Starting phenix.real_space_refine on Tue Jul 7 02:56:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cdv_16596/07_2026/8cdv_16596.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cdv_16596/07_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_16596/07_2026/8cdv_16596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cdv_16596/07_2026/8cdv_16596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cdv_16596/07_2026/8cdv_16596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cdv_16596/07_2026/8cdv_16596.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8cdv_16596/07_2026/8cdv_16596.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cdv_16596/07_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-dev-6108/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: {'RNA': 1247} Modifications used: {'rna2p_pur': 97, 'rna2p_pyr': 64, 'rna3p_pur': 614, 'rna3p_pyr': 472} Link IDs: {'rna2p': 161, 'rna3p': 1085} Chain breaks: 4 Chain: "B" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 242 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 9} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "C" Number of atoms: 3687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3687 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 17, 'TRANS': 439} Chain breaks: 1 Chain: "F" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1490 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 2 Chain: "G" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1170 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain: "H" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 727 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1036 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "J" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 776 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "K" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 489 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain breaks: 1 Chain: "L" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1052 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 128} Chain: "M" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 868 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "O" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 710 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "P" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 82} Chain: "Q" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 691 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "R" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 637 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain: "T" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 755 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "V" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 662 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Time building chain proxies: 7.79, 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: 3.41 Conformation dependent library (CDL) restraints added in 982.9 milliseconds 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 21 sheets defined 48.7% alpha, 19.0% beta 342 base pairs and 689 stacking pairs defined. Time for finding SS restraints: 7.18 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: 16.09 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3953 1.28 - 1.42: 17935 1.42 - 1.56: 22571 1.56 - 1.70: 2510 1.70 - 1.84: 84 Bond restraints: 47053 Sorted by residual: bond pdb=" C LYS P 13 " pdb=" O LYS P 13 " ideal model delta sigma weight residual 1.235 1.143 0.092 1.26e-02 6.30e+03 5.36e+01 bond pdb=" C SER K 94 " pdb=" O SER K 94 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.26e-02 6.30e+03 3.50e+01 bond pdb=" O5' G A 764 " pdb=" C5' G A 764 " ideal model delta sigma weight residual 1.420 1.478 -0.058 1.50e-02 4.44e+03 1.50e+01 bond pdb=" O5' C A 668 " pdb=" C5' C A 668 " ideal model delta sigma weight residual 1.420 1.478 -0.058 1.50e-02 4.44e+03 1.47e+01 bond pdb=" O5' G A 736 " pdb=" C5' G A 736 " ideal model delta sigma weight residual 1.420 1.476 -0.056 1.50e-02 4.44e+03 1.40e+01 ... (remaining 47048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 67519 3.39 - 6.79: 2164 6.79 - 10.18: 55 10.18 - 13.57: 9 13.57 - 16.97: 2 Bond angle restraints: 69749 Sorted by residual: angle pdb=" CA LYS P 13 " pdb=" C LYS P 13 " pdb=" N LYS P 14 " ideal model delta sigma weight residual 116.84 129.59 -12.75 1.71e+00 3.42e-01 5.56e+01 angle pdb=" CB LYS S 81 " pdb=" CG LYS S 81 " pdb=" CD LYS S 81 " ideal model delta sigma weight residual 111.30 128.27 -16.97 2.30e+00 1.89e-01 5.44e+01 angle pdb=" CA SER K 94 " pdb=" C SER K 94 " pdb=" O SER K 94 " ideal model delta sigma weight residual 120.51 110.34 10.17 1.43e+00 4.89e-01 5.06e+01 angle pdb=" O3' G A1148 " pdb=" C3' G A1148 " pdb=" C2' G A1148 " ideal model delta sigma weight residual 109.50 119.27 -9.77 1.50e+00 4.44e-01 4.24e+01 angle pdb=" CA SER K 94 " pdb=" C SER K 94 " pdb=" N GLY K 95 " ideal model delta sigma weight residual 116.84 127.88 -11.04 1.71e+00 3.42e-01 4.17e+01 ... (remaining 69744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 25756 35.19 - 70.38: 2742 70.38 - 105.57: 489 105.57 - 140.76: 25 140.76 - 175.95: 24 Dihedral angle restraints: 29036 sinusoidal: 23006 harmonic: 6030 Sorted by residual: dihedral pdb=" CA ASP G 5 " pdb=" C ASP G 5 " pdb=" N PRO G 6 " pdb=" CA PRO G 6 " ideal model delta harmonic sigma weight residual -180.00 -126.42 -53.58 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA LYS R 28 " pdb=" C LYS R 28 " pdb=" N GLN R 29 " pdb=" CA GLN R 29 " ideal model delta harmonic sigma weight residual -180.00 -130.21 -49.79 0 5.00e+00 4.00e-02 9.92e+01 dihedral pdb=" C4' G A 641 " pdb=" C3' G A 641 " pdb=" C2' G A 641 " pdb=" C1' G A 641 " ideal model delta sinusoidal sigma weight residual -35.00 33.54 -68.54 1 8.00e+00 1.56e-02 9.51e+01 ... (remaining 29033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 6102 0.122 - 0.244: 2597 0.244 - 0.366: 148 0.366 - 0.488: 7 0.488 - 0.610: 7 Chirality restraints: 8861 Sorted by residual: chirality pdb=" P A B -1 " pdb=" OP1 A B -1 " pdb=" OP2 A B -1 " pdb=" O5' A B -1 " both_signs ideal model delta sigma weight residual True 2.41 3.02 -0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" P C A 815 " pdb=" OP1 C A 815 " pdb=" OP2 C A 815 " pdb=" O5' C A 815 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" P G A 8 " pdb=" OP1 G A 8 " pdb=" OP2 G A 8 " pdb=" O5' G A 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.57 