Starting phenix.real_space_refine on Tue Nov 19 02:32:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdu_16595/11_2024/8cdu_16595.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdu_16595/11_2024/8cdu_16595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdu_16595/11_2024/8cdu_16595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdu_16595/11_2024/8cdu_16595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdu_16595/11_2024/8cdu_16595.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdu_16595/11_2024/8cdu_16595.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 1340 5.49 5 S 71 5.16 5 C 27407 2.51 5 N 9534 2.21 5 O 13612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 186 residue(s): 2.60s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 51964 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 28597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 28597 Classifications: {'RNA': 1333} Modifications used: {'rna2p_pur': 113, 'rna2p_pyr': 81, 'rna3p_pur': 643, 'rna3p_pyr': 496} Link IDs: {'rna2p': 194, 'rna3p': 1138} Chain breaks: 3 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 154 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "C" Number of atoms: 5650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5650 Classifications: {'peptide': 708} Link IDs: {'PTRANS': 27, 'TRANS': 680} Chain: "D" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1757 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "E" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1615 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 3, 'TRANS': 201} 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: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1181 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} 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: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} 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: "N" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} 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: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 93} 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: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 730 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "K" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 761 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Time building chain proxies: 27.17, per 1000 atoms: 0.52 Number of scatterers: 51964 At special positions: 0 Unit cell: (191.2, 220.8, 205.6, 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 71 16.00 P 1340 15.00 O 13612 8.00 N 9534 7.00 C 27407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 27 " distance=2.06 Simple disulfide: pdb=" SG CYS N 27 " - pdb=" SG CYS N 43 " distance=2.06 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: 10.48 Conformation dependent library (CDL) restraints added in 3.3 seconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5444 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 32 sheets defined 42.2% alpha, 19.0% beta 418 base pairs and 795 stacking pairs defined. Time for finding SS restraints: 23.39 Creating SS restraints... Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.501A pdb=" N GLU C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 31 removed outlier: 3.631A pdb=" N GLU C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C 29 " --> pdb=" O GLN C 25 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 removed outlier: 4.066A pdb=" N VAL C 43 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LYS C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 removed outlier: 4.235A pdb=" N LEU C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.229A 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 414 Processing helix chain 'C' and resid 442 through 467 Processing helix chain 'C' and resid 479 through 490 Processing helix chain 'C' and resid 505 through 516 removed outlier: 3.759A pdb=" N LEU C 509 " --> pdb=" O HIS C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 533 removed outlier: 3.713A pdb=" N ILE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 576 Processing helix chain 'C' and resid 582 through 623 Proline residue: C 594 - end of helix Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.620A pdb=" N LYS D 28 " --> pdb=" O PRO D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 62 removed outlier: 3.691A pdb=" N THR D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.654A pdb=" N ARG D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 124 " --> pdb=" O MET D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 148 removed outlier: 3.610A pdb=" N VAL D 134 " --> pdb=" O PRO D 130 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 179 Processing helix chain 'D' and resid 206 through 226 removed outlier: 3.655A pdb=" N MET D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 27 through 46 Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.846A pdb=" N GLY E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 95 removed outlier: 3.534A pdb=" N GLY E 95 " --> pdb=" O ASN E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.531A pdb=" N GLU E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 144 removed outlier: 3.744A pdb=" N LYS E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 16 removed outlier: 4.358A pdb=" N LEU F 11 " --> pdb=" O PRO F 7 " (cutoff:3.500A) removed outlier: 3.698A 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 77 removed outlier: 3.774A pdb=" N LYS F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 93 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 removed outlier: 3.750A pdb=" N ARG F 146 " --> pdb=" O GLU F 143 " (cutoff:3.500A) No H-bonds generated for '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: 3.766A pdb=" N ILE F 194 " --> pdb=" O ASN F 190 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG F 200 " --> pdb=" O GLU F 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 70 Processing helix chain 'G' and resid 109 through 119 Processing helix chain 'G' and resid 132 through 146 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: 3.595A pdb=" N SER H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 70 Processing helix chain 'H' and resid 92 through 111 removed outlier: 3.523A pdb=" N THR H 97 " --> pdb=" O PRO H 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU H 110 " --> pdb=" O ASN H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 129 Processing helix chain 'H' and resid 133 through 148 Processing helix chain 'I' and resid 5 through 20 Processing helix chain 'I' and resid 30 through 44 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 114 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: 3.941A pdb=" N GLU J 89 " --> pdb=" O ARG J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 101 removed outlier: 3.706A pdb=" N ALA J 101 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 127 through 131 removed outlier: 3.503A pdb=" N GLY L 131 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.737A pdb=" N TYR M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.807A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 82 removed outlier: 3.506A pdb=" N ASN M 76 " --> pdb=" O GLU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.715A pdb=" N THR O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.636A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 61 Processing helix chain 'P' and resid 67 through 78 Processing helix chain 'P' and resid 78 through 89 removed outlier: 3.550A pdb=" N GLN P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 25 removed outlier: 3.536A pdb=" N LYS R 18 " --> pdb=" O HIS R 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR R 25 " --> pdb=" O LYS R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 45 Processing helix chain 'R' and resid 70 through 75 Processing helix chain 'S' and resid 5 through 42 Processing helix chain 'S' and resid 43 through 64 Processing helix chain 'S' and resid 68 through 85 removed outlier: 3.573A pdb=" N LYS S 82 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 33 Processing helix chain 'T' and resid 68 through 82 removed outlier: 3.739A pdb=" N VAL T 72 " --> pdb=" O ASP T 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 30 through 36 removed outlier: 3.632A pdb=" N LYS U 36 " --> pdb=" O ASP U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 51 Processing helix chain 'U' and resid 53 through 70 Processing helix chain 'V' and resid 56 through 61 removed outlier: 4.149A pdb=" N SER V 60 " --> pdb=" O GLY V 56 " (cutoff:3.500A) removed outlier: 3.519A 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: 3.773A pdb=" N HIS V 79 " --> pdb=" O GLY V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 106 removed outlier: 3.730A pdb=" N GLY V 106 " --> pdb=" O LEU V 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 33 removed outlier: 3.542A pdb=" N LYS K 24 " --> pdb=" O GLN K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 90 removed outlier: 3.538A pdb=" N MET K 88 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'C' and resid 75 through 78 Processing sheet with id=AA3, first strand: chain 'C' and resid 194 through 195 removed outlier: 3.846A pdb=" N GLY C 151 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N HIS C 178 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 203 " --> pdb=" O LYS C 179 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL C 181 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE C 201 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 249 through 250 removed outlier: 3.580A pdb=" N GLU C 355 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 258 through 260 removed outlier: 6.139A pdb=" N THR C 258 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 312 Processing sheet with id=AA7, first strand: chain 'C' and resid 423 through 427 removed outlier: 3.554A pdb=" N VAL C 437 " --> pdb=" O LYS C 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 472 through 475 Processing sheet with id=AA9, first strand: chain 'C' and resid 651 through 654 removed outlier: 3.770A pdb=" N ILE C 651 " --> pdb=" O LEU C 647 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU C 646 " --> pdb=" O ILE C 635 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE C 635 " --> pdb=" O GLU C 646 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 689 " --> pdb=" O GLY C 633 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 666 through 668 Processing sheet with id=AB2, first strand: chain 'D' and resid 16 through 19 removed outlier: 5.558A pdb=" N PHE D 