cc_final: 0.7025 (mt) outliers start: 1 outliers final: 1 residues processed: 392 average time/residue: 0.2736 time to fit residues: 175.2368 Evaluate side-chains 315 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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: 9.9990 chunk 240 optimal weight: 0.0970 chunk 306 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 226 optimal weight: 0.1980 chunk 261 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 overall best weight: 3.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 286 HIS C 535 GLN ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 115 ASN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN M 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.111372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092118 restraints weight = 189126.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092536 restraints weight = 125798.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092628 restraints weight = 87753.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.092808 restraints weight = 73872.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.093058 restraints weight = 68746.981| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.7442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 47053 Z= 0.258 Angle : 1.205 17.669 69749 Z= 0.487 Chirality : 0.089 1.090 8861 Planarity : 0.006 0.091 4164 Dihedral : 25.505 179.665 20906 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.71 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.18), residues: 2050 helix: 0.57 (0.17), residues: 919 sheet: -0.51 (0.27), residues: 329 loop : -0.94 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 119 TYR 0.031 0.003 TYR H 107 PHE 0.039 0.003 PHE C 556 TRP 0.013 0.002 TRP F 9 HIS 0.012 0.002 HIS I 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.26 (47053) covalent geometry : angle 1.20507 / 0.49 (69749) hydrogen bonds : bond 0.07893 / 4.20 ( 1731) hydrogen bonds : angle 4.28822 / 1.72 ( 3858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6654.09 seconds wall clock time: 117 minutes 7.91 seconds (7027.91 seconds total)