2.00e-01 2.50e+01 8.26e+00 ... (remaining 8858 not shown) Planarity restraints: 4164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 89 " 1.019 9.50e-02 1.11e+02 4.57e-01 1.27e+02 pdb=" NE ARG K 89 " -0.068 2.00e-02 2.50e+03 pdb=" CZ ARG K 89 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG K 89 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 89 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 39 " -0.925 9.50e-02 1.11e+02 4.15e-01 1.12e+02 pdb=" NE ARG Q 39 " 0.073 2.00e-02 2.50e+03 pdb=" CZ ARG Q 39 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 39 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 78 " -0.918 9.50e-02 1.11e+02 4.12e-01 1.07e+02 pdb=" NE ARG R 78 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG R 78 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG R 78 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG R 78 " -0.012 2.00e-02 2.50e+03 ... (remaining 4161 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 4 1.93 - 2.67: 2293 2.67 - 3.41: 62382 3.41 - 4.16: 147745 4.16 - 4.90: 206452 Nonbonded interactions: 418876 Sorted by model distance: nonbonded pdb=" O2' G A 641 " pdb=" OP1 U A 642 " model vdw 1.187 3.040 nonbonded pdb=" C5' A B 6 " pdb=" N3 A B 6 " model vdw 1.659 3.520 nonbonded pdb=" O5' A B 6 " pdb=" N3 A B 6 " model vdw 1.808 3.120 nonbonded pdb=" O2' U A1198 " pdb=" OP1 G A1199 " model vdw 1.920 3.040 nonbonded pdb=" OP1 U A 64 " pdb=" O2' U A 393 " model vdw 1.972 3.040 ... (remaining 418871 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.960 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 47.610 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.960 ------------------------------------------------------------------------------- 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= 0.597 Angle : 1.435 16.966 69749 Z= 0.900 Chirality : 0.114 0.610 8861 Planarity : 0.025 0.457 4164 Dihedral : 24.149 175.951 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 0.00934 / 0.60 (47053) covalent geometry : angle 1.43529 / 0.90 (69749) hydrogen bonds : bond 0.17028 / 10.11 ( 1731) hydrogen bonds : angle 11.06224 / 6.23 ( 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 : 0.969 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: 0.3056 time to fit residues: 331.8356 Evaluate side-chains 421 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 397 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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: 9.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 333 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 HIS C 535 GLN F 64 ASN F 67 GLN F 112 GLN F 115 ASN H 56 ASN H 106 ASN H 122 ASN I 22 HIS I 57 GLN I 69 ASN J 66 ASN J 81 HIS L 5 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 ASN O 18 HIS O 72 ASN O 83 ASN Q 52 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.111940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094101 restraints weight = 184740.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.092656 restraints weight = 182065.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093949 restraints weight = 125500.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093720 restraints weight = 89882.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093909 restraints weight = 83009.863| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.2770 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= 0.220 Angle : 0.812 9.512 69749 Z= 0.429 Chirality : 0.048 0.332 8861 Planarity : 0.006 0.116 4164 Dihedral : 24.427 178.442 20906 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.46 % Favored : 98.24 % Rotamer: Outliers : 0.33 % Allowed : 3.40 % Favored : 96.27 % 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: 0.27 (0.18), residues: 2050 helix: 1.07 (0.16), residues: 931 sheet: -0.86 (0.26), residues: 328 loop : -0.27 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 106 TYR 0.021 0.002 TYR L 108 PHE 0.029 0.003 PHE U 18 TRP 0.009 0.002 TRP T 43 HIS 0.007 0.001 HIS J 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.22 (47053) covalent geometry : angle 0.81218 / 0.43 (69749) hydrogen bonds : bond 0.07796 / 4.62 ( 1731) hydrogen bonds : angle 4.13032 / 2.40 ( 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 510 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 504 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 GLU cc_start: 0.5294 (tt0) cc_final: 0.5039 (tt0) REVERT: C 407 ARG cc_start: 0.5411 (ttt180) cc_final: 0.4272 (mtm180) REVERT: C 458 THR cc_start: 0.6376 (m) cc_final: 0.5823 (m) REVERT: C 538 TYR cc_start: 0.4795 (m-80) cc_final: 0.4564 (m-10) REVERT: C 539 ASP cc_start: 0.4936 (t0) cc_final: 0.4279 (t0) REVERT: C 604 GLU cc_start: 0.5216 (tt0) cc_final: 0.4959 (mm-30) REVERT: F 9 TRP cc_start: 0.3338 (m-10) cc_final: 0.3011 (m-10) REVERT: F 86 PHE cc_start: 0.5930 (t80) cc_final: 0.5542 (t80) REVERT: F 87 MET cc_start: 0.7706 (mmm) cc_final: 0.7179 (mmm) REVERT: F 125 ARG cc_start: 0.5637 (ttt180) cc_final: 0.5049 (mtt180) REVERT: F 127 ASP cc_start: 0.7211 (p0) cc_final: 0.6980 (p0) REVERT: F 146 ARG cc_start: 0.5291 (mtp180) cc_final: 0.4662 (ttp80) REVERT: F 147 ASN cc_start: 0.7327 (p0) cc_final: 0.6834 (p0) REVERT: F 167 PHE cc_start: 0.6726 (t80) cc_final: 0.6010 (t80) REVERT: G 132 THR cc_start: 0.8051 (m) cc_final: 0.7622 (p) REVERT: H 114 LYS cc_start: 0.6519 (mttt) cc_final: 0.6313 (tttm) REVERT: I 35 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7818 (tp30) REVERT: I 45 PHE cc_start: 0.7077 (m-80) cc_final: 0.6237 (m-80) REVERT: I 66 TYR cc_start: 0.5218 (m-80) cc_final: 0.4222 (m-10) REVERT: I 114 THR cc_start: 0.6726 (p) cc_final: 0.6152 (p) REVERT: L 3 THR cc_start: 0.7187 (m) cc_final: 0.6978 (m) REVERT: L 50 VAL cc_start: 0.6385 (t) cc_final: 0.5896 (p) REVERT: L 55 PRO cc_start: 0.7321 (Cg_endo) cc_final: 0.6652 (Cg_exo) REVERT: L 76 VAL cc_start: 0.7364 (m) cc_final: 0.6759 (p) REVERT: L 77 THR cc_start: 0.7163 (m) cc_final: 0.6449 (p) REVERT: L 102 ASP cc_start: 0.4567 (p0) cc_final: 0.4021 (p0) REVERT: L 130 TYR cc_start: 0.7419 (m-80) cc_final: 0.7155 (m-80) REVERT: M 46 ARG cc_start: 0.5154 (mtt-85) cc_final: 0.4670 (tpp80) REVERT: O 7 ARG cc_start: 0.6463 (tpt170) cc_final: 0.6191 (tpp-160) REVERT: O 8 LYS cc_start: 0.6810 (mtmm) cc_final: 0.6442 (mmtp) REVERT: O 32 LEU cc_start: 0.7702 (mt) cc_final: 0.7414 (mt) REVERT: O 41 GLU cc_start: 0.6249 (tp30) cc_final: 0.5798 (tp30) REVERT: O 46 