16 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE D 41 " --> pdb=" O PHE D 16 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS D 18 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU D 34 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE D 40 " --> pdb=" O PHE D 32 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 90 through 92 removed outlier: 6.630A pdb=" N ILE D 67 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL D 92 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE D 69 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU D 68 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE D 164 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL D 70 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU D 161 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE D 186 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE D 163 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 20 through 21 removed outlier: 7.668A pdb=" N LYS E 21 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE E 56 " --> pdb=" O LYS E 21 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS E 53 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS E 68 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 152 removed outlier: 3.904A pdb=" N THR E 150 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR E 167 " --> pdb=" O THR E 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 179 through 189 removed outlier: 6.008A pdb=" N ASP E 180 " --> pdb=" O ARG E 203 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 124 through 125 removed outlier: 3.631A pdb=" N SER F 124 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 12 through 25 removed outlier: 5.465A pdb=" N GLU G 13 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY G 40 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU G 15 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL G 38 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR G 17 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 85 through 89 Processing sheet with id=AC1, first strand: chain 'H' and resid 73 through 78 Processing sheet with id=AC2, first strand: chain 'I' and resid 24 through 28 removed outlier: 6.702A pdb=" N ILE I 59 " --> pdb=" O PHE I 51 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE I 51 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG I 61 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL I 49 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE I 63 " --> pdb=" O ARG I 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 66 through 67 Processing sheet with id=AC4, first strand: chain 'I' and resid 76 through 79 Processing sheet with id=AC5, first strand: chain 'I' and resid 76 through 79 removed outlier: 5.319A pdb=" N VAL I 127 " --> pdb=" O SER I 107 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER I 107 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA I 129 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 6 through 12 Processing sheet with id=AC7, first strand: chain 'L' and resid 43 through 53 removed outlier: 6.630A pdb=" N ARG L 67 " --> pdb=" O THR L 48 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL L 50 " --> pdb=" O TYR L 65 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR L 65 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR L 52 " --> pdb=" O ARG L 63 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG L 63 " --> pdb=" O THR L 52 " (cutoff:3.500A) removed outlier: 13.616A pdb=" N GLU L 75 " --> pdb=" O VAL L 106 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N TYR L 108 " --> pdb=" O GLU L 75 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR L 77 " --> pdb=" O TYR L 108 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE L 110 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR L 79 " --> pdb=" O ILE L 110 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ARG L 112 " --> pdb=" O TYR L 79 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS L 109 " --> pdb=" O ARG L 96 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU L 94 " --> pdb=" O VAL L 111 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLY L 113 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 11.930A pdb=" N VAL L 92 " --> pdb=" O GLY L 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 56 through 58 removed outlier: 7.341A pdb=" N LYS K 59 " --> pdb=" O ALA K 54 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA K 54 " --> pdb=" O LYS K 59 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER K 61 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU K 52 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU K 63 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR K 50 " --> pdb=" O GLU K 63 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE K 65 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL K 48 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET K 67 " --> pdb=" O LYS K 46 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS K 46 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR K 69 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR K 44 " --> pdb=" O THR K 69 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS K 71 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASP K 75 " --> pdb=" O GLY K 38 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY K 38 " --> pdb=" O ASP K 75 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL K 77 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL K 36 " --> pdb=" O VAL K 77 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 56 through 58 removed outlier: 3.602A pdb=" N LYS K 11 " --> pdb=" O ASP K 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.525A pdb=" N GLU P 35 " --> pdb=" O VAL P 22 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE P 20 " --> pdb=" O VAL P 37 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR P 39 " --> pdb=" O TYR P 18 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR P 18 " --> pdb=" O THR P 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 9 through 14 removed outlier: 16.649A pdb=" N VAL Q 9 " --> pdb=" O TYR Q 30 " (cutoff:3.500A) removed outlier: 13.171A pdb=" N TYR Q 30 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLN Q 11 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLU Q 28 " --> pdb=" O GLN Q 11 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N PHE Q 75 " --> pdb=" O LYS Q 45 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS Q 47 " --> pdb=" O PHE Q 75 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU Q 77 " --> pdb=" O LYS Q 47 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS Q 49 " --> pdb=" O LEU Q 77 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLU Q 79 " --> pdb=" O HIS Q 49 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL Q 78 " --> pdb=" O MET Q 64 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N MET Q 64 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL Q 80 " --> pdb=" O LYS Q 62 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS Q 62 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 31 through 33 removed outlier: 6.301A pdb=" N VAL R 31 " --> pdb=" O ALA R 50 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR R 52 " --> pdb=" O VAL R 31 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR R 33 " --> pdb=" O TYR R 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 36 through 47 removed outlier: 7.354A pdb=" N THR T 38 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N GLN T 66 " --> pdb=" O THR T 38 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR T 40 " --> pdb=" O ASN T 64 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASN T 64 " --> pdb=" O THR T 40 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASP T 42 " --> pdb=" O ILE T 62 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE T 62 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY T 44 " --> pdb=" O TYR T 60 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR T 60 " --> pdb=" O GLY T 44 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG T 87 " --> pdb=" O ILE T 9 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'V' and resid 43 through 48 removed outlier: 7.058A pdb=" N ILE V 36 " --> pdb=" O ILE V 44 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP V 46 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL V 34 " --> pdb=" O TRP V 46 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER V 48 " --> pdb=" O THR V 32 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR V 32 " --> pdb=" O SER V 48 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY V 21 " --> pdb=" O GLU V 85 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR V 87 " --> pdb=" O GLY V 21 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA V 23 " --> pdb=" O THR V 87 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LYS V 89 " --> pdb=" O ALA V 23 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE V 25 " --> pdb=" O LYS V 89 " (cutoff:3.500A) 1078 hydrogen bonds defined for protein. 3099 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1034 hydrogen bonds 1632 hydrogen bond angles 0 basepair planarities 418 basepair parallelities 795 stacking parallelities Total time for adding SS restraints: 40.43 Time building geometry restraints manager: 12.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7707 1.33 - 1.46: 25528 1.46 - 1.60: 19918 1.60 - 1.73: 2457 1.73 - 1.86: 133 Bond restraints: 55743 Sorted by residual: bond pdb=" O3' G A1395 " pdb=" P G A1396 " ideal model delta sigma weight residual 1.607 1.712 -0.105 1.50e-02 4.44e+03 4.88e+01 bond pdb=" O5' A A 364 " pdb=" C5' A A 364 " ideal model delta sigma weight residual 1.420 1.485 -0.065 1.50e-02 4.44e+03 1.90e+01 bond pdb=" O5' U A1088 " pdb=" C5' U A1088 " ideal model delta sigma weight residual 1.420 1.483 -0.063 1.50e-02 4.44e+03 1.79e+01 bond pdb=" P G A 8 " pdb=" O5' G A 8 " ideal model delta sigma weight residual 1.593 1.655 -0.062 1.50e-02 4.44e+03 1.69e+01 bond pdb=" P A B9002 " pdb=" O5' A B9002 " ideal model delta sigma weight residual 1.593 1.655 -0.062 1.50e-02 4.44e+03 1.68e+01 ... (remaining 55738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 73398 2.56 - 5.11: 7891 5.11 - 7.67: 525 7.67 - 10.22: 52 10.22 - 12.78: 6 Bond angle restraints: 81872 Sorted by residual: angle pdb=" CA HIS C 656 " pdb=" CB HIS C 656 " pdb=" CG HIS C 656 " ideal model delta sigma weight residual 113.80 123.42 -9.62 1.00e+00 1.00e+00 9.25e+01 angle pdb=" C TYR Q 36 " pdb=" CA TYR Q 36 " pdb=" CB TYR Q 36 " ideal model delta sigma weight residual 110.79 123.57 -12.78 1.68e+00 3.54e-01 5.78e+01 angle pdb=" N ALA G 22 " pdb=" CA ALA G 22 " pdb=" C ALA G 22 " ideal model delta sigma weight residual 107.61 119.29 -11.68 1.74e+00 3.30e-01 4.51e+01 angle pdb=" O3' C A 980 " pdb=" C3' C A 980 " pdb=" C2' C A 980 " ideal model delta sigma weight residual 109.50 119.24 -9.74 1.50e+00 4.44e-01 4.21e+01 angle pdb=" O3' G A 113 " pdb=" C3' G A 113 " pdb=" C2' G A 113 " ideal model delta sigma weight residual 109.50 119.11 -9.61 1.50e+00 4.44e-01 4.11e+01 ... (remaining 81867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 31961 35.76 - 71.52: 3090 71.52 - 107.29: 411 107.29 - 143.05: 29 143.05 - 178.81: 25 Dihedral angle restraints: 35516 sinusoidal: 27085 harmonic: 8431 Sorted by residual: dihedral pdb=" C5' C A 980 " pdb=" C4' C A 980 " pdb=" C3' C A 980 " pdb=" O3' C A 980 " ideal model delta sinusoidal sigma weight residual 147.00 64.69 82.31 1 8.00e+00 1.56e-02 1.30e+02 dihedral pdb=" O4' C A 980 " pdb=" C4' C A 980 " pdb=" C3' C A 980 " pdb=" C2' C A 980 " ideal model delta sinusoidal sigma weight residual 24.00 -44.82 68.82 1 8.00e+00 1.56e-02 9.58e+01 dihedral pdb=" C4' C A 980 " pdb=" C3' C A 980 " pdb=" C2' C A 980 " pdb=" C1' C A 980 " ideal model delta sinusoidal sigma weight residual -35.00 33.06 -68.06 1 8.00e+00 1.56e-02 9.40e+01 ... (remaining 35513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 8062 0.130 - 0.260: 2157 0.260 - 0.390: 50 0.390 - 0.520: 3 0.520 - 0.650: 5 Chirality restraints: 10277 Sorted by residual: 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 -3.06 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P A A 979 " pdb=" OP1 A A 979 " pdb=" OP2 A A 979 " pdb=" O5' A A 979 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.36e+00 chirality pdb=" P C A 817 " pdb=" OP1 C A 817 " pdb=" OP2 C A 817 " pdb=" O5' C A 817 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.23e+00 ... (remaining 10274 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 47 " -0.589 9.50e-02 1.11e+02 2.64e-01 4.58e+01 pdb=" NE ARG I 47 " 0.046 2.00e-02 2.50e+03 pdb=" CZ ARG I 47 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG I 47 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG I 47 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 58 " -0.588 9.50e-02 1.11e+02 2.63e-01 4.24e+01 pdb=" NE ARG F 58 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG F 58 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG F 58 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 58 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 3 " 0.521 9.50e-02 1.11e+02 2.34e-01 3.77e+01 pdb=" NE ARG F 3 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG F 3 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG F 3 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG F 3 " 0.030 2.00e-02 2.50e+03 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 7015 2.76 - 3.30: 48667 3.30 - 3.83: 107388 3.83 - 4.37: 133594 4.37 - 4.90: 182786 Nonbonded interactions: 479450 Sorted by model distance: nonbonded pdb=" O2' A A 979 " pdb=" O2 C A 980 " model vdw 2.229 3.040 nonbonded pdb=" O2' U A1072 " pdb=" O5' C A1073 " model vdw 2.242 3.040 nonbonded pdb=" OP2 C A 531 " pdb=" OH TYR L 79 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR N 49 " pdb=" OE2 GLU K 63 " model vdw 2.259 3.040 nonbonded pdb=" O2' A A 190 " pdb=" O5' C A 191 " model vdw 2.296 3.040 ... (remaining 479445 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.910 Check model and map are aligned: 0.360 Set scattering table: 0.390 Process input model: 133.870 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.010 0.105 55743 Z= 0.579 Angle : 1.552 12.776 81872 Z= 0.989 Chirality : 0.102 0.650 10277 Planarity : 0.020 0.264 5424 Dihedral : 23.320 178.809 30066 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.87 % Allowed : 5.96 % Favored : 93.17 % Rotamer: Outliers : 4.95 % Allowed : 6.74 % Favored : 88.31 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.13), residues: 2884 helix: -2.52 (0.11), residues: 1150 sheet: -2.36 (0.21), residues: 455 loop : -1.82 (0.16), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.008 TRP E 200 HIS 0.016 0.004 HIS L 109 PHE 0.057 0.007 PHE O 15 TYR 0.066 0.008 TYR L 130 ARG 0.037 0.004 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 656 time to evaluate : 2.769 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 59 ARG cc_start: 0.3345 (mtt-85) cc_final: 0.3019 (ptm-80) REVERT: C 67 GLU cc_start: 0.4815 (mm-30) cc_final: 0.4426 (tp30) REVERT: C 68 LYS cc_start: 0.2960 (mmtt) cc_final: 0.2669 (ttpt) REVERT: C 69 MET cc_start: 0.3261 (OUTLIER) cc_final: 0.2398 (tpp) REVERT: C 72 ILE cc_start: 0.3906 (OUTLIER) cc_final: 0.3571 (pt) REVERT: C 101 ASN cc_start: 0.2282 (OUTLIER) cc_final: 0.1826 (t0) REVERT: C 103 LEU cc_start: 0.4234 (OUTLIER) cc_final: 0.3639 (pp) REVERT: C 107 MET cc_start: 0.3554 (mtp) cc_final: 0.3114 (mtt) REVERT: C 195 GLU cc_start: 0.5021 (OUTLIER) cc_final: 0.4018 (tm-30) REVERT: C 199 GLU cc_start: 0.4309 (tt0) cc_final: 0.4083 (tm-30) REVERT: C 218 LYS cc_start: 0.5911 (tttt) cc_final: 0.5361 (mtpp) REVERT: C 230 MET cc_start: 0.3270 (mmm) cc_final: 0.3004 (mtp) REVERT: C 248 ARG cc_start: 0.2078 (mtt-85) cc_final: 0.1655 (mtt-85) REVERT: C 266 ASP cc_start: 0.1718 (OUTLIER) cc_final: 0.0359 (p0) REVERT: C 271 VAL cc_start: 0.5913 (m) cc_final: 0.5687 (p) REVERT: C 281 TYR cc_start: 0.4982 (m-80) cc_final: 0.4711 (m-10) REVERT: C 287 ILE cc_start: 0.2918 (mm) cc_final: 0.2250 (mm) REVERT: C 346 THR cc_start: 0.5897 (m) cc_final: 0.5207 (p) REVERT: C 348 ASN cc_start: 0.2883 (p0) cc_final: 0.2661 (m-40) REVERT: C 360 GLN cc_start: 0.3505 (mt0) cc_final: 0.2678 (mt0) REVERT: C 389 TYR cc_start: 0.5123 (m-80) cc_final: 0.4896 (m-80) REVERT: C 395 MET cc_start: 0.4178 (ttp) cc_final: 0.3886 (ttp) REVERT: C 410 ARG cc_start: 0.4540 (ttp-170) cc_final: 0.4173 (mtm110) REVERT: C 422 GLU cc_start: 0.5569 (mt-10) cc_final: 0.5296 (tm-30) REVERT: C 434 LYS cc_start: 0.4082 (OUTLIER) cc_final: 0.3718 (tptm) REVERT: C 441 ARG cc_start: 0.3849 (mtm180) cc_final: 0.2994 (mtm180) REVERT: C 445 GLU cc_start: 0.6149 (mp0) cc_final: 0.5828 (mp0) REVERT: C 449 GLU cc_start: 0.5223 (tt0) cc_final: 0.4860 (mm-30) REVERT: C 466 MET cc_start: 0.4245 (ttm) cc_final: 0.3355 (mmp) REVERT: C 476 GLU cc_start: 0.5648 (mt-10) cc_final: 0.5145 (tp30) REVERT: C 479 ASN cc_start: 0.5724 (t0) cc_final: 0.5309 (t0) REVERT: C 496 VAL cc_start: 0.6484 (t) cc_final: 0.6215 (p) REVERT: C 518 ASP cc_start: 0.5886 (m-30) cc_final: 0.5652 (t70) REVERT: C 556 PHE cc_start: 0.4347 (t80) cc_final: 0.3938 (t80) REVERT: C 572 ILE cc_start: 0.4075 (mt) cc_final: 0.3454 (mt) REVERT: C 575 TYR cc_start: 0.4851 (m-80) cc_final: 0.4508 (m-80) REVERT: C 578 ASN cc_start: 0.3169 (m-40) cc_final: 0.2955 (m110) REVERT: C 604 GLU cc_start: 0.5670 (tt0) cc_final: 0.5092 (tm-30) REVERT: C 613 GLU cc_start: 0.5969 (tt0) cc_final: 0.5476 (tp30) REVERT: C 629 GLU cc_start: 0.3920 (mt-10) cc_final: 0.3376 (mm-30) REVERT: C 656 HIS cc_start: 0.4112 (OUTLIER) cc_final: 0.3600 (m-70) REVERT: C 660 MET cc_start: 0.2913 (mtp) cc_final: 0.2370 (mmm) REVERT: C 678 ARG cc_start: 0.2454 (ttp80) cc_final: 0.1062 (mtt-85) REVERT: C 707 ILE cc_start: 0.5439 (mt) cc_final: 0.4569 (mm) REVERT: D 21 ARG cc_start: 0.6135 (mtp-110) cc_final: 0.5782 (ttm170) REVERT: D 24 ASN cc_start: 0.7912 (t0) cc_final: 0.7658 (t0) REVERT: D 36 ASN cc_start: 0.5290 (m110) cc_final: 0.5080 (m110) REVERT: D 82 GLU cc_start: 0.5407 (mt-10) cc_final: 0.5184 (mm-30) REVERT: D 105 GLU cc_start: 0.6451 (mt-10) cc_final: 0.5995 (mp0) REVERT: D 108 GLN cc_start: 0.6822 (mt0) cc_final: 0.6531 (mm-40) REVERT: D 129 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.5078 (pp) REVERT: D 132 LYS cc_start: 0.4745 (OUTLIER) cc_final: 0.3939 (tptt) REVERT: D 140 GLU cc_start: 0.6564 (tt0) cc_final: 0.6072 (tp30) REVERT: D 142 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6633 (mm-30) REVERT: D 170 ARG cc_start: 0.5846 (ptt180) cc_final: 0.5417 (ptm160) REVERT: D 178 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6415 (tptm) REVERT: D 197 ASP cc_start: 0.6739 (m-30) cc_final: 0.6321 (t0) REVERT: D 204 ASP cc_start: 0.6038 (OUTLIER) cc_final: 0.5483 (p0) REVERT: D 219 ASP cc_start: 0.5317 (m-30) cc_final: 0.5031 (t70) REVERT: D 223 GLU cc_start: 0.5155 (mt-10) cc_final: 0.4713 (mm-30) REVERT: E 26 LYS cc_start: 0.6264 (mttt) cc_final: 0.5330 (tttt) REVERT: E 65 ILE cc_start: 0.6455 (mm) cc_final: 0.6137 (mt) REVERT: E 98 VAL cc_start: 0.5690 (t) cc_final: 0.5217 (p) REVERT: E 126 ARG cc_start: 0.4599 (mtt-85) cc_final: 0.3968 (tpp-160) REVERT: E 135 GLN cc_start: 0.6075 (tt0) cc_final: 0.5719 (mm-40) REVERT: E 148 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7892 (m) REVERT: E 163 ARG cc_start: 0.3528 (OUTLIER) cc_final: 0.1926 (tmt170) REVERT: E 205 GLU cc_start: 0.6704 (mt-10) cc_final: 0.5788 (mm-30) REVERT: F 66 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.7043 (ttm170) REVERT: F 152 LYS cc_start: 0.6498 (mtpp) cc_final: 0.6272 (mttt) REVERT: F 168 ASP cc_start: 0.4952 (t0) cc_final: 0.4730 (m-30) REVERT: F 178 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5597 (ptt-90) REVERT: G 8 LYS cc_start: 0.6243 (OUTLIER) cc_final: 0.5696 (tmtt) REVERT: G 30 ARG cc_start: 0.7343 (mmm-85) cc_final: 0.6511 (tmm160) REVERT: G 32 ARG cc_start: 0.7750 (mtt90) cc_final: 0.7537 (mtp180) REVERT: G 55 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6769 (tp30) REVERT: G 66 ASP cc_start: 0.8137 (t70) cc_final: 0.7932 (t0) REVERT: G 73 GLU cc_start: 0.7903 (tt0) cc_final: 0.7473 (mt-10) REVERT: G 155 LYS cc_start: 0.7563 (ttmm) cc_final: 0.7094 (mmtm) REVERT: H 13 LEU cc_start: 0.5031 (OUTLIER) cc_final: 0.4827 (mt) REVERT: H 45 LYS cc_start: 0.5180 (mttt) cc_final: 0.4977 (mttp) REVERT: H 59 MET cc_start: 0.3047 (OUTLIER) cc_final: 0.2400 (tmm) REVERT: H 60 GLU cc_start: 0.4194 (tt0) cc_final: 0.3841 (mm-30) REVERT: H 63 GLU cc_start: 0.3757 (mt-10) cc_final: 0.3113 (pt0) REVERT: H 67 LYS cc_start: 0.5733 (ttmt) cc_final: 0.5529 (mtmt) REVERT: H 94 GLU cc_start: 0.4563 (mt-10) cc_final: 0.4358 (mm-30) REVERT: H 103 TRP cc_start: 0.5409 (m-10) cc_final: 0.5064 (m-10) REVERT: H 118 GLU cc_start: 0.6328 (mt-10) cc_final: 0.6047 (tt0) REVERT: I 34 ARG cc_start: 0.6995 (ttm170) cc_final: 0.6361 (ttt180) REVERT: I 35 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6389 (mt-10) REVERT: I 38 GLU cc_start: 0.7715 (tt0) cc_final: 0.7330 (mm-30) REVERT: I 53 GLU cc_start: 0.6985 (mp0) cc_final: 0.6714 (mm-30) REVERT: I 54 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6450 (p0) REVERT: I 55 SER cc_start: 0.5423 (p) cc_final: 