HIS cc_start: 0.6252 (m90) cc_final: 0.5968 (m90) REVERT: O 56 LEU cc_start: 0.8319 (tt) cc_final: 0.7880 (tp) REVERT: O 69 TYR cc_start: 0.7866 (t80) cc_final: 0.7472 (t80) REVERT: O 81 LEU cc_start: 0.7005 (tp) cc_final: 0.6520 (tp) REVERT: P 60 LEU cc_start: 0.8598 (mt) cc_final: 0.8366 (mm) REVERT: R 49 ILE cc_start: 0.5393 (mt) cc_final: 0.5137 (mt) REVERT: S 25 LYS cc_start: 0.6734 (mtmt) cc_final: 0.6193 (mtpt) REVERT: S 39 VAL cc_start: 0.7514 (p) cc_final: 0.7254 (p) REVERT: S 57 ARG cc_start: 0.6833 (tpp-160) cc_final: 0.6512 (tpp-160) REVERT: T 11 ARG cc_start: 0.5361 (ptp-170) cc_final: 0.4391 (ptp-170) REVERT: T 25 ARG cc_start: 0.7247 (ptp-170) cc_final: 0.6951 (ptp-170) REVERT: T 41 LYS cc_start: 0.6438 (mttt) cc_final: 0.6173 (tptt) REVERT: T 50 TYR cc_start: 0.5850 (p90) cc_final: 0.5448 (p90) REVERT: U 17 TYR cc_start: 0.7300 (t80) cc_final: 0.7041 (t80) REVERT: U 56 TYR cc_start: 0.7470 (m-80) cc_final: 0.6890 (m-80) REVERT: U 60 LEU cc_start: 0.7362 (tp) cc_final: 0.7013 (tp) outliers start: 6 outliers final: 0 residues processed: 506 average time/residue: 0.2865 time to fit residues: 232.4387 Evaluate side-chains 360 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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: 1.9990 chunk 78 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 288 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 264 optimal weight: 0.0980 chunk 300 optimal weight: 7.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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 64 ASN F 112 GLN F 115 ASN H 64 GLN I 57 GLN I 69 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.109513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.091894 restraints weight = 186007.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.091449 restraints weight = 171708.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.092015 restraints weight = 119318.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.091807 restraints weight = 89199.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.092039 restraints weight = 75647.248| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 47053 Z= 0.232 Angle : 0.783 9.142 69749 Z= 0.408 Chirality : 0.045 0.294 8861 Planarity : 0.006 0.054 4164 Dihedral : 24.363 179.244 20906 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Rotamer: Outliers : 0.28 % Allowed : 4.46 % Favored : 95.26 % 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: 0.06 (0.18), residues: 2050 helix: 0.80 (0.16), residues: 932 sheet: -0.41 (0.27), residues: 333 loop : -0.52 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 7 TYR 0.021 0.002 TYR C 371 PHE 0.035 0.003 PHE U 18 TRP 0.025 0.003 TRP C 589 HIS 0.014 0.002 HIS C 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.23 (47053) covalent geometry : angle 0.78267 / 0.41 (69749) hydrogen bonds : bond 0.07768 / 4.62 ( 1731) hydrogen bonds : angle 4.19009 / 2.43 ( 3858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 432 time to evaluate : 1.111 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: 0.6948 (t0) cc_final: 0.6743 (t0) REVERT: C 404 GLN cc_start: 0.5500 (mt0) cc_final: 0.4743 (mt0) REVERT: C 407 ARG cc_start: 0.5619 (ttt180) cc_final: 0.4378 (mtm180) REVERT: C 538 TYR cc_start: 0.4773 (m-80) cc_final: 0.4434 (m-10) REVERT: C 563 TYR cc_start: 0.3830 (t80) cc_final: 0.3328 (t80) REVERT: F 47 TYR cc_start: 0.6993 (t80) cc_final: 0.6149 (t80) REVERT: F 58 ARG cc_start: 0.4794 (ttp80) cc_final: 0.4339 (ttp80) REVERT: F 60 MET cc_start: 0.7251 (ttt) cc_final: 0.7014 (ttt) REVERT: F 64 ASN cc_start: 0.7336 (m-40) cc_final: 0.6054 (m110) REVERT: F 91 ASP cc_start: 0.5667 (t0) cc_final: 0.5242 (t0) REVERT: F 111 ARG cc_start: 0.5968 (ttt-90) cc_final: 0.5700 (ttt-90) REVERT: F 112 GLN cc_start: 0.7459 (tm130) cc_final: 0.7177 (tm-30) REVERT: F 125 ARG cc_start: 0.5429 (ttt180) cc_final: 0.5226 (mtt180) REVERT: F 127 ASP cc_start: 0.7312 (p0) cc_final: 0.7080 (p0) REVERT: F 146 ARG cc_start: 0.5435 (mtp180) cc_final: 0.5003 (ttp80) REVERT: F 182 ARG cc_start: 0.4933 (tpt170) cc_final: 0.4692 (tpm170) REVERT: G 9 LEU cc_start: 0.5942 (mt) cc_final: 0.5724 (mt) REVERT: G 96 LEU cc_start: 0.6911 (mt) cc_final: 0.6673 (mt) REVERT: G 132 THR cc_start: 0.8048 (m) cc_final: 0.7589 (p) REVERT: I 45 PHE cc_start: 0.7309 (m-80) cc_final: 0.6858 (m-80) REVERT: I 62 VAL cc_start: 0.7889 (p) cc_final: 0.7610 (p) REVERT: I 66 TYR cc_start: 0.5731 (m-80) cc_final: 0.5221 (m-80) REVERT: I 114 THR cc_start: 0.6586 (p) cc_final: 0.6108 (p) REVERT: L 21 SER cc_start: 0.4808 (m) cc_final: 0.4361 (p) REVERT: L 25 ASN cc_start: 0.7533 (m-40) cc_final: 0.7182 (m-40) REVERT: L 32 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7730 (tttt) REVERT: L 75 GLU cc_start: 0.6262 (tt0) cc_final: 0.5457 (mp0) REVERT: O 32 LEU cc_start: 0.7926 (mt) cc_final: 0.7575 (mp) REVERT: O 41 GLU cc_start: 0.6659 (tp30) cc_final: 0.6233 (tp30) REVERT: O 45 THR cc_start: 0.8427 (p) cc_final: 0.8028 (p) REVERT: O 46 HIS cc_start: 0.6626 (m90) cc_final: 0.6341 (m90) REVERT: O 81 LEU cc_start: 0.7283 (tp) cc_final: 0.6626 (tp) REVERT: Q 39 ARG cc_start: 0.7471 (mtp85) cc_final: 0.7190 (mtp85) REVERT: Q 79 GLU cc_start: 0.6018 (tm-30) cc_final: 0.5329 (pt0) REVERT: R 49 ILE cc_start: 0.4998 (mt) cc_final: 0.4704 (mt) REVERT: S 71 THR cc_start: 0.7629 (m) cc_final: 0.5369 (m) REVERT: S 75 TYR cc_start: 0.7176 (m-10) cc_final: 0.6903 (m-80) REVERT: T 5 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6167 (tm-30) REVERT: T 9 ILE cc_start: 0.5367 (mt) cc_final: 0.5141 (mt) REVERT: T 41 LYS cc_start: 0.6403 (mttt) cc_final: 0.6052 (tptt) REVERT: T 50 TYR cc_start: 0.6302 (p90) cc_final: 0.5786 (p90) REVERT: U 16 CYS cc_start: 0.7712 (t) cc_final: 0.7040 (t) REVERT: V 108 GLU cc_start: 0.5672 (pm20) cc_final: 0.5401 (mm-30) outliers start: 5 outliers final: 1 residues processed: 432 average time/residue: 0.2854 time to fit residues: 198.1850 Evaluate side-chains 329 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 328 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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: 0.6980 chunk 185 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 167 optimal weight: 0.0970 chunk 34 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 overall best weight: 3.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 286 HIS C 541 GLN F 59 HIS F 115 ASN G 54 GLN G 142 GLN J 66 ASN S 68 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.109936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.091983 restraints weight = 185622.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.091394 restraints weight = 163543.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092507 restraints weight = 112300.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.092166 restraints weight = 85244.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.092359 restraints weight = 70499.708| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 47053 Z= 0.199 Angle : 0.717 12.420 69749 Z= 0.374 Chirality : 0.043 0.296 8861 Planarity : 0.006 0.057 4164 Dihedral : 24.258 178.560 20906 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.39 % Favored : 97.37 % Rotamer: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.99 % 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: 0.90 (0.17), residues: 928 sheet: -0.52 (0.27), residues: 322 loop : -0.52 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 561 TYR 0.031 0.002 TYR I 130 PHE 0.029 0.003 PHE R 74 TRP 0.036 0.004 TRP V 46 HIS 0.011 0.002 HIS C 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.20 (47053) covalent geometry : angle 0.71744 / 0.37 (69749) hydrogen bonds : bond 0.07028 / 4.21 ( 1731) hydrogen bonds : angle 4.08467 / 2.38 ( 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 409 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 408 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 ASN cc_start: 0.6994 (t0) cc_final: 0.6718 (t0) REVERT: C 69 MET cc_start: 0.1263 (tmm) cc_final: 0.1042 (tmm) REVERT: C 407 ARG cc_start: 0.5599 (ttt180) cc_final: 0.4235 (mtm180) REVERT: C 518 ASP cc_start: 0.3467 (m-30) cc_final: 0.2775 (t0) REVERT: C 529 MET cc_start: 0.1999 (mtt) cc_final: 0.1777 (mtt) REVERT: C 535 GLN cc_start: 0.5554 (mt0) cc_final: 0.4786 (mm-40) REVERT: C 563 TYR cc_start: 0.4120 (t80) cc_final: 0.3786 (t80) REVERT: C 604 GLU cc_start: 0.5211 (tt0) cc_final: 0.5000 (mm-30) REVERT: F 47 TYR cc_start: 0.7009 (t80) cc_final: 0.6643 (t80) REVERT: F 60 MET cc_start: 0.7143 (ttt) cc_final: 0.6905 (ttt) REVERT: F 64 ASN cc_start: 0.7297 (m-40) cc_final: 0.7084 (m-40) REVERT: F 125 ARG cc_start: 0.5419 (ttt180) cc_final: 0.5182 (mtt180) REVERT: F 164 TYR cc_start: 0.4832 (p90) cc_final: 0.4612 (p90) REVERT: G 41 ASP cc_start: 0.7713 (m-30) cc_final: 0.7473 (m-30) REVERT: G 96 LEU cc_start: 0.6839 (mt) cc_final: 0.6573 (mt) REVERT: G 127 SER cc_start: 0.6906 (t) cc_final: 0.6500 (p) REVERT: G 132 THR cc_start: 0.8086 (m) cc_final: 0.7535 (p) REVERT: I 35 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7964 (mm-30) REVERT: I 45 PHE cc_start: 0.7450 (m-80) cc_final: 0.6922 (m-80) REVERT: I 63 PHE cc_start: 0.6772 (m-10) cc_final: 0.6572 (m-10) REVERT: I 66 TYR cc_start: 0.5751 (m-80) cc_final: 0.5512 (m-80) REVERT: I 117 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6718 (mm-30) REVERT: L 75 GLU cc_start: 0.6058 (tt0) cc_final: 0.5267 (mp0) REVERT: L 76 VAL cc_start: 0.7256 (m) cc_final: 0.6834 (t) REVERT: O 32 LEU cc_start: 0.7831 (mt) cc_final: 0.7596 (mt) REVERT: O 33 THR cc_start: 0.7872 (p) cc_final: 0.7660 (p) REVERT: O 41 GLU cc_start: 0.6691 (tp30) cc_final: 0.6466 (tp30) REVERT: O 45 THR cc_start: 0.8462 (p) cc_final: 0.8187 (p) REVERT: O 46 HIS cc_start: 0.6640 (m90) cc_final: 0.6394 (m90) REVERT: O 81 LEU cc_start: 0.7135 (tp) cc_final: 0.6811 (tp) REVERT: Q 18 LYS cc_start: 0.8747 (mttt) cc_final: 0.7674 (tptp) REVERT: R 49 ILE cc_start: 0.5078 (mt) cc_final: 0.4774 (mt) REVERT: R 79 THR cc_start: 0.3827 (m) cc_final: 0.3573 (m) REVERT: S 32 ILE cc_start: 0.8042 (mm) cc_final: 0.7804 (mm) REVERT: T 78 LEU cc_start: 0.7658 (tp) cc_final: 0.7175 (pp) REVERT: U 16 CYS cc_start: 0.7324 (t) cc_final: 0.6788 (t) REVERT: U 64 ILE cc_start: 0.7595 (mm) cc_final: 0.7067 (mm) REVERT: V 67 MET cc_start: 0.4429 (ttm) cc_final: 0.3173 (tmm) REVERT: V 89 LYS cc_start: 0.6050 (mptt) cc_final: 0.5731 (tptp) outliers start: 1 outliers final: 0 residues processed: 408 average time/residue: 0.2832 time to fit residues: 185.9580 Evaluate side-chains 306 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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: 3.9990 chunk 86 optimal weight: 10.0000 chunk 239 optimal weight: 0.2980 chunk 180 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 115 ASN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 ASN O 13 ASN O 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.109435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.090837 restraints weight = 186180.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090295 restraints weight = 167845.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.091459 restraints weight = 114867.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.091331 restraints weight = 77682.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091363 restraints weight = 71171.321| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 47053 Z= 0.206 Angle : 0.726 10.089 69749 Z= 0.375 Chirality : 0.042 0.301 8861 Planarity : 0.006 0.074 4164 Dihedral : 24.246 179.781 20906 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.22 % Favored : 96.54 % Rotamer: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % 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: -0.06 (0.18), residues: 2050 helix: 0.76 (0.16), residues: 930 sheet: -0.64 (0.26), residues: 328 loop : -0.58 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 39 TYR 0.028 0.002 TYR C 19 PHE 0.033 0.003 PHE R 74 TRP 0.016 0.002 TRP T 43 HIS 0.014 0.002 HIS C 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.21 (47053) covalent geometry : angle 0.72639 / 0.38 (69749) hydrogen bonds : bond 0.07273 / 4.35 ( 1731) hydrogen bonds : angle 4.15016 / 2.42 ( 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 400 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 399 time to evaluate : 0.979 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 32 ASN cc_start: 0.6941 (t0) cc_final: 0.6709 (t0) REVERT: C 399 MET cc_start: 0.1299 (ttm) cc_final: 0.0764 (tmm) REVERT: C 407 ARG cc_start: 0.5796 (ttt180) cc_final: 0.3973 (mtm180) REVERT: C 518 ASP cc_start: 0.3172 (m-30) cc_final: 0.2510 (t0) REVERT: C 529 MET cc_start: 0.1934 (mtt) cc_final: 0.1725 (mtt) REVERT: C 533 MET cc_start: 0.3420 (ppp) cc_final: 0.3215 (ptm) REVERT: C 560 ILE cc_start: 0.5884 (mp) cc_final: 0.5586 (mp) REVERT: C 563 TYR cc_start: 0.4189 (t80) cc_final: 0.3722 (t80) REVERT: F 64 ASN cc_start: 0.6859 (m-40) cc_final: 0.6416 (m-40) REVERT: F 125 ARG cc_start: 0.5521 (ttt180) cc_final: 0.5300 (mtt180) REVERT: G 96 LEU cc_start: 0.6817 (mt) cc_final: 0.6582 (mt) REVERT: G 127 SER cc_start: 0.6963 (t) cc_final: 0.6484 (p) REVERT: G 130 SER cc_start: 0.6448 (t) cc_final: 0.5935 (t) REVERT: G 132 THR cc_start: 0.8091 (m) cc_final: 0.7458 (p) REVERT: H 119 ARG cc_start: 0.4649 (tpp80) cc_final: 0.4299 (ttm-80) REVERT: I 34 ARG cc_start: 0.7109 (ttm170) cc_final: 0.6277 (mtt180) REVERT: I 45 PHE cc_start: 0.7266 (m-80) cc_final: 0.6859 (m-80) REVERT: I 114 THR cc_start: 0.6423 (p) cc_final: 0.5990 (p) REVERT: J 98 LEU cc_start: 0.6381 (mm) cc_final: 0.5798 (tp) REVERT: L 17 GLU cc_start: 0.5924 (tt0) cc_final: 0.5623 (tp30) REVERT: L 55 PRO cc_start: 0.6942 (Cg_endo) cc_final: 0.6710 (Cg_exo) REVERT: L 75 GLU cc_start: 0.6018 (tt0) cc_final: 0.5189 (mp0) REVERT: L 76 VAL cc_start: 0.7109 (m) cc_final: 0.6752 (t) REVERT: O 19 GLU cc_start: 0.6989 (mp0) cc_final: 0.6013 (tt0) REVERT: O 32 LEU cc_start: 0.7925 (mt) cc_final: 0.7661 (mp) REVERT: O 41 GLU cc_start: 0.6798 (tp30) cc_final: 0.6240 (tp30) REVERT: O 53 ARG cc_start: 0.7715 (mtp85) cc_final: 0.6721 (tpt170) REVERT: O 56 LEU cc_start: 0.8308 (tt) cc_final: 0.8093 (tp) REVERT: O 81 LEU cc_start: 0.6579 (tp) cc_final: 0.6223 (tp) REVERT: P 50 LYS cc_start: 0.6856 (mptt) cc_final: 0.6485 (mptt) REVERT: Q 18 LYS cc_start: 0.8811 (mttt) cc_final: 0.7701 (tptt) REVERT: Q 79 GLU cc_start: 0.6780 (tp30) cc_final: 0.5809 (pt0) REVERT: R 49 ILE cc_start: 0.5018 (mt) cc_final: 0.4644 (mt) REVERT: R 79 THR cc_start: 0.4097 (m) cc_final: 0.3838 (m) REVERT: S 75 TYR cc_start: 0.7105 (m-80) cc_final: 0.6843 (m-80) REVERT: T 5 GLU cc_start: 0.7511 (tm-30) cc_final: 0.6415 (tm-30) REVERT: T 78 LEU cc_start: 0.7679 (tp) cc_final: 0.7158 (pp) REVERT: U 16 CYS cc_start: 0.7531 (t) cc_final: 0.6894 (t) REVERT: V 46 TRP cc_start: 0.0339 (p90) cc_final: -0.0571 (p90) REVERT: V 89 LYS cc_start: 0.5946 (mptt) cc_final: 0.5681 (mptt) REVERT: V 107 LEU cc_start: 0.7124 (mm) cc_final: 0.6888 (mt) outliers start: 1 outliers final: 0 residues processed: 399 average time/residue: 0.2860 time to fit residues: 183.2427 Evaluate side-chains 321 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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: 0.5980 chunk 312 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 307 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 569 HIS ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 112 GLN F 115 ASN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS L 42 GLN M 32 GLN T 73 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.108871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.090954 restraints weight = 187057.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.090571 restraints weight = 154220.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.091320 restraints weight = 109138.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.091199 restraints weight = 81485.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091357 restraints weight = 69452.312| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 47053 Z= 0.226 Angle : 0.751 10.113 69749 Z= 0.386 Chirality : 0.043 0.321 8861 Planarity : 0.006 0.062 4164 Dihedral : 24.258 177.368 20906 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.56 % Favored : 96.20 % Rotamer: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % 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: -0.36 (0.18), residues: 2050 helix: 0.53 (0.16), residues: 914 sheet: -0.71 (0.26), residues: 324 loop : -0.80 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 106 TYR 0.036 0.003 TYR Q 36 PHE 0.033 0.003 PHE F 86 TRP 0.011 0.002 TRP R 34 HIS 0.022 0.002 HIS R 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.23 (47053) covalent geometry : angle 0.75077 / 0.39 (69749) hydrogen bonds : bond 0.07486 / 4.49 ( 1731) hydrogen bonds : angle 4.30296 / 2.51 ( 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 385 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 384 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 407 ARG cc_start: 0.5544 (ttt180) cc_final: 0.3944 (mtm180) REVERT: C 518 ASP cc_start: 0.3231 (m-30) cc_final: 0.2414 (t0) REVERT: C 560 ILE cc_start: 0.6194 (mp) cc_final: 0.5889 (mp) REVERT: F 125 ARG cc_start: 0.5740 (ttt180) cc_final: 0.5411 (mtt180) REVERT: F 153 GLU cc_start: 0.6628 (pt0) cc_final: 0.6313 (tm-30) REVERT: G 33 PHE cc_start: 0.5574 (m-80) cc_final: 0.5227 (m-80) REVERT: G 36 LEU cc_start: 0.6388 (tp) cc_final: 0.6134 (tp) REVERT: G 127 SER cc_start: 0.6881 (t) cc_final: 0.6448 (p) REVERT: G 130 SER cc_start: 0.6454 (t) cc_final: 0.5945 (t) REVERT: G 132 THR cc_start: 0.8148 (m) cc_final: 0.7566 (p) REVERT: I 66 TYR cc_start: 0.5840 (m-80) cc_final: 0.5287 (m-10) REVERT: I 117 GLU cc_start: 0.6835 (pt0) cc_final: 0.6575 (mp0) REVERT: L 55 PRO cc_start: 0.6978 (Cg_endo) cc_final: 0.6737 (Cg_exo) REVERT: L 75 GLU cc_start: 0.6117 (tt0) cc_final: 0.5271 (mp0) REVERT: L 76 VAL cc_start: 0.6987 (m) cc_final: 0.6707 (t) REVERT: L 95 ILE cc_start: 0.7847 (pt) cc_final: 0.7578 (pt) REVERT: O 19 GLU cc_start: 0.7044 (mp0) cc_final: 0.6038 (tt0) REVERT: O 32 LEU cc_start: 0.7996 (mt) cc_final: 0.7563 (mt) REVERT: O 41 GLU cc_start: 0.6865 (tp30) cc_final: 0.6344 (tp30) REVERT: O 53 ARG cc_start: 0.7772 (mtp85) cc_final: 0.6754 (tpt170) REVERT: O 56 LEU cc_start: 0.8326 (tt) cc_final: 0.8126 (tp) REVERT: O 81 LEU cc_start: 0.6916 (tp) cc_final: 0.6487 (tp) REVERT: Q 18 LYS cc_start: 0.8859 (mttt) cc_final: 0.7801 (tptp) REVERT: Q 39 ARG cc_start: 0.7912 (mtp-110) cc_final: 0.7651 (mtp85) REVERT: Q 79 GLU cc_start: 0.6998 (tp30) cc_final: 0.5789 (pt0) REVERT: R 49 ILE cc_start: 0.4794 (mt) cc_final: 0.4436 (mt) REVERT: R 79 THR cc_start: 0.4410 (m) cc_final: 0.4135 (m) REVERT: S 75 TYR cc_start: 0.7215 (m-80) cc_final: 0.6409 (m-80) REVERT: T 41 LYS cc_start: 0.6572 (mttt) cc_final: 0.6045 (tppt) REVERT: T 78 LEU cc_start: 0.7680 (tp) cc_final: 0.7190 (pp) REVERT: U 16 CYS cc_start: 0.7588 (t) cc_final: 0.6882 (t) REVERT: V 46 TRP cc_start: 0.0297 (p90) cc_final: -0.0293 (p90) REVERT: V 63 PHE cc_start: 0.6294 (t80) cc_final: 0.6051 (t80) outliers start: 1 outliers final: 1 residues processed: 384 average time/residue: 0.2821 time to fit residues: 175.1906 Evaluate side-chains 312 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 ASN C 356 HIS ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN F 112 GLN F 115 ASN G 45 HIS ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 65 ASN O 72 ASN ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.109916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.092098 restraints weight = 184824.