0.4843 (m) REVERT: I 56 LYS cc_start: 0.5789 (mttt) cc_final: 0.5376 (mtmt) REVERT: I 71 GLU cc_start: 0.6703 (tp30) cc_final: 0.6298 (tp30) REVERT: I 93 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6349 (mm-30) REVERT: I 99 ASN cc_start: 0.8176 (t0) cc_final: 0.7737 (t0) REVERT: J 38 HIS cc_start: 0.5672 (t70) cc_final: 0.5372 (t70) REVERT: J 50 GLN cc_start: 0.5700 (tt0) cc_final: 0.5358 (mm-40) REVERT: J 68 HIS cc_start: 0.6005 (m-70) cc_final: 0.5002 (p-80) REVERT: J 100 ARG cc_start: 0.6083 (OUTLIER) cc_final: 0.5531 (mmt90) REVERT: J 106 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7376 (tmt-80) REVERT: J 112 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.4770 (tt0) REVERT: L 3 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8213 (p) REVERT: L 17 GLU cc_start: 0.5345 (mp0) cc_final: 0.4988 (pm20) REVERT: L 32 LYS cc_start: 0.7162 (mmmt) cc_final: 0.6939 (mtpp) REVERT: L 34 GLU cc_start: 0.5913 (pt0) cc_final: 0.5710 (tt0) REVERT: L 49 ARG cc_start: 0.5681 (ttp-110) cc_final: 0.5014 (mtm110) REVERT: L 69 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7121 (ttp80) REVERT: L 121 GLU cc_start: 0.6687 (mp0) cc_final: 0.6396 (pt0) REVERT: M 93 ARG cc_start: 0.4299 (mtt180) cc_final: 0.3608 (mtt180) REVERT: N 15 LYS cc_start: 0.4960 (ttpt) cc_final: 0.4705 (tptt) REVERT: N 23 ARG cc_start: 0.7087 (mtp85) cc_final: 0.6282 (ptp-170) REVERT: N 25 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6920 (mm-30) REVERT: N 35 ARG cc_start: 0.7392 (mtt180) cc_final: 0.6279 (mtp-110) REVERT: N 61 TRP cc_start: 0.5046 (t60) cc_final: 0.4252 (p-90) REVERT: O 41 GLU cc_start: 0.7636 (tp30) cc_final: 0.7293 (tm-30) REVERT: O 74 ASP cc_start: 0.7608 (t70) cc_final: 0.7160 (t0) REVERT: O 77 ARG cc_start: 0.7275 (mtp180) cc_final: 0.7030 (mtm-85) REVERT: P 10 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7888 (mtm) REVERT: P 35 GLU cc_start: 0.8512 (tp30) cc_final: 0.8293 (tt0) REVERT: P 54 GLU cc_start: 0.7729 (pp20) cc_final: 0.7391 (tp30) REVERT: Q 6 GLN cc_start: 0.7640 (mp10) cc_final: 0.7066 (tt0) REVERT: Q 7 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8237 (mmt180) REVERT: Q 28 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7522 (mm-30) REVERT: Q 56 LYS cc_start: 0.7586 (mttt) cc_final: 0.7119 (ptmt) REVERT: Q 59 ASP cc_start: 0.8551 (m-30) cc_final: 0.8234 (m-30) REVERT: Q 64 MET cc_start: 0.8550 (ttm) cc_final: 0.8297 (ttm) REVERT: R 16 MET cc_start: 0.6610 (tpp) cc_final: 0.5656 (ptt) REVERT: R 81 LYS cc_start: 0.4060 (OUTLIER) cc_final: 0.2024 (tptt) REVERT: S 14 ASN cc_start: 0.7598 (t0) cc_final: 0.7042 (m-40) REVERT: S 29 ARG cc_start: 0.7036 (mtt90) cc_final: 0.6658 (mtm180) REVERT: S 57 ARG cc_start: 0.7702 (mmp-170) cc_final: 0.7080 (mpt-90) REVERT: T 1 MET cc_start: 0.5197 (ptt) cc_final: 0.4892 (ptp) REVERT: T 2 ARG cc_start: 0.5209 (OUTLIER) cc_final: 0.4712 (ptp-170) REVERT: T 3 LYS cc_start: 0.7333 (mttt) cc_final: 0.6468 (tptp) REVERT: T 28 ASN cc_start: 0.5896 (t0) cc_final: 0.5666 (t0) REVERT: T 92 LYS cc_start: 0.7251 (mtmt) cc_final: 0.6960 (mtmt) REVERT: T 94 GLU cc_start: 0.2900 (OUTLIER) cc_final: 0.2179 (mp0) REVERT: U 21 ASN cc_start: 0.6617 (m110) cc_final: 0.6301 (m110) REVERT: U 32 ASP cc_start: 0.6555 (m-30) cc_final: 0.6276 (p0) REVERT: U 41 ARG cc_start: 0.6217 (mtp180) cc_final: 0.5524 (mtt-85) REVERT: U 47 ARG cc_start: 0.7330 (mtp85) cc_final: 0.5843 (mtm-85) REVERT: U 48 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.5783 (mtt180) REVERT: K 20 GLN cc_start: 0.6032 (mt0) cc_final: 0.5456 (tt0) REVERT: K 45 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6339 (mm-30) REVERT: K 46 LYS cc_start: 0.6882 (tttm) cc_final: 0.6637 (tttp) REVERT: K 53 ARG cc_start: 0.5910 (mtm-85) cc_final: 0.5658 (ttm110) REVERT: K 57 LYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6498 (tptt) REVERT: K 69 THR cc_start: 0.7425 (m) cc_final: 0.7156 (p) REVERT: K 96 VAL cc_start: 0.7999 (t) cc_final: 0.7762 (m) REVERT: K 98 ILE cc_start: 0.4902 (OUTLIER) cc_final: 0.4641 (mt) REVERT: K 99 GLU cc_start: 0.4156 (tt0) cc_final: 0.3159 (mm-30) outliers start: 124 outliers final: 28 residues processed: 733 average time/residue: 0.6518 time to fit residues: 758.4180 Evaluate side-chains 487 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 427 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 656 HIS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 130 PRO Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain P residue 10 MET Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 7 ARG Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain T residue 2 ARG Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 87 ARG Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 98 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 chunk 324 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 375 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN C 671 HIS D 44 GLN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN H 64 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN M 105 ASN O 18 HIS O 37 ASN O 46 HIS O 72 ASN O 83 ASN P 72 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 57 HIS S 84 ASN T 33 ASN T 66 GLN ** V 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 ASN V 42 ASN K 56 HIS K 82 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 55743 Z= 0.238 Angle : 0.725 8.249 81872 Z= 0.383 Chirality : 0.044 0.335 10277 Planarity : 0.005 0.079 5424 Dihedral : 23.990 177.438 24295 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.50 % Favored : 96.22 % Rotamer: Outliers : 4.79 % Allowed : 11.37 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 2884 helix: 0.09 (0.14), residues: 1166 sheet: -1.47 (0.21), residues: 497 loop : -1.24 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 200 HIS 0.007 0.001 HIS E 99 PHE 0.026 0.002 PHE C 6 TYR 0.026 0.002 TYR L 130 ARG 0.007 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 435 time to evaluate : 2.711 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 55 ILE cc_start: 0.0396 (pt) cc_final: -0.0052 (mm) REVERT: C 59 ARG cc_start: 0.3526 (mtt-85) cc_final: 0.3056 (ppt170) REVERT: C 68 LYS cc_start: 0.3047 (mmtt) cc_final: 0.2797 (ttpt) REVERT: C 101 ASN cc_start: 0.2576 (OUTLIER) cc_final: 0.2207 (t0) REVERT: C 103 LEU cc_start: 0.4180 (OUTLIER) cc_final: 0.3611 (pp) REVERT: C 137 ILE cc_start: 0.4898 (mt) cc_final: 0.4694 (tt) REVERT: C 218 LYS cc_start: 0.5806 (tttt) cc_final: 0.5043 (tppt) REVERT: C 224 GLU cc_start: 0.4143 (mt-10) cc_final: 0.3816 (mp0) REVERT: C 230 MET cc_start: 0.2926 (mmm) cc_final: 0.2674 (mtp) REVERT: C 287 ILE cc_start: 0.2971 (mm) cc_final: 0.2390 (mm) REVERT: C 389 TYR cc_start: 0.5134 (m-80) cc_final: 0.4833 (m-80) REVERT: C 434 LYS cc_start: 0.3920 (OUTLIER) cc_final: 0.3683 (tttp) REVERT: C 445 GLU cc_start: 0.6431 (mp0) cc_final: 0.6178 (mp0) REVERT: C 457 GLU cc_start: 0.6053 (mt-10) cc_final: 0.5748 (tm-30) REVERT: C 466 MET cc_start: 0.4234 (ttm) cc_final: 0.3564 (mmp) REVERT: C 485 LYS cc_start: 0.6609 (mttt) cc_final: 0.6241 (ttpp) REVERT: C 556 PHE cc_start: 0.4143 (t80) cc_final: 0.3721 (t80) REVERT: C 573 ARG cc_start: 0.3389 (ttm-80) cc_final: 0.2813 (mtp-110) REVERT: C 575 TYR cc_start: 0.4981 (m-80) cc_final: 0.4510 (m-10) REVERT: C 604 GLU cc_start: 0.5643 (tt0) cc_final: 0.5085 (tm-30) REVERT: C 613 GLU cc_start: 0.6166 (tt0) cc_final: 0.5651 (mm-30) REVERT: C 629 GLU cc_start: 0.4325 (mt-10) cc_final: 0.3600 (mm-30) REVERT: C 660 MET cc_start: 0.2667 (mtp) cc_final: 0.2307 (mmm) REVERT: C 678 ARG cc_start: 0.2424 (ttp80) cc_final: 0.1110 (mtt180) REVERT: C 707 ILE cc_start: 0.5381 (mt) cc_final: 0.4457 (mm) REVERT: D 21 ARG cc_start: 0.6075 (mtp-110) cc_final: 0.5823 (ttm110) REVERT: D 22 ARG cc_start: 0.6124 (OUTLIER) cc_final: 0.5379 (ttt180) REVERT: D 105 GLU cc_start: 0.6242 (mt-10) cc_final: 0.5831 (mp0) REVERT: D 108 GLN cc_start: 0.6502 (mt0) cc_final: 0.6180 (mm-40) REVERT: D 132 LYS cc_start: 0.4551 (OUTLIER) cc_final: 0.4043 (tptt) REVERT: D 140 GLU cc_start: 0.5959 (tt0) cc_final: 0.5392 (mm-30) REVERT: D 142 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6501 (mm-30) REVERT: D 170 ARG cc_start: 0.5658 (ptt180) cc_final: 0.5301 (ptm160) REVERT: D 204 ASP cc_start: 0.5899 (OUTLIER) cc_final: 0.5291 (p0) REVERT: D 219 ASP cc_start: 0.5376 (m-30) cc_final: 0.4964 (t70) REVERT: E 26 LYS cc_start: 0.6333 (mttt) cc_final: 0.5591 (tttt) REVERT: E 65 ILE cc_start: 0.6416 (OUTLIER) cc_final: 0.6084 (mt) REVERT: E 103 LEU cc_start: 0.4742 (mm) cc_final: 0.4295 (mt) REVERT: E 126 ARG cc_start: 0.4657 (mtt-85) cc_final: 0.3911 (tpp-160) REVERT: E 138 GLN cc_start: 0.5952 (mt0) cc_final: 0.5673 (mp10) REVERT: E 163 ARG cc_start: 0.3438 (OUTLIER) cc_final: 0.1835 (ttt180) REVERT: E 175 HIS cc_start: 0.6795 (m-70) cc_final: 0.6470 (m170) REVERT: E 187 GLU cc_start: 0.5254 (mt-10) cc_final: 0.4977 (pt0) REVERT: E 205 GLU cc_start: 0.6603 (mt-10) cc_final: 0.5817 (mm-30) REVERT: F 152 LYS cc_start: 0.6391 (mtpp) cc_final: 0.6144 (mttt) REVERT: F 178 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5342 (ptt-90) REVERT: G 8 LYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5686 (tmtt) REVERT: G 30 ARG cc_start: 0.7402 (mmm-85) cc_final: 0.6485 (tmm160) REVERT: G 88 ARG cc_start: 0.7645 (mtt-85) cc_final: 0.7236 (ttt90) REVERT: G 155 LYS cc_start: 0.7418 (ttmm) cc_final: 0.6934 (mmtm) REVERT: H 30 MET cc_start: 0.6198 (mtm) cc_final: 0.5465 (mpp) REVERT: H 60 GLU cc_start: 0.4803 (tt0) cc_final: 0.4381 (mt-10) REVERT: H 70 MET cc_start: 0.5293 (mtp) cc_final: 0.5040 (mtp) REVERT: H 86 GLN cc_start: 0.3426 (mm-40) cc_final: 0.3082 (mm-40) REVERT: H 94 GLU cc_start: 0.4482 (mt-10) cc_final: 0.4237 (mm-30) REVERT: H 103 TRP cc_start: 0.5406 (m-10) cc_final: 0.5134 (m-10) REVERT: I 34 ARG cc_start: 0.7117 (ttm170) cc_final: 0.6455 (ttt180) REVERT: I 38 GLU cc_start: 0.7662 (tt0) cc_final: 0.7402 (mm-30) REVERT: I 47 ARG cc_start: 0.7719 (mtt90) cc_final: 0.6767 (ttp-170) REVERT: I 53 GLU cc_start: 0.7040 (mp0) cc_final: 0.6553 (mm-30) REVERT: I 55 SER cc_start: 0.5272 (p) cc_final: 0.5042 (m) REVERT: I 71 GLU cc_start: 0.6911 (tp30) cc_final: 0.6407 (tp30) REVERT: I 93 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6335 (mm-30) REVERT: I 99 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7827 (t0) REVERT: J 50 GLN cc_start: 0.5054 (tt0) cc_final: 0.4812 (mm-40) REVERT: J 66 ASN cc_start: 0.5720 (t0) cc_final: 0.5342 (t0) REVERT: J 100 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.5598 (mmt90) REVERT: J 112 GLU cc_start: 0.5771 (OUTLIER) cc_final: 0.4683 (tt0) REVERT: L 17 GLU cc_start: 0.5147 (mp0) cc_final: 0.4840 (pm20) REVERT: L 32 LYS cc_start: 0.7077 (mmmt) cc_final: 0.6697 (mtmm) REVERT: L 36 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.6996 (p) REVERT: L 49 ARG cc_start: 0.5595 (ttp-110) cc_final: 0.4944 (mtm110) REVERT: L 69 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7049 (tmt170) REVERT: M 27 ARG cc_start: 0.3863 (ttm-80) cc_final: 0.3549 (mtt180) REVERT: N 23 ARG cc_start: 0.7229 (mtp85) cc_final: 0.6275 (ptp-170) REVERT: N 25 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6690 (mm-30) REVERT: N 35 ARG cc_start: 0.7327 (mtt180) cc_final: 0.6307 (mtp-110) REVERT: N 49 TYR cc_start: 0.7508 (m-10) cc_final: 0.7055 (m-10) REVERT: N 50 LYS cc_start: 0.6898 (mtmt) cc_final: 0.6687 (mttt) REVERT: P 35 GLU cc_start: 0.8573 (tp30) cc_final: 0.8313 (tt0) REVERT: Q 6 GLN cc_start: 0.7572 (mp10) cc_final: 0.7096 (tt0) REVERT: Q 17 ASP cc_start: 0.6466 (p0) cc_final: 0.6252 (t0) REVERT: Q 82 GLU cc_start: 0.6253 (tt0) cc_final: 0.5851 (mm-30) REVERT: R 16 MET cc_start: 0.6478 (tpp) cc_final: 0.5581 (ptt) REVERT: R 52 TYR cc_start: 0.6390 (t80) cc_final: 0.6173 (t80) REVERT: R 81 LYS cc_start: 0.4228 (OUTLIER) cc_final: 0.1800 (pptt) REVERT: S 29 ARG cc_start: 0.6821 (mtt90) cc_final: 0.6483 (mtm110) REVERT: T 1 MET cc_start: 0.5144 (ptt) cc_final: 0.4411 (ptp) REVERT: T 2 ARG cc_start: 0.4493 (OUTLIER) cc_final: 0.4231 (ptp-170) REVERT: T 3 LYS cc_start: 0.7081 (mttt) cc_final: 0.6354 (tptt) REVERT: T 23 ILE cc_start: 0.4960 (OUTLIER) cc_final: 0.4734 (tp) REVERT: T 66 GLN cc_start: 0.6000 (mt0) cc_final: 0.5526 (tt0) REVERT: T 87 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6272 (mmt90) REVERT: U 21 ASN cc_start: 0.6591 (m110) cc_final: 0.6238 (m110) REVERT: U 32 ASP cc_start: 0.6628 (m-30) cc_final: 0.6278 (p0) REVERT: U 33 LEU cc_start: 0.6714 (tp) cc_final: 0.6461 (mt) REVERT: U 41 ARG cc_start: 0.5950 (mtp180) cc_final: 0.5327 (mtt-85) REVERT: U 47 ARG cc_start: 0.7251 (mtp85) cc_final: 0.6164 (mtm-85) REVERT: U 48 ARG cc_start: 0.6344 (OUTLIER) cc_final: 0.5823 (mtt180) REVERT: K 20 GLN cc_start: 0.5958 (mt0) cc_final: 0.5489 (tt0) REVERT: K 40 ILE cc_start: 0.6440 (mp) cc_final: 0.6220 (mm) REVERT: K 45 GLU cc_start: 0.6483 (mt-10) cc_final: 0.6249 (mm-30) REVERT: K 53 ARG cc_start: 0.5975 (mtm-85) cc_final: 0.5578 (ttm110) REVERT: K 69 THR cc_start: 0.7449 (m) cc_final: 0.7111 (p) REVERT: K 96 VAL cc_start: 0.7901 (t) cc_final: 0.7468 (m) outliers start: 120 outliers final: 68 residues processed: 521 average time/residue: 0.7273 time to fit residues: 603.7549 Evaluate side-chains 443 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 356 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain T residue 2 ARG Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 87 ARG Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 312 optimal weight: 0.3980 chunk 256 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 376 optimal weight: 9.9990 chunk 406 optimal weight: 10.0000 chunk 335 optimal weight: 5.9990 chunk 373 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 302 optimal weight: 8.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN D 18 HIS E 68 HIS E 113 GLN F 115 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 ASN O 38 ASN O 83 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 HIS S 84 ASN V 40 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 55743 Z= 0.352 Angle : 0.791 10.396 81872 Z= 0.408 Chirality : 0.047 0.480 10277 Planarity : 0.006 0.061 5424 Dihedral : 24.093 174.506 24243 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.51 % Favored : 95.32 % Rotamer: Outliers : 5.66 % Allowed : 13.96 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 2884 helix: 0.28 (0.14), residues: 1166 sheet: -1.12 (0.22), residues: 481 loop : -1.30 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 200 HIS 0.011 0.002 HIS J 38 PHE 0.030 0.003 PHE R 74 TYR 0.027 0.003 TYR H 85 ARG 0.009 0.001 ARG C 606 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 368 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.3138 (mtt-85) cc_final: 0.2764 (ppt170) REVERT: C 68 LYS cc_start: 0.3334 (mmtt) cc_final: 0.3013 (ttpt) REVERT: C 101 ASN cc_start: 0.2659 (OUTLIER) cc_final: 0.2129 (t0) REVERT: C 103 LEU cc_start: 0.3880 (OUTLIER) cc_final: 0.3350 (pp) REVERT: C 137 ILE cc_start: 0.4276 (mt) cc_final: 0.3983 (tt) REVERT: C 138 GLN cc_start: 0.4331 (mt0) cc_final: 0.4120 (tp-100) REVERT: C 171 LYS cc_start: 0.4827 (tttt) cc_final: 0.4593 (ttpp) REVERT: C 218 LYS cc_start: 0.5753 (tttt) cc_final: 0.4976 (tppt) REVERT: C 230 MET cc_start: 0.2872 (mmm) cc_final: 0.2617 (mtp) REVERT: C 323 HIS cc_start: 0.3596 (m-70) cc_final: 0.3261 (t-170) REVERT: C 346 THR cc_start: 0.5380 (m) cc_final: 0.5002 (p) REVERT: C 430 GLU cc_start: 0.3181 (mp0) cc_final: 0.2698 (tt0) REVERT: C 445 GLU cc_start: 0.6507 (mp0) cc_final: 0.6135 (mp0) REVERT: C 457 GLU cc_start: 0.5934 (mt-10) cc_final: 0.5614 (tm-30) REVERT: C 466 MET cc_start: 0.3800 (ttm) cc_final: 0.3321 (mmp) REVERT: C 573 ARG cc_start: 0.3350 (ttm-80) cc_final: 0.2349 (mtp-110) REVERT: C 604 GLU cc_start: 0.5541 (tt0) cc_final: 0.4978 (tm-30) REVERT: C 613 GLU cc_start: 0.6190 (tt0) cc_final: 0.5760 (mm-30) REVERT: C 629 GLU cc_start: 0.4019 (mt-10) cc_final: 0.3414 (mm-30) REVERT: C 678 ARG cc_start: 0.2067 (ttp80) cc_final: 0.0915 (ttt180) REVERT: D 21 ARG cc_start: 0.5915 (mtp-110) cc_final: 0.5658 (ttm110) REVERT: D 22 ARG cc_start: 0.6227 (OUTLIER) cc_final: 0.5394 (ttt180) REVERT: D 39 TYR cc_start: 0.6505 (m-10) cc_final: 0.6227 (m-10) REVERT: D 105 GLU cc_start: 0.6466 (mt-10) cc_final: 0.5999 (mp0) REVERT: D 108 GLN cc_start: 0.6504 (mt0) cc_final: 0.6151 (mm-40) REVERT: D 132 LYS cc_start: 0.4352 (OUTLIER) cc_final: 0.3882 (tptt) REVERT: D 142 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6519 (mm-30) REVERT: D 170 ARG cc_start: 0.5758 (ptt180) cc_final: 0.5333 (ptm160) REVERT: D 204 ASP cc_start: 0.5908 (OUTLIER) cc_final: 0.5233 (p0) REVERT: D 219 ASP cc_start: 0.5431 (m-30) cc_final: 0.4968 (t70) REVERT: D 223 GLU cc_start: 0.5127 (mt-10) cc_final: 0.4813 (mm-30) REVERT: E 26 LYS cc_start: 0.5975 (mttt) cc_final: 0.5384 (ttmt) REVERT: E 65 ILE cc_start: 0.6378 (OUTLIER) cc_final: 0.5919 (mt) REVERT: E 74 MET cc_start: 0.3215 (tmm) cc_final: 0.2969 (tmm) REVERT: E 99 HIS cc_start: 0.5671 (OUTLIER) cc_final: 0.5016 (m-70) REVERT: E 126 ARG cc_start: 0.4802 (mtt-85) cc_final: 0.3958 (tpp-160) REVERT: E 141 MET cc_start: 0.6090 (mmm) cc_final: 0.5590 (mmm) REVERT: E 163 ARG cc_start: 0.3416 (OUTLIER) cc_final: 0.1798 (ttt180) REVERT: E 167 TYR cc_start: 0.5488 (m-80) cc_final: 0.5231 (m-80) REVERT: E 187 GLU cc_start: 0.5437 (mt-10) cc_final: 0.5117 (pt0) REVERT: E 205 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6074 (mm-30) REVERT: F 152 LYS cc_start: 0.6379 (mtpp) cc_final: 0.6107 (mttt) REVERT: F 178 ARG cc_start: 0.5965 (OUTLIER) cc_final: 0.5246 (ptt-90) REVERT: G 8 LYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5667 (tmtt) REVERT: G 30 ARG cc_start: 0.7378 (mmm-85) cc_final: 0.6453 (tmm160) REVERT: G 88 ARG cc_start: 0.7654 (mtt-85) cc_final: 0.6857 (ttp-170) REVERT: G 155 LYS cc_start: 0.7412 (ttmm) cc_final: 0.6872 (mmtm) REVERT: H 60 GLU cc_start: 0.5353 (tt0) cc_final: 0.4852 (mt-10) REVERT: H 70 MET cc_start: 0.5148 (mtt) cc_final: 0.4895 (mtm) REVERT: H 86 GLN cc_start: 0.3349 (OUTLIER) cc_final: 0.3000 (mm-40) REVERT: H 94 GLU cc_start: 0.4264 (mt-10) cc_final: 0.4015 (mm-30) REVERT: H 116 MET cc_start: 0.5106 (tpt) cc_final: 0.4745 (tpp) REVERT: I 34 ARG cc_start: 0.7153 (ttm170) cc_final: 0.6601 (ttt180) REVERT: I 53 GLU cc_start: 0.6757 (mp0) cc_final: 0.6434 (mm-30) REVERT: I 55 SER cc_start: 0.5479 (p) cc_final: 0.5205 (m) REVERT: J 66 ASN cc_start: 0.5983 (t0) cc_final: 0.5593 (t0) REVERT: J 68 HIS cc_start: 0.5521 (m-70) cc_final: 0.4628 (p-80) REVERT: J 100 ARG cc_start: 0.6213 (OUTLIER) cc_final: 0.5595 (mmt90) REVERT: J 112 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.4724 (tt0) REVERT: L 17 GLU cc_start: 0.5225 (mp0) cc_final: 0.4970 (pm20) REVERT: L 32 LYS cc_start: 0.7014 (mmmt) cc_final: 0.6745 (mtpt) REVERT: L 36 THR cc_start: 0.7574 (OUTLIER) cc_final: 0.7244 (p) REVERT: L 69 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7064 (tmt170) REVERT: L 121 GLU cc_start: 0.6482 (mm-30) cc_final: 0.5954 (pt0) REVERT: N 23 ARG cc_start: 0.7395 (mtp85) cc_final: 0.6303 (ptp-170) REVERT: N 25 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6879 (mm-30) REVERT: N 35 ARG cc_start: 0.7013 (mtt180) cc_final: 0.6782 (mtp180) REVERT: N 49 TYR cc_start: 0.7624 (m-10) cc_final: 0.7203 (m-10) REVERT: N 61 TRP cc_start: 0.5207 (OUTLIER) cc_final: 0.4516 (p-90) REVERT: P 8 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8223 (ptmt) REVERT: P 48 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7065 (mm-30) REVERT: Q 6 GLN cc_start: 0.7736 (mp10) cc_final: 0.7406 (tt0) REVERT: Q 19 MET cc_start: 0.8079 (mtm) cc_final: 0.7857 (mtm) REVERT: Q 50 ASP cc_start: 0.8274 (p0) cc_final: 0.7984 (p0) REVERT: R 16 MET cc_start: 0.6552 (tpp) cc_final: 0.5767 (ptt) REVERT: R 52 TYR cc_start: 0.6413 (t80) cc_final: 0.5984 (t80) REVERT: S 29 ARG cc_start: 0.6692 (mtt90) cc_final: 0.6317 (mtm110) REVERT: T 1 MET cc_start: 0.5350 (OUTLIER) cc_final: 0.4978 (ptp) REVERT: T 3 LYS cc_start: 0.7164 (mttt) cc_final: 0.6401 (tptp) REVERT: T 23 ILE cc_start: 0.5056 (OUTLIER) cc_final: 0.4822 (tt) REVERT: T 72 VAL cc_start: 0.6301 (OUTLIER) cc_final: 0.5703 (m) REVERT: T 76 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6900 (m-30) REVERT: U 41 ARG cc_start: 0.5815 (mtp180) cc_final: 0.5397 (mtt-85) REVERT: U 47 ARG cc_start: 0.7163 (mtp85) cc_final: 0.6038 (mtm-85) REVERT: U 48 ARG cc_start: 0.6813 (mtm110) cc_final: 0.5873 (mtt180) REVERT: K 20 GLN cc_start: 0.5920 (mt0) cc_final: 0.5536 (tt0) REVERT: K 45 GLU cc_start: 0.6366 (mt-10) cc_final: 0.6154 (mm-30) REVERT: K 53 ARG cc_start: 0.6006 (mtm-85) cc_final: 0.5624 (ttm110) REVERT: K 69 THR cc_start: 0.7619 (m) cc_final: 0.7353 (p) REVERT: K 96 VAL cc_start: 0.7852 (t) cc_final: 0.7420 (m) outliers start: 142 outliers final: 89 residues processed: 472 average time/residue: 0.6906 time to fit residues: 526.9286 Evaluate side-chains 428 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 318 time to evaluate : 3.