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.091599 restraints weight = 157275.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.092370 restraints weight = 116769.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.092279 restraints weight = 81946.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.092351 restraints weight = 75573.847| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 47053 Z= 0.173 Angle : 0.684 12.171 69749 Z= 0.355 Chirality : 0.040 0.345 8861 Planarity : 0.006 0.104 4164 Dihedral : 24.185 178.055 20906 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.27 % Favored : 96.44 % Rotamer: Outliers : 0.06 % Allowed : 1.73 % Favored : 98.22 % 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: -0.17 (0.18), residues: 2050 helix: 0.71 (0.17), residues: 915 sheet: -0.67 (0.26), residues: 330 loop : -0.71 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 106 TYR 0.028 0.002 TYR L 65 PHE 0.031 0.002 PHE C 451 TRP 0.009 0.001 TRP R 34 HIS 0.014 0.002 HIS R 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (47053) covalent geometry : angle 0.68392 / 0.35 (69749) hydrogen bonds : bond 0.06849 / 4.12 ( 1731) hydrogen bonds : angle 4.22925 / 2.46 ( 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 384 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 320 MET cc_start: 0.5440 (tpt) cc_final: 0.5217 (tpt) REVERT: C 399 MET cc_start: 0.2398 (tpt) cc_final: 0.2075 (tpp) REVERT: C 407 ARG cc_start: 0.5464 (ttt180) cc_final: 0.3678 (mtm180) REVERT: C 560 ILE cc_start: 0.6347 (mp) cc_final: 0.6043 (mp) REVERT: C 563 TYR cc_start: 0.4243 (t80) cc_final: 0.3836 (t80) REVERT: F 125 ARG cc_start: 0.5565 (ttt180) cc_final: 0.5254 (mtt180) REVERT: G 33 PHE cc_start: 0.5584 (m-80) cc_final: 0.5226 (m-80) REVERT: G 112 ARG cc_start: 0.4833 (mtp85) cc_final: 0.4610 (mtp85) REVERT: G 127 SER cc_start: 0.6957 (t) cc_final: 0.6559 (p) REVERT: G 130 SER cc_start: 0.6385 (t) cc_final: 0.6013 (t) REVERT: G 132 THR cc_start: 0.8180 (m) cc_final: 0.7597 (p) REVERT: I 45 PHE cc_start: 0.7283 (m-80) cc_final: 0.6880 (m-80) REVERT: I 66 TYR cc_start: 0.5925 (m-80) cc_final: 0.5262 (m-10) REVERT: I 117 GLU cc_start: 0.6931 (pt0) cc_final: 0.6458 (mp0) REVERT: J 98 LEU cc_start: 0.6680 (mm) cc_final: 0.6356 (tp) REVERT: L 75 GLU cc_start: 0.6152 (tt0) cc_final: 0.5314 (pm20) REVERT: O 19 GLU cc_start: 0.6823 (mp0) cc_final: 0.6079 (tt0) REVERT: O 41 GLU cc_start: 0.6819 (tp30) cc_final: 0.6601 (tp30) REVERT: O 53 ARG cc_start: 0.7746 (mtp85) cc_final: 0.6640 (tpt170) REVERT: O 56 LEU cc_start: 0.8325 (tt) cc_final: 0.8057 (tp) REVERT: P 4 LYS cc_start: 0.5415 (tptm) cc_final: 0.5070 (tptp) REVERT: P 58 LYS cc_start: 0.7559 (tttt) cc_final: 0.7175 (tptp) REVERT: Q 79 GLU cc_start: 0.6782 (tp30) cc_final: 0.5737 (pt0) REVERT: R 49 ILE cc_start: 0.4703 (mt) cc_final: 0.4307 (mt) REVERT: R 79 THR cc_start: 0.4366 (m) cc_final: 0.4103 (m) REVERT: S 75 TYR cc_start: 0.7194 (m-80) cc_final: 0.6483 (m-80) REVERT: T 41 LYS cc_start: 0.6515 (mttt) cc_final: 0.6017 (tppt) REVERT: T 46 ARG cc_start: 0.7098 (mtp180) cc_final: 0.6364 (ptp-170) REVERT: T 50 TYR cc_start: 0.6649 (p90) cc_final: 0.6381 (p90) REVERT: T 78 LEU cc_start: 0.7679 (tp) cc_final: 0.7062 (pp) REVERT: U 16 CYS cc_start: 0.7627 (t) cc_final: 0.7009 (t) REVERT: V 46 TRP cc_start: 0.0336 (p90) cc_final: -0.0436 (p90) REVERT: V 63 PHE cc_start: 0.6287 (t80) cc_final: 0.5998 (t80) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.2836 time to fit residues: 175.4545 Evaluate side-chains 307 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 103 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 170 optimal weight: 0.0370 chunk 90 optimal weight: 20.0000 chunk 306 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 chunk 268 optimal weight: 0.8980 chunk 313 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 311 optimal weight: 2.9990 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 356 HIS C 555 HIS ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 112 GLN F 115 ASN G 54 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.110143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.091004 restraints weight = 185329.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.090774 restraints weight = 140772.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091525 restraints weight = 93339.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.091562 restraints weight = 81607.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091641 restraints weight = 71276.190| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 47053 Z= 0.174 Angle : 0.680 11.679 69749 Z= 0.351 Chirality : 0.040 0.357 8861 Planarity : 0.005 0.097 4164 Dihedral : 24.139 179.149 20906 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.32 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -0.20 (0.18), residues: 2050 helix: 0.71 (0.17), residues: 915 sheet: -0.60 (0.26), residues: 327 loop : -0.79 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 106 TYR 0.027 0.002 TYR C 538 PHE 0.025 0.002 PHE C 451 TRP 0.009 0.001 TRP R 34 HIS 0.008 0.001 HIS C 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (47053) covalent geometry : angle 0.68048 / 0.35 (69749) hydrogen bonds : bond 0.06830 / 4.09 ( 1731) hydrogen bonds : angle 4.19328 / 2.43 ( 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 361 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 MET cc_start: 0.1542 (tmm) cc_final: 0.1169 (tmm) REVERT: C 399 MET cc_start: 0.2019 (tpt) cc_final: 0.1737 (tpp) REVERT: C 407 ARG cc_start: 0.5212 (ttt180) cc_final: 0.3640 (mtm180) REVERT: C 545 HIS cc_start: 0.0690 (t-90) cc_final: 0.0488 (t-90) REVERT: C 560 ILE cc_start: 0.6327 (mp) cc_final: 0.6086 (mp) REVERT: C 563 TYR cc_start: 0.3909 (t80) cc_final: 0.3531 (t80) REVERT: C 603 MET cc_start: 0.4627 (mpp) cc_final: 0.4382 (mmm) REVERT: F 64 ASN cc_start: 0.6979 (m-40) cc_final: 0.6621 (m-40) REVERT: F 125 ARG cc_start: 0.5597 (ttt180) cc_final: 0.5250 (mtt180) REVERT: G 33 PHE cc_start: 0.5520 (m-80) cc_final: 0.5218 (m-80) REVERT: G 112 ARG cc_start: 0.5053 (mtp85) cc_final: 0.4801 (mtp85) REVERT: G 127 SER cc_start: 0.6928 (t) cc_final: 0.6466 (p) REVERT: G 130 SER cc_start: 0.6442 (t) cc_final: 0.6029 (t) REVERT: G 132 THR cc_start: 0.8153 (m) cc_final: 0.7585 (p) REVERT: I 66 TYR cc_start: 0.5790 (m-80) cc_final: 0.5227 (m-10) REVERT: I 117 GLU cc_start: 0.6957 (pt0) cc_final: 0.6489 (mp0) REVERT: J 98 LEU cc_start: 0.6490 (mm) cc_final: 0.6148 (tp) REVERT: L 75 GLU cc_start: 0.6443 (tt0) cc_final: 0.5479 (pm20) REVERT: O 19 GLU cc_start: 0.6856 (mp0) cc_final: 0.6138 (tt0) REVERT: O 41 GLU cc_start: 0.6797 (tp30) cc_final: 0.6582 (tp30) REVERT: O 53 ARG cc_start: 0.7817 (mtp85) cc_final: 0.6579 (tpt170) REVERT: O 56 LEU cc_start: 0.8218 (tt) cc_final: 0.8014 (tp) REVERT: P 4 LYS cc_start: 0.5122 (tptm) cc_final: 0.4820 (tptp) REVERT: P 67 SER cc_start: 0.8670 (m) cc_final: 0.8461 (m) REVERT: Q 18 LYS cc_start: 0.8977 (mttt) cc_final: 0.7655 (tptp) REVERT: Q 22 THR cc_start: 0.7505 (m) cc_final: 0.7142 (m) REVERT: Q 79 GLU cc_start: 0.6858 (tp30) cc_final: 0.5777 (pt0) REVERT: R 49 ILE cc_start: 0.4312 (mt) cc_final: 0.3963 (mt) REVERT: S 75 TYR cc_start: 0.7208 (m-80) cc_final: 0.6451 (m-80) REVERT: T 5 GLU cc_start: 0.7783 (tm-30) cc_final: 0.6657 (tm-30) REVERT: T 41 LYS cc_start: 0.6444 (mttt) cc_final: 0.5964 (tppt) REVERT: T 50 TYR cc_start: 0.6562 (p90) cc_final: 0.6338 (p90) REVERT: T 78 LEU cc_start: 0.7601 (tp) cc_final: 0.7043 (pp) REVERT: U 16 CYS cc_start: 0.7636 (t) cc_final: 0.6962 (t) REVERT: U 52 THR cc_start: 0.6675 (t) cc_final: 0.6453 (t) REVERT: V 46 TRP cc_start: 0.0437 (p90) cc_final: -0.0467 (p90) REVERT: V 63 PHE cc_start: 0.6420 (t80) cc_final: 0.6202 (t80) REVERT: V 107 LEU cc_start: 0.7172 (mm) cc_final: 0.6970 (mt) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.2718 time to fit residues: 160.6357 Evaluate side-chains 295 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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: 5.9990 chunk 234 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 312 optimal weight: 7.9990 chunk 229 optimal weight: 20.0000 chunk 323 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 285 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 ASN ** C 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN F 112 GLN F 115 ASN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN O 9 ASN O 65 ASN P 72 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.107858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.090088 restraints weight = 186693.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.089476 restraints weight = 167326.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090294 restraints weight = 122328.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.090173 restraints weight = 93757.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.090384 restraints weight = 83351.965| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 47053 Z= 0.282 Angle : 0.844 10.813 69749 Z= 0.429 Chirality : 0.046 0.356 8861 Planarity : 0.007 0.100 4164 Dihedral : 24.350 176.705 20906 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.88 % Favored : 94.93 % Rotamer: Outliers : 0.06 % Allowed : 1.34 % Favored : 98.61 % 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: -0.87 (0.18), residues: 2050 helix: 0.11 (0.16), residues: 905 sheet: -0.69 (0.27), residues: 321 loop : -1.19 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 439 TYR 0.031 0.003 TYR I 130 PHE 0.030 0.004 PHE R 74 TRP 0.027 0.003 TRP R 34 HIS 0.014 0.002 HIS C 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.28 (47053) covalent geometry : angle 0.84385 / 0.43 (69749) hydrogen bonds : bond 0.08497 / 5.06 ( 1731) hydrogen bonds : angle 4.73769 / 2.70 ( 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 370 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 369 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 MET cc_start: 0.1883 (tmm) cc_final: 0.1510 (tmm) REVERT: C 399 MET cc_start: 0.2275 (tpt) cc_final: 0.1816 (tpp) REVERT: C 407 ARG cc_start: 0.5279 (ttt180) cc_final: 0.3921 (mtm180) REVERT: C 473 ARG cc_start: 0.4536 (tpt170) cc_final: 0.3474 (mmt180) REVERT: C 538 TYR cc_start: 0.5130 (m-10) cc_final: 0.4177 (m-10) REVERT: C 563 TYR cc_start: 0.4463 (t80) cc_final: 0.4140 (t80) REVERT: C 603 MET cc_start: 0.4822 (mpp) cc_final: 0.4377 (mmm) REVERT: C 604 GLU cc_start: 0.5313 (tt0) cc_final: 0.4809 (tt0) REVERT: F 64 ASN cc_start: 0.6929 (m-40) cc_final: 0.6549 (m-40) REVERT: F 125 ARG cc_start: 0.5682 (ttt180) cc_final: 0.5369 (mtt180) REVERT: G 33 PHE cc_start: 0.5484 (m-80) cc_final: 0.5235 (m-80) REVERT: G 36 LEU cc_start: 0.6544 (tp) cc_final: 0.6336 (tp) REVERT: G 127 SER cc_start: 0.6912 (t) cc_final: 0.6493 (p) REVERT: G 130 SER cc_start: 0.6579 (t) cc_final: 0.6110 (t) REVERT: G 132 THR cc_start: 0.8189 (m) cc_final: 0.7556 (p) REVERT: I 21 ARG cc_start: 0.6853 (mtt-85) cc_final: 0.6306 (mtm180) REVERT: I 63 PHE cc_start: 0.6289 (m-80) cc_final: 0.5835 (t80) REVERT: I 66 TYR cc_start: 0.6029 (m-80) cc_final: 0.5430 (m-10) REVERT: I 117 GLU cc_start: 0.7105 (pt0) cc_final: 0.6540 (mp0) REVERT: J 103 LEU cc_start: 0.6211 (mt) cc_final: 0.4909 (tp) REVERT: L 75 GLU cc_start: 0.6043 (tt0) cc_final: 0.5419 (pm20) REVERT: L 77 THR cc_start: 0.7481 (m) cc_final: 0.6688 (p) REVERT: M 11 ARG cc_start: 0.3349 (mpp80) cc_final: 0.2884 (mtt90) REVERT: O 12 ILE cc_start: 0.5789 (pt) cc_final: 0.5580 (pt) REVERT: O 19 GLU cc_start: 0.7024 (mp0) cc_final: 0.6201 (tt0) REVERT: P 67 SER cc_start: 0.8941 (m) cc_final: 0.8627 (m) REVERT: Q 19 MET cc_start: 0.7606 (ptp) cc_final: 0.7157 (ptp) REVERT: R 34 TRP cc_start: 0.0218 (m-90) cc_final: -0.0157 (m-90) REVERT: R 49 ILE cc_start: 0.4524 (mt) cc_final: 0.4219 (mt) REVERT: S 75 TYR cc_start: 0.7353 (m-80) cc_final: 0.6623 (m-80) REVERT: T 5 GLU cc_start: 0.7798 (tm-30) cc_final: 0.6672 (tm-30) REVERT: T 25 ARG cc_start: 0.7140 (ptt180) cc_final: 0.6549 (ptt90) REVERT: T 41 LYS cc_start: 0.6485 (mttt) cc_final: 0.5936 (tppt) REVERT: T 46 ARG cc_start: 0.6920 (mtp180) cc_final: 0.5628 (mtp85) REVERT: T 55 PHE cc_start: 0.3840 (m-10) cc_final: 0.3075 (m-80) REVERT: U 16 CYS cc_start: 0.7560 (t) cc_final: 0.6836 (t) REVERT: V 46 TRP cc_start: 0.0275 (p90) cc_final: -0.0366 (p90) REVERT: V 63 PHE cc_start: 0.6472 (t80) cc_final: 0.6122 (t80) outliers start: 1 outliers final: 0 residues processed: 369 average time/residue: 0.2729 time to fit residues: 164.0948 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 : 1.032 ------------------------------------------------------------------------------- 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: 0.2980 chunk 203 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 315 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 135 optimal weight: 0.2980 chunk 284 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 541 GLN F 109 GLN F 115 ASN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.109786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091696 restraints weight = 185966.