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 73 GLU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 61 TRP Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain P residue 8 LYS Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 48 GLU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 87 ARG Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 252 optimal weight: 0.8980 chunk 377 optimal weight: 3.9990 chunk 400 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 358 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN E 118 ASN E 136 GLN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN J 5 GLN J 75 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN M 104 ASN O 83 ASN Q 52 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN V 40 HIS V 79 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 55743 Z= 0.227 Angle : 0.653 8.540 81872 Z= 0.340 Chirality : 0.041 0.322 10277 Planarity : 0.005 0.047 5424 Dihedral : 23.900 175.574 24227 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.16 % Favored : 96.67 % Rotamer: Outliers : 4.83 % Allowed : 16.31 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 2884 helix: 0.73 (0.15), residues: 1167 sheet: -0.81 (0.22), residues: 499 loop : -1.08 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 200 HIS 0.006 0.001 HIS R 14 PHE 0.017 0.002 PHE R 74 TYR 0.020 0.002 TYR K 58 ARG 0.005 0.001 ARG J 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 334 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 LYS cc_start: 0.3332 (mmtt) cc_final: 0.2947 (ttpt) REVERT: C 101 ASN cc_start: 0.2837 (OUTLIER) cc_final: 0.2354 (t0) REVERT: C 103 LEU cc_start: 0.3580 (OUTLIER) cc_final: 0.3194 (pp) REVERT: C 171 LYS cc_start: 0.4839 (tttt) cc_final: 0.4580 (ttpp) REVERT: C 218 LYS cc_start: 0.5780 (tttt) cc_final: 0.4991 (tppt) REVERT: C 230 MET cc_start: 0.3067 (mmm) cc_final: 0.2774 (mtp) REVERT: C 289 ASP cc_start: 0.0974 (OUTLIER) cc_final: 0.0502 (m-30) REVERT: C 323 HIS cc_start: 0.3494 (m-70) cc_final: 0.3143 (t-170) REVERT: C 346 THR cc_start: 0.5406 (m) cc_final: 0.5049 (p) REVERT: C 445 GLU cc_start: 0.6503 (mp0) cc_final: 0.6158 (mp0) REVERT: C 457 GLU cc_start: 0.5908 (mt-10) cc_final: 0.5474 (tm-30) REVERT: C 461 GLU cc_start: 0.4178 (OUTLIER) cc_final: 0.3956 (pt0) REVERT: C 466 MET cc_start: 0.4049 (ttm) cc_final: 0.3442 (mmp) REVERT: C 599 HIS cc_start: 0.5772 (OUTLIER) cc_final: 0.5404 (t70) REVERT: C 604 GLU cc_start: 0.5512 (tt0) cc_final: 0.4974 (tm-30) REVERT: C 613 GLU cc_start: 0.6111 (tt0) cc_final: 0.5676 (mm-30) REVERT: C 660 MET cc_start: 0.2389 (mtp) cc_final: 0.2139 (mmm) REVERT: C 678 ARG cc_start: 0.2147 (ttp80) cc_final: 0.1249 (ttt180) REVERT: D 18 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.5878 (m-70) REVERT: D 21 ARG cc_start: 0.5891 (mtp-110) cc_final: 0.5634 (ttm110) REVERT: D 22 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5373 (ttt180) REVERT: D 34 GLU cc_start: 0.6572 (pt0) cc_final: 0.5927 (pp20) REVERT: D 105 GLU cc_start: 0.6504 (mt-10) cc_final: 0.6059 (mp0) REVERT: D 108 GLN cc_start: 0.6478 (mt0) cc_final: 0.6112 (mm-40) REVERT: D 132 LYS cc_start: 0.4456 (OUTLIER) cc_final: 0.4027 (tptt) REVERT: D 133 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5940 (mt-10) REVERT: D 142 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6494 (mm-30) REVERT: D 170 ARG cc_start: 0.5767 (ptt180) cc_final: 0.5351 (ptm160) REVERT: D 204 ASP cc_start: 0.5707 (OUTLIER) cc_final: 0.5066 (p0) REVERT: D 219 ASP cc_start: 0.5579 (m-30) cc_final: 0.5137 (t70) REVERT: D 223 GLU cc_start: 0.5153 (mt-10) cc_final: 0.4909 (mm-30) REVERT: E 18 TRP cc_start: 0.6575 (m100) cc_final: 0.6373 (m-90) REVERT: E 26 LYS cc_start: 0.5944 (mttt) cc_final: 0.5340 (ttmt) REVERT: E 65 ILE cc_start: 0.6376 (OUTLIER) cc_final: 0.5913 (mt) REVERT: E 87 ARG cc_start: 0.5187 (mtp-110) cc_final: 0.4757 (mtt180) REVERT: E 99 HIS cc_start: 0.5571 (OUTLIER) cc_final: 0.4901 (m-70) REVERT: E 103 LEU cc_start: 0.4609 (mm) cc_final: 0.4145 (mt) REVERT: E 126 ARG cc_start: 0.4596 (mtt-85) cc_final: 0.3826 (tpp-160) REVERT: E 163 ARG cc_start: 0.3285 (OUTLIER) cc_final: 0.1812 (ttt180) REVERT: E 167 TYR cc_start: 0.5369 (m-80) cc_final: 0.5162 (m-80) REVERT: E 175 HIS cc_start: 0.6590 (m-70) cc_final: 0.6231 (m170) REVERT: E 187 GLU cc_start: 0.5510 (mt-10) cc_final: 0.5063 (pt0) REVERT: E 205 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6003 (mm-30) REVERT: F 54 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.6738 (tmmm) REVERT: F 152 LYS cc_start: 0.6504 (mtpp) cc_final: 0.6229 (mttt) REVERT: F 178 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5278 (ptt-90) REVERT: F 184 GLU cc_start: 0.6353 (mp0) cc_final: 0.6006 (mp0) REVERT: G 8 LYS cc_start: 0.6225 (OUTLIER) cc_final: 0.5721 (tmtt) REVERT: G 30 ARG cc_start: 0.7269 (mmm-85) cc_final: 0.6521 (tmm160) REVERT: G 155 LYS cc_start: 0.7412 (ttmm) cc_final: 0.6876 (mmtm) REVERT: H 30 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5343 (mpp) REVERT: H 60 GLU cc_start: 0.5343 (tt0) cc_final: 0.4849 (mt-10) REVERT: H 70 MET cc_start: 0.5172 (mtt) cc_final: 0.4895 (mtp) REVERT: I 34 ARG cc_start: 0.7128 (ttm170) cc_final: 0.6549 (ttt180) REVERT: I 55 SER cc_start: 0.5529 (p) cc_final: 0.5254 (m) REVERT: I 110 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.6875 (mt0) REVERT: J 66 ASN cc_start: 0.5801 (t0) cc_final: 0.5368 (t0) REVERT: J 68 HIS cc_start: 0.5534 (m-70) cc_final: 0.4607 (p-80) REVERT: J 100 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5555 (mmt90) REVERT: J 112 GLU cc_start: 0.5621 (OUTLIER) cc_final: 0.4681 (tt0) REVERT: L 17 GLU cc_start: 0.5295 (mp0) cc_final: 0.4893 (pm20) REVERT: L 32 LYS cc_start: 0.7027 (mmmt) cc_final: 0.6754 (mtpt) REVERT: L 36 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7315 (p) REVERT: L 69 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7043 (tmt170) REVERT: L 121 GLU cc_start: 0.6387 (mm-30) cc_final: 0.5861 (pt0) REVERT: N 25 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6579 (mm-30) REVERT: N 35 ARG cc_start: 0.7101 (mtt180) cc_final: 0.6319 (mtp-110) REVERT: N 49 TYR cc_start: 0.7461 (m-10) cc_final: 0.6998 (m-10) REVERT: O 26 GLU cc_start: 0.7591 (mp0) cc_final: 0.7367 (mp0) REVERT: P 8 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8130 (ptmt) REVERT: P 48 GLU cc_start: 0.7474 (tp30) cc_final: 0.7077 (mm-30) REVERT: Q 6 GLN cc_start: 0.7751 (mp10) cc_final: 0.7279 (tt0) REVERT: Q 50 ASP cc_start: 0.8252 (p0) cc_final: 0.7987 (p0) REVERT: R 16 MET cc_start: 0.6572 (tpp) cc_final: 0.5754 (ptt) REVERT: R 52 TYR cc_start: 0.6270 (t80) cc_final: 0.5918 (t80) REVERT: R 81 LYS cc_start: 0.3636 (OUTLIER) cc_final: 0.2143 (mmtm) REVERT: S 29 ARG cc_start: 0.6694 (mtt90) cc_final: 0.6348 (mtm110) REVERT: T 1 MET cc_start: 0.5202 (ptt) cc_final: 0.4835 (ptp) REVERT: T 3 LYS cc_start: 0.7133 (mttt) cc_final: 0.6381 (tptt) REVERT: T 5 GLU cc_start: 0.8378 (tt0) cc_final: 0.8115 (tm-30) REVERT: T 23 ILE cc_start: 0.4985 (OUTLIER) cc_final: 0.4775 (tt) REVERT: T 72 VAL cc_start: 0.6084 (OUTLIER) cc_final: 0.5417 (m) REVERT: T 76 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: U 41 ARG cc_start: 0.5939 (mtp180) cc_final: 0.5430 (mtt-85) REVERT: U 47 ARG cc_start: 0.7101 (mtp85) cc_final: 0.5931 (mtm-85) REVERT: U 48 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.5734 (mtt180) REVERT: V 19 GLU cc_start: 0.5233 (mt-10) cc_final: 0.4742 (mp0) REVERT: V 112 ILE cc_start: 0.5917 (mm) cc_final: 0.5523 (mm) REVERT: K 20 GLN cc_start: 0.5864 (mt0) cc_final: 0.5417 (tt0) REVERT: K 45 GLU cc_start: 0.6415 (mt-10) cc_final: 0.6170 (mm-30) REVERT: K 53 ARG cc_start: 0.5971 (mtm-85) cc_final: 0.5534 (ttm110) REVERT: K 69 THR cc_start: 0.7582 (m) cc_final: 0.7277 (p) REVERT: K 88 MET cc_start: 0.4255 (mpp) cc_final: 0.4048 (mpp) REVERT: K 96 VAL cc_start: 0.7821 (t) cc_final: 0.7400 (m) outliers start: 121 outliers final: 74 residues processed: 420 average time/residue: 0.6718 time to fit residues: 461.9589 Evaluate side-chains 406 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 305 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 599 HIS Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 61 TRP Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain P residue 8 LYS Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 333 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 341 optimal weight: 0.0980 chunk 276 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 359 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 40 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 55743 Z= 0.288 Angle : 0.701 9.132 81872 Z= 0.362 Chirality : 0.043 0.342 10277 Planarity : 0.005 0.107 5424 Dihedral : 23.938 175.384 24220 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.26 % Favored : 95.60 % Rotamer: Outliers : 5.15 % Allowed : 17.35 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 2884 helix: 0.65 (0.15), residues: 1168 sheet: -0.81 (0.22), residues: 489 loop : -1.11 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 200 HIS 0.011 0.002 HIS E 99 PHE 0.024 0.002 PHE C 641 TYR 0.020 0.002 TYR K 58 ARG 0.006 0.001 ARG J 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 321 time to evaluate : 3.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 LYS cc_start: 0.3468 (mmtt) cc_final: 0.3076 (ttpt) REVERT: C 101 ASN cc_start: 0.2766 (OUTLIER) cc_final: 0.2040 (t0) REVERT: C 103 LEU cc_start: 0.3571 (OUTLIER) cc_final: 0.3086 (pp) REVERT: C 113 MET cc_start: 0.4661 (ptt) cc_final: 0.3996 (ttm) REVERT: C 171 LYS cc_start: 0.4818 (tttt) cc_final: 0.4597 (ttpp) REVERT: C 218 LYS cc_start: 0.5789 (tttt) cc_final: 0.4971 (tppt) REVERT: C 230 MET cc_start: 0.3011 (mmm) cc_final: 0.2721 (mtp) REVERT: C 323 HIS cc_start: 0.3540 (m-70) cc_final: 0.3206 (t-170) REVERT: C 346 THR cc_start: 0.5449 (m) cc_final: 0.5074 (p) REVERT: C 399 MET cc_start: 0.4607 (ptp) cc_final: 0.4399 (ptm) REVERT: C 430 GLU cc_start: 0.3461 (mp0) cc_final: 0.2937 (tt0) REVERT: C 445 GLU cc_start: 0.6512 (mp0) cc_final: 0.6266 (mp0) REVERT: C 457 GLU cc_start: 0.5906 (mt-10) cc_final: 0.5590 (tm-30) REVERT: C 466 MET cc_start: 0.3761 (ttm) cc_final: 0.3197 (mmp) REVERT: C 593 LEU cc_start: 0.3401 (OUTLIER) cc_final: 0.3110 (mp) REVERT: C 599 HIS cc_start: 0.5775 (OUTLIER) cc_final: 0.5402 (t70) REVERT: C 604 GLU cc_start: 0.5507 (tt0) cc_final: 0.4960 (tm-30) REVERT: C 613 GLU cc_start: 0.6200 (tt0) cc_final: 0.5703 (mm-30) REVERT: C 660 MET cc_start: 0.2588 (mtp) cc_final: 0.2263 (mmm) REVERT: C 669 GLU cc_start: 0.5728 (tt0) cc_final: 0.5439 (mp0) REVERT: C 678 ARG cc_start: 0.1986 (ttp80) cc_final: 0.1166 (ttt180) REVERT: D 21 ARG cc_start: 0.5861 (mtp-110) cc_final: 0.5612 (ttm110) REVERT: D 22 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.5413 (ttt180) REVERT: D 34 GLU cc_start: 0.6579 (pt0) cc_final: 0.5926 (pp20) REVERT: D 105 GLU cc_start: 0.6514 (mt-10) cc_final: 0.6030 (mp0) REVERT: D 108 GLN cc_start: 0.6454 (mt0) cc_final: 0.6071 (mm-40) REVERT: D 132 LYS cc_start: 0.4452 (OUTLIER) cc_final: 0.4021 (tptt) REVERT: D 133 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5943 (mp0) REVERT: D 142 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6516 (mm-30) REVERT: D 170 ARG cc_start: 0.5778 (ptt180) cc_final: 0.5336 (ptm160) REVERT: D 204 ASP cc_start: 0.5727 (OUTLIER) cc_final: 0.5085 (p0) REVERT: D 219 ASP cc_start: 0.5681 (m-30) cc_final: 0.5262 (t70) REVERT: D 223 GLU cc_start: 0.5326 (mt-10) cc_final: 0.4976 (mm-30) REVERT: E 26 LYS cc_start: 0.5927 (mttt) cc_final: 0.5324 (ttmt) REVERT: E 65 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6045 (mt) REVERT: E 87 ARG cc_start: 0.5203 (mtp-110) cc_final: 0.4759 (mtt180) REVERT: E 99 HIS cc_start: 0.5428 (OUTLIER) cc_final: 0.5091 (m-70) REVERT: E 103 LEU cc_start: 0.4585 (mm) cc_final: 0.4115 (mt) REVERT: E 126 ARG cc_start: 0.4581 (mtt-85) cc_final: 0.3806 (tpp-160) REVERT: E 163 ARG cc_start: 0.3383 (OUTLIER) cc_final: 0.1757 (ttt180) REVERT: E 175 HIS cc_start: 0.6769 (m-70) cc_final: 0.6370 (m170) REVERT: E 187 GLU cc_start: 0.5452 (mt-10) cc_final: 0.5023 (pt0) REVERT: E 205 GLU cc_start: 0.6706 (mt-10) cc_final: 0.5932 (mm-30) REVERT: F 54 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.6792 (tmmm) REVERT: F 152 LYS cc_start: 0.6552 (mtpp) cc_final: 0.6273 (mttt) REVERT: F 178 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.5328 (ptt-90) REVERT: G 8 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5691 (tmtt) REVERT: G 30 ARG cc_start: 0.7226 (mmm-85) cc_final: 0.6450 (tmm160) REVERT: G 155 LYS cc_start: 0.7440 (ttmm) cc_final: 0.7050 (ttpt) REVERT: H 60 GLU cc_start: 0.5354 (tt0) cc_final: 0.4856 (mt-10) REVERT: H 70 MET cc_start: 0.5187 (mtt) cc_final: 0.4893 (mtm) REVERT: H 86 GLN cc_start: 0.4525 (OUTLIER) cc_final: 0.3990 (mp10) REVERT: I 34 ARG cc_start: 0.7129 (ttm170) cc_final: 0.6532 (ttt180) REVERT: I 55 SER cc_start: 0.5532 (p) cc_final: 0.5262 (m) REVERT: I 110 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.6888 (mt0) REVERT: J 66 ASN cc_start: 0.5924 (t0) cc_final: 0.5535 (t0) REVERT: J 68 HIS cc_start: 0.5547 (m-70) cc_final: 0.4642 (p-80) REVERT: J 100 ARG cc_start: 0.6120 (OUTLIER) cc_final: 0.5525 (mmt90) REVERT: J 112 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.4631 (tt0) REVERT: L 17 GLU cc_start: 0.5422 (mp0) cc_final: 0.4939 (pm20) REVERT: L 32 LYS cc_start: 0.7014 (mmmt) cc_final: 0.6757 (mtpt) REVERT: L 36 THR cc_start: 0.7566 (OUTLIER) cc_final: 0.7250 (p) REVERT: L 69 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7070 (tmt170) REVERT: L 121 GLU cc_start: 0.6379 (mm-30) cc_final: 0.5913 (pt0) REVERT: M 17 ILE cc_start: 0.4288 (mp) cc_final: 0.4047 (mt) REVERT: N 25 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6550 (mm-30) REVERT: N 35 ARG cc_start: 0.7114 (mtt180) cc_final: 0.6388 (mtp-110) REVERT: N 49 TYR cc_start: 0.7610 (m-10) cc_final: 0.7211 (m-10) REVERT: P 8 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8134 (ptmt) REVERT: P 48 GLU cc_start: 0.7484 (tp30) cc_final: 0.7088 (mm-30) REVERT: Q 6 GLN cc_start: 0.7759 (mp10) cc_final: 0.7275 (tt0) REVERT: Q 50 ASP cc_start: 0.8257 (p0) cc_final: 0.7989 (p0) REVERT: R 16 MET cc_start: 0.6596 (tpp) cc_final: 0.5789 (ptt) REVERT: R 52 TYR cc_start: 0.6252 (t80) cc_final: 0.5864 (t80) REVERT: S 29 ARG cc_start: 0.6693 (mtt90) cc_final: 0.6372 (mtm110) REVERT: T 1 MET cc_start: 0.5342 (OUTLIER) cc_final: 0.4811 (ptp) REVERT: T 3 LYS cc_start: 0.7071 (mttt) cc_final: 0.6366 (tptp) REVERT: T 5 GLU cc_start: 0.8376 (tt0) cc_final: 0.8149 (tm-30) REVERT: T 10 ILE cc_start: 0.6821 (mt) cc_final: 0.6396 (mm) REVERT: T 23 ILE cc_start: 0.4933 (OUTLIER) cc_final: 0.4672 (tt) REVERT: T 50 TYR cc_start: 0.6018 (p90) cc_final: 0.5616 (p90) REVERT: T 66 GLN cc_start: 0.5967 (mt0) cc_final: 0.5603 (tt0) REVERT: T 72 VAL cc_start: 0.5977 (OUTLIER) cc_final: 0.5357 (m) REVERT: T 76 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6927 (m-30) REVERT: U 41 ARG cc_start: 0.5964 (mtp180) cc_final: 0.5472 (mtt-85) REVERT: U 47 ARG cc_start: 0.7090 (mtp85) cc_final: 0.5935 (mtm-85) REVERT: U 48 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.5686 (mtt180) REVERT: V 19 GLU cc_start: 0.5264 (mt-10) cc_final: 0.4760 (mp0) REVERT: V 112 ILE cc_start: 0.5729 (mm) cc_final: 0.5326 (mm) REVERT: K 20 GLN cc_start: 0.6061 (mt0) cc_final: 0.5503 (tt0) REVERT: K 45 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6142 (mm-30) REVERT: K 53 ARG cc_start: 0.5915 (mtm-85) cc_final: 0.5468 (ttm110) REVERT: K 69 THR cc_start: 0.7554 (m) cc_final: 0.7288 (p) REVERT: K 88 MET cc_start: 0.4431 (mpp) cc_final: 0.4139 (mpp) REVERT: K 96 VAL cc_start: 0.7874 (t) cc_final: 0.7454 (m) outliers start: 129 outliers final: 91 residues processed: 417 average time/residue: 0.6636 time to fit residues: 458.4557 Evaluate side-chains 421 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 305 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 599 HIS Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 61 TRP Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain P residue 8 LYS Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 40 HIS Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 134 optimal weight: 0.6980 chunk 360 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 234 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 400 optimal weight: 7.9990 chunk 332 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 210 optimal weight: 4.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 113 GLN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 55743 Z= 0.380 Angle : 0.802 10.215 81872 Z= 0.409 Chirality : 0.047 0.395 10277 Planarity : 0.006 0.091 5424 Dihedral : 24.100 174.828 24217 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.89 % Favored : 94.97 % Rotamer: Outliers : 5.74 % Allowed : 18.15 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2884 helix: 0.25 (0.14), residues: 1173 sheet: -0.81 (0.23), residues: 456 loop : -1.38 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 200 HIS 0.036 0.002 HIS V 40 PHE 0.026 0.003 PHE C 641 TYR 0.020 0.003 TYR K 58 ARG 0.008 0.001 ARG C 439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 312 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 LYS cc_start: 0.3404 (mmtt) cc_final: 0.2955 (ttpt) REVERT: C 101 ASN cc_start: 0.2788 (OUTLIER) cc_final: 0.2432 (p0) REVERT: C 103 LEU cc_start: 0.3916 (OUTLIER) cc_final: 0.3362 (pp) REVERT: C 171 LYS cc_start: 0.4899 (tttt) cc_final: 0.4665 (ttpp) REVERT: C 218 LYS cc_start: 0.5801 (tttt) cc_final: 0.4955 (tppt) REVERT: C 230 MET cc_start: 0.2926 (mmm) cc_final: 0.2645 (mtp) REVERT: C 255 VAL cc_start: 0.4211 (t) cc_final: 0.3833 (p) REVERT: C 277 ASP cc_start: 0.4759 (m-30) cc_final: 0.4266 (t0) REVERT: C 346 THR cc_start: 0.5529 (m) cc_final: 0.5227 (p) REVERT: C 399 MET cc_start: 0.4598 (ptp) cc_final: 0.4389 (ptm) REVERT: C 430 GLU cc_start: 0.3499 (mp0) cc_final: 0.2736 (tp30) REVERT: C 445 GLU cc_start: 0.6354 (mp0) cc_final: 0.6112 (mp0) REVERT: C 457 GLU cc_start: 0.5853 (mt-10) cc_final: 0.5521 (tm-30) REVERT: C 466 MET cc_start: 0.4004 (ttm) cc_final: 0.3421 (mmp) REVERT: C 593 LEU cc_start: 0.3291 (OUTLIER) cc_final: 0.3047 (mp) REVERT: C 599 HIS cc_start: 0.5789 (OUTLIER) cc_final: 0.5450 (t70) REVERT: C 604 GLU cc_start: 0.5548 (tt0) cc_final: 0.4978 (tm-30) REVERT: C 613 GLU cc_start: 0.6243 (tt0) cc_final: 0.5797 (mm-30) REVERT: C 660 MET cc_start: 0.2601 (mtp) cc_final: 0.2310 (mmm) REVERT: C 669 GLU cc_start: 0.5739 (tt0) cc_final: 0.5442 (mp0) REVERT: C 678 ARG cc_start: 0.2084 (ttp80) cc_final: 0.1281 (ttt180) REVERT: D 11 GLU cc_start: 0.4800 (OUTLIER) cc_final: 0.3614 (mp0) REVERT: D 21 ARG cc_start: 0.5869 (mtp-110) cc_final: 0.5668 (ttm110) REVERT: D 22 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.5383 (ttt180) REVERT: D 34 GLU cc_start: 0.6498 (pt0) cc_final: 0.5897 (pp20) REVERT: D 105 GLU cc_start: 0.6558 (mt-10) cc_final: 0.6068 (mp0) REVERT: D 108 GLN cc_start: 0.6421 (mt0) cc_final: 0.6030 (mm-40) REVERT: D 132 LYS cc_start: 0.4543 (OUTLIER) cc_final: 0.4255 (pttp) REVERT: D 133 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5902 (mt-10) REVERT: D 142 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6555 (mm-30) REVERT: D 170 ARG cc_start: 0.5811 (ptt180) cc_final: 0.5360 (ptm160) REVERT: D 204 ASP cc_start: 0.5724 (OUTLIER) cc_final: 0.5071 (p0) REVERT: E 26 LYS cc_start: 0.5871 (mttt) cc_final: 0.5287 (ttmt) REVERT: E 65 ILE cc_start: 0.6421 (OUTLIER) cc_final: 0.5972 (mt) REVERT: E 74 MET cc_start: 0.3081 (tmm) cc_final: 0.2833 (tmm) REVERT: E 126 ARG cc_start: 0.4683 (mtt-85) cc_final: 0.3921 (tpp-160) REVERT: E 135 GLN cc_start: 0.6234 (tt0) cc_final: 0.5832 (mm-40) REVERT: E 163 ARG cc_start: 0.3480 (OUTLIER) cc_final: 0.1803 (ttt180) REVERT: E 187 GLU cc_start: 0.5390 (mt-10) cc_final: 0.4966 (pt0) REVERT: F 54 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.6874 (tmmm) REVERT: F 152 LYS cc_start: 0.6376 (mtpp) cc_final: 0.6124 (mttt) REVERT: G 8 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5573 (tmtt) REVERT: G 30 ARG cc_start: 0.7209 (mmm-85) cc_final: 0.6445 (tmm160) REVERT: G 155 LYS cc_start: 0.7446 (ttmm) cc_final: 0.7126 (ttpt) REVERT: H 60 GLU cc_start: 0.5423 (tt0) cc_final: 0.4910 (mt-10) REVERT: H 86 GLN cc_start: 0.3158 (OUTLIER) cc_final: 0.2770 (mm-40) REVERT: I 34 ARG cc_start: 0.7126 (ttm170) cc_final: 0.6524 (ttt180) REVERT: I 110 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.6926 (mt0) REVERT: J 68 HIS cc_start: 0.5584 (m-70) cc_final: 0.4715 (p-80) REVERT: J 112 GLU cc_start: 0.5543 (OUTLIER) cc_final: 0.4691 (tt0) REVERT: L 17 GLU cc_start: 0.5576 (mp0) cc_final: 0.4972 (pm20) REVERT: L 32 LYS cc_start: 0.6994 (mmmt) cc_final: 0.6744 (mtpt) REVERT: L 36 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7297 (p) REVERT: L 69 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7036 (tmt170) REVERT: L 121 GLU cc_start: 0.6432 (mm-30) cc_final: 0.5954 (pt0) REVERT: N 35 ARG cc_start: 0.7028 (mtt180) cc_final: 0.6227 (mtp-110) REVERT: P 8 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8160 (ptmt) REVERT: Q 6 GLN cc_start: 0.7707 (mp10) cc_final: 0.7231 (tt0) REVERT: Q 50 ASP cc_start: 0.8327 (p0) cc_final: 0.8062 (p0) REVERT: R 16 MET cc_start: 0.6557 (tpp) cc_final: 0.5803 (ptt) REVERT: R 52 TYR cc_start: 0.6170 (t80) cc_final: 0.5789 (t80) REVERT: S 14 ASN cc_start: 0.7572 (t0) cc_final: 0.7261 (m110) REVERT: S 16 GLU cc_start: 0.7894 (mt-10) cc_final: 0.6778 (tm-30) REVERT: S 29 ARG cc_start: 0.6646 (mtt90) cc_final: 