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.091380 restraints weight = 158795.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.091634 restraints weight = 105297.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091795 restraints weight = 90317.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091806 restraints weight = 88451.726| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 47053 Z= 0.183 Angle : 0.710 14.790 69749 Z= 0.366 Chirality : 0.041 0.347 8861 Planarity : 0.006 0.097 4164 Dihedral : 24.240 178.069 20906 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.56 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.18), residues: 2050 helix: 0.27 (0.16), residues: 917 sheet: -0.61 (0.27), residues: 323 loop : -1.21 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 13 TYR 0.037 0.003 TYR O 78 PHE 0.024 0.002 PHE R 74 TRP 0.019 0.002 TRP F 9 HIS 0.013 0.002 HIS C 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (47053) covalent geometry : angle 0.70957 / 0.37 (69749) hydrogen bonds : bond 0.07144 / 4.28 ( 1731) hydrogen bonds : angle 4.42668 / 2.54 ( 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 371 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 MET cc_start: 0.1830 (tmm) cc_final: 0.1500 (tmm) REVERT: C 320 MET cc_start: 0.4714 (tpt) cc_final: 0.4005 (mmm) REVERT: C 345 MET cc_start: 0.0889 (tpp) cc_final: 0.0220 (mpp) REVERT: C 399 MET cc_start: 0.2025 (tpt) cc_final: 0.1680 (tpp) REVERT: C 407 ARG cc_start: 0.5226 (ttt180) cc_final: 0.3912 (mtm180) REVERT: C 472 TYR cc_start: 0.0973 (m-10) cc_final: -0.0643 (m-80) REVERT: C 473 ARG cc_start: 0.4328 (tpt170) cc_final: 0.3505 (mmt90) REVERT: C 538 TYR cc_start: 0.5117 (m-10) cc_final: 0.3886 (m-10) REVERT: C 603 MET cc_start: 0.4845 (mpp) cc_final: 0.4379 (mmm) REVERT: C 604 GLU cc_start: 0.5427 (tt0) cc_final: 0.5053 (tt0) REVERT: F 64 ASN cc_start: 0.7018 (m-40) cc_final: 0.6661 (m-40) REVERT: F 125 ARG cc_start: 0.5640 (ttt180) cc_final: 0.5435 (mtt180) REVERT: F 134 LYS cc_start: 0.7121 (tppt) cc_final: 0.6522 (mttt) REVERT: G 127 SER cc_start: 0.6914 (t) cc_final: 0.6494 (p) REVERT: G 130 SER cc_start: 0.6571 (t) cc_final: 0.6182 (t) REVERT: G 132 THR cc_start: 0.8239 (m) cc_final: 0.7635 (p) REVERT: H 30 MET cc_start: 0.3815 (mmt) cc_final: 0.3331 (mmm) REVERT: I 66 TYR cc_start: 0.6103 (m-80) cc_final: 0.5234 (m-10) REVERT: I 117 GLU cc_start: 0.6878 (pt0) cc_final: 0.6445 (mp0) REVERT: J 103 LEU cc_start: 0.6103 (mt) cc_final: 0.4687 (tp) REVERT: L 75 GLU cc_start: 0.5865 (tt0) cc_final: 0.5400 (pm20) REVERT: L 76 VAL cc_start: 0.6970 (m) cc_final: 0.6526 (t) REVERT: L 77 THR cc_start: 0.7114 (m) cc_final: 0.5967 (p) REVERT: L 95 ILE cc_start: 0.7891 (pt) cc_final: 0.7675 (pt) REVERT: M 11 ARG cc_start: 0.3310 (mpp80) cc_final: 0.2909 (mtt90) REVERT: O 19 GLU cc_start: 0.6882 (mp0) cc_final: 0.6161 (tt0) REVERT: O 32 LEU cc_start: 0.7899 (mt) cc_final: 0.7410 (mp) REVERT: O 46 HIS cc_start: 0.6444 (m90) cc_final: 0.6182 (m90) REVERT: P 50 LYS cc_start: 0.7671 (tmmt) cc_final: 0.7032 (mttp) REVERT: Q 19 MET cc_start: 0.7634 (ptp) cc_final: 0.7181 (ptp) REVERT: Q 54 GLN cc_start: 0.7558 (mp10) cc_final: 0.7220 (mp10) REVERT: R 34 TRP cc_start: -0.0180 (m-90) cc_final: -0.0524 (m-90) REVERT: R 49 ILE cc_start: 0.4611 (mt) cc_final: 0.4304 (mt) REVERT: S 75 TYR cc_start: 0.7365 (m-80) cc_final: 0.6595 (m-80) REVERT: T 5 GLU cc_start: 0.7992 (tm-30) cc_final: 0.6794 (tm-30) REVERT: T 25 ARG cc_start: 0.7077 (ptt180) cc_final: 0.6710 (ptt90) REVERT: T 41 LYS cc_start: 0.6358 (mttt) cc_final: 0.5918 (tptt) REVERT: T 46 ARG cc_start: 0.6654 (mtp180) cc_final: 0.5353 (mtp85) REVERT: U 16 CYS cc_start: 0.7510 (t) cc_final: 0.6817 (t) REVERT: V 46 TRP cc_start: 0.0245 (p90) cc_final: -0.0614 (p90) REVERT: V 63 PHE cc_start: 0.6463 (t80) cc_final: 0.6238 (t80) REVERT: V 107 LEU cc_start: 0.7348 (mm) cc_final: 0.7081 (mp) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.2745 time to fit residues: 166.5205 Evaluate side-chains 305 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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: 6.9990 chunk 240 optimal weight: 0.0980 chunk 306 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 chunk 126 optimal weight: 0.0570 chunk 211 optimal weight: 0.0020 chunk 143 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 226 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 229 optimal weight: 0.9980 overall best weight: 1.0308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 510 GLN F 115 ASN G 45 HIS G 54 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN ** 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 = 0.3923 r_free = 0.3923 target = 0.112443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.094395 restraints weight = 186019.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094260 restraints weight = 156973.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.094695 restraints weight = 109326.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.094986 restraints weight = 87890.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.095154 restraints weight = 73588.133| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.7027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 47053 Z= 0.131 Angle : 0.635 11.403 69749 Z= 0.328 Chirality : 0.038 0.346 8861 Planarity : 0.005 0.057 4164 Dihedral : 24.053 179.184 20906 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.02 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2050 helix: 0.69 (0.16), residues: 919 sheet: -0.43 (0.28), residues: 310 loop : -0.95 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG T 46 TYR 0.037 0.002 TYR L 65 PHE 0.027 0.002 PHE G 33 TRP 0.030 0.002 TRP F 9 HIS 0.017 0.002 HIS O 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (47053) covalent geometry : angle 0.63511 / 0.33 (69749) hydrogen bonds : bond 0.06275 / 3.74 ( 1731) hydrogen bonds : angle 4.17016 / 2.43 ( 3858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6538.71 seconds wall clock time: 115 minutes 20.69 seconds (6920.69 seconds total)