0.6257 (mtm110) REVERT: T 1 MET cc_start: 0.5366 (OUTLIER) cc_final: 0.4574 (ptp) REVERT: T 3 LYS cc_start: 0.6951 (mttt) cc_final: 0.6280 (tptt) REVERT: T 10 ILE cc_start: 0.6802 (mt) cc_final: 0.6379 (mm) REVERT: T 23 ILE cc_start: 0.4876 (OUTLIER) cc_final: 0.4622 (tp) REVERT: T 33 ASN cc_start: 0.5714 (m110) cc_final: 0.5421 (p0) REVERT: T 36 GLU cc_start: 0.5661 (pt0) cc_final: 0.5160 (pm20) REVERT: T 66 GLN cc_start: 0.6005 (mt0) cc_final: 0.5440 (tt0) REVERT: T 72 VAL cc_start: 0.6163 (OUTLIER) cc_final: 0.5553 (m) REVERT: T 76 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6959 (m-30) REVERT: U 41 ARG cc_start: 0.5931 (mtp180) cc_final: 0.5450 (mtt-85) REVERT: U 47 ARG cc_start: 0.7108 (mtp85) cc_final: 0.6004 (mtm-85) REVERT: U 48 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.5654 (mtt180) REVERT: V 19 GLU cc_start: 0.5287 (mt-10) cc_final: 0.4694 (mp0) REVERT: K 20 GLN cc_start: 0.6061 (mt0) cc_final: 0.5528 (tt0) REVERT: K 45 GLU cc_start: 0.6307 (mt-10) cc_final: 0.6096 (mm-30) REVERT: K 53 ARG cc_start: 0.5875 (mtm-85) cc_final: 0.5431 (ttm110) REVERT: K 57 LYS cc_start: 0.6361 (OUTLIER) cc_final: 0.4944 (tmtm) REVERT: K 88 MET cc_start: 0.4423 (mpp) cc_final: 0.4140 (mpp) REVERT: K 96 VAL cc_start: 0.7983 (t) cc_final: 0.7733 (m) outliers start: 144 outliers final: 104 residues processed: 423 average time/residue: 0.6485 time to fit residues: 455.8944 Evaluate side-chains 422 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 294 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 599 HIS Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 73 GLU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 61 TRP Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain P residue 8 LYS Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 386 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 337 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 399 optimal weight: 4.9990 chunk 249 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 HIS E 113 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 55743 Z= 0.196 Angle : 0.623 8.835 81872 Z= 0.323 Chirality : 0.039 0.295 10277 Planarity : 0.004 0.050 5424 Dihedral : 23.857 175.351 24213 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.60 % Rotamer: Outliers : 4.59 % Allowed : 19.23 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 2884 helix: 0.75 (0.15), residues: 1173 sheet: -0.77 (0.22), residues: 490 loop : -1.16 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 200 HIS 0.025 0.001 HIS E 99 PHE 0.017 0.002 PHE C 39 TYR 0.020 0.002 TYR K 58 ARG 0.006 0.000 ARG J 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 334 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 LYS cc_start: 0.3432 (mmtt) cc_final: 0.3083 (ttpt) REVERT: C 69 MET cc_start: 0.2504 (OUTLIER) cc_final: 0.2063 (mmp) REVERT: C 101 ASN cc_start: 0.3063 (OUTLIER) cc_final: 0.2715 (p0) REVERT: C 103 LEU cc_start: 0.3610 (OUTLIER) cc_final: 0.3111 (pp) REVERT: C 171 LYS cc_start: 0.4752 (tttt) cc_final: 0.4531 (ttpp) REVERT: C 218 LYS cc_start: 0.5792 (tttt) cc_final: 0.4949 (tppt) REVERT: C 230 MET cc_start: 0.3024 (mmm) cc_final: 0.2714 (mtp) REVERT: C 277 ASP cc_start: 0.4698 (m-30) cc_final: 0.4182 (t0) REVERT: C 346 THR cc_start: 0.5543 (m) cc_final: 0.5189 (p) REVERT: C 399 MET cc_start: 0.4673 (ptp) cc_final: 0.4467 (ptm) REVERT: C 430 GLU cc_start: 0.3779 (mp0) cc_final: 0.3214 (tt0) REVERT: C 445 GLU cc_start: 0.6351 (mp0) cc_final: 0.6062 (mp0) REVERT: C 457 GLU cc_start: 0.5912 (mt-10) cc_final: 0.5539 (tm-30) REVERT: C 466 MET cc_start: 0.4121 (ttm) cc_final: 0.3483 (mmp) REVERT: C 593 LEU cc_start: 0.3266 (OUTLIER) cc_final: 0.3005 (mp) REVERT: C 599 HIS cc_start: 0.5821 (OUTLIER) cc_final: 0.5471 (t70) REVERT: C 604 GLU cc_start: 0.5403 (tt0) cc_final: 0.4885 (tm-30) REVERT: C 613 GLU cc_start: 0.6193 (tt0) cc_final: 0.5703 (mm-30) REVERT: C 660 MET cc_start: 0.2573 (mtp) cc_final: 0.1903 (mmm) REVERT: C 669 GLU cc_start: 0.5729 (tt0) cc_final: 0.5414 (mp0) REVERT: C 678 ARG cc_start: 0.2147 (ttp80) cc_final: 0.1340 (ttm-80) REVERT: D 11 GLU cc_start: 0.4652 (OUTLIER) cc_final: 0.3523 (mp0) REVERT: D 18 HIS cc_start: 0.6804 (OUTLIER) cc_final: 0.5879 (m-70) REVERT: D 21 ARG cc_start: 0.5852 (mtp-110) cc_final: 0.5638 (ttm110) REVERT: D 22 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5420 (ttt180) REVERT: D 34 GLU cc_start: 0.6532 (pt0) cc_final: 0.5893 (pp20) REVERT: D 105 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6119 (mp0) REVERT: D 108 GLN cc_start: 0.6470 (mt0) cc_final: 0.6100 (mm-40) REVERT: D 132 LYS cc_start: 0.4580 (OUTLIER) cc_final: 0.4147 (mmtt) REVERT: D 133 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.5994 (mt-10) REVERT: D 142 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6546 (mm-30) REVERT: D 170 ARG cc_start: 0.5714 (ptt180) cc_final: 0.5298 (ptm160) REVERT: D 204 ASP cc_start: 0.5651 (OUTLIER) cc_final: 0.5022 (p0) REVERT: E 26 LYS cc_start: 0.5907 (mttt) cc_final: 0.5275 (ttmt) REVERT: E 65 ILE cc_start: 0.6396 (OUTLIER) cc_final: 0.5948 (mt) REVERT: E 74 MET cc_start: 0.3275 (tmm) cc_final: 0.3024 (tmm) REVERT: E 87 ARG cc_start: 0.5062 (mtp-110) cc_final: 0.4633 (mtt180) REVERT: E 103 LEU cc_start: 0.4688 (mm) cc_final: 0.4226 (mt) REVERT: E 126 ARG cc_start: 0.4721 (mtt-85) cc_final: 0.3919 (tpp-160) REVERT: E 135 GLN cc_start: 0.6199 (tt0) cc_final: 0.5818 (mm-40) REVERT: E 163 ARG cc_start: 0.3499 (OUTLIER) cc_final: 0.1708 (ttt180) REVERT: E 187 GLU cc_start: 0.5392 (mt-10) cc_final: 0.4880 (pt0) REVERT: E 205 GLU cc_start: 0.6693 (mt-10) cc_final: 0.5912 (pt0) REVERT: F 54 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.6705 (tmmm) REVERT: F 152 LYS cc_start: 0.6376 (mtpp) cc_final: 0.6157 (mttt) REVERT: G 8 LYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5767 (tmtt) REVERT: G 30 ARG cc_start: 0.7193 (mmm-85) cc_final: 0.6451 (tmm160) REVERT: G 88 ARG cc_start: 0.7613 (mtt-85) cc_final: 0.6874 (ttp-170) REVERT: G 155 LYS cc_start: 0.7426 (ttmm) cc_final: 0.7049 (ttpt) REVERT: H 30 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.5006 (mpp) REVERT: H 60 GLU cc_start: 0.5461 (tt0) cc_final: 0.4952 (mt-10) REVERT: H 103 TRP cc_start: 0.5743 (m-10) cc_final: 0.5325 (m100) REVERT: H 139 GLU cc_start: 0.5069 (OUTLIER) cc_final: 0.4565 (tp30) REVERT: I 34 ARG cc_start: 0.7180 (ttm170) cc_final: 0.6589 (ttt180) REVERT: I 55 SER cc_start: 0.5558 (p) cc_final: 0.5274 (m) REVERT: I 110 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.6884 (mt0) REVERT: J 66 ASN cc_start: 0.5988 (t0) cc_final: 0.5632 (t0) REVERT: J 68 HIS cc_start: 0.5534 (m-70) cc_final: 0.4615 (p-80) REVERT: J 100 ARG cc_start: 0.6187 (OUTLIER) cc_final: 0.5524 (mmt90) REVERT: J 112 GLU cc_start: 0.5602 (OUTLIER) cc_final: 0.4695 (tt0) REVERT: L 17 GLU cc_start: 0.5647 (mp0) cc_final: 0.5275 (tp30) REVERT: L 32 LYS cc_start: 0.6981 (mmmt) cc_final: 0.6735 (mtpt) REVERT: L 36 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7353 (p) REVERT: L 69 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7046 (tmt170) REVERT: L 121 GLU cc_start: 0.6387 (mm-30) cc_final: 0.5914 (pt0) REVERT: M 17 ILE cc_start: 0.4199 (mp) cc_final: 0.3866 (pt) REVERT: N 35 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6329 (mtp-110) REVERT: Q 6 GLN cc_start: 0.7786 (mp10) cc_final: 0.7256 (tt0) REVERT: Q 50 ASP cc_start: 0.8299 (p0) cc_final: 0.8042 (p0) REVERT: R 16 MET cc_start: 0.6687 (tpp) cc_final: 0.5875 (ptt) REVERT: R 52 TYR cc_start: 0.6170 (t80) cc_final: 0.5840 (t80) REVERT: S 29 ARG cc_start: 0.6560 (mtt90) cc_final: 0.6174 (mtm110) REVERT: S 30 THR cc_start: 0.7298 (t) cc_final: 0.7083 (p) REVERT: S 34 GLN cc_start: 0.6459 (tp-100) cc_final: 0.6170 (tt0) REVERT: T 1 MET cc_start: 0.5269 (OUTLIER) cc_final: 0.4754 (ptp) REVERT: T 3 LYS cc_start: 0.7019 (mttt) cc_final: 0.6320 (tptt) REVERT: T 10 ILE cc_start: 0.6831 (mt) cc_final: 0.6398 (mm) REVERT: T 23 ILE cc_start: 0.4683 (OUTLIER) cc_final: 0.4437 (tt) REVERT: T 33 ASN cc_start: 0.5643 (m110) cc_final: 0.5225 (t0) REVERT: T 36 GLU cc_start: 0.5652 (pt0) cc_final: 0.5162 (pm20) REVERT: T 72 VAL cc_start: 0.6025 (t) cc_final: 0.5356 (m) REVERT: U 41 ARG cc_start: 0.5962 (mtp180) cc_final: 0.5445 (mtt-85) REVERT: U 47 ARG cc_start: 0.7040 (mtp85) cc_final: 0.5918 (mtm-85) REVERT: U 48 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.5645 (mtt180) REVERT: V 19 GLU cc_start: 0.5348 (mt-10) cc_final: 0.4732 (mp0) REVERT: K 20 GLN cc_start: 0.6041 (mt0) cc_final: 0.5433 (tt0) REVERT: K 45 GLU cc_start: 0.6350 (mt-10) cc_final: 0.6133 (mm-30) REVERT: K 53 ARG cc_start: 0.5787 (mtm-85) cc_final: 0.5415 (ttm110) REVERT: K 88 MET cc_start: 0.4424 (mpp) cc_final: 0.4201 (mpp) outliers start: 115 outliers final: 76 residues processed: 418 average time/residue: 0.7368 time to fit residues: 510.0722 Evaluate side-chains 404 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 304 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 599 HIS Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 98 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 246 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 253 optimal weight: 3.9990 chunk 271 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 313 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 HIS C 464 HIS ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 55743 Z= 0.391 Angle : 0.805 10.265 81872 Z= 0.408 Chirality : 0.047 0.395 10277 Planarity : 0.006 0.092 5424 Dihedral : 24.065 175.211 24212 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.06 % Favored : 94.80 % Rotamer: Outliers : 5.50 % Allowed : 19.35 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 2884 helix: 0.28 (0.14), residues: 1172 sheet: -0.80 (0.23), residues: 459 loop : -1.43 (0.16), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 200 HIS 0.008 0.002 HIS E 175 PHE 0.026 0.003 PHE C 641 TYR 0.021 0.003 TYR J 7 ARG 0.009 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 296 time to evaluate : 3.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 LYS cc_start: 0.3488 (mmtt) cc_final: 0.3037 (ttpt) REVERT: C 101 ASN cc_start: 0.3151 (OUTLIER) cc_final: 0.2793 (p0) REVERT: C 103 LEU cc_start: 0.3728 (OUTLIER) cc_final: 0.3175 (pp) REVERT: C 171 LYS cc_start: 0.4826 (tttt) cc_final: 0.4620 (ttpp) REVERT: C 218 LYS cc_start: 0.5693 (tttt) cc_final: 0.4867 (tppt) REVERT: C 230 MET cc_start: 0.2898 (mmm) cc_final: 0.2545 (mtp) REVERT: C 277 ASP cc_start: 0.4773 (m-30) cc_final: 0.4268 (t0) REVERT: C 346 THR cc_start: 0.5463 (m) cc_final: 0.5161 (p) REVERT: C 430 GLU cc_start: 0.3692 (mp0) cc_final: 0.2920 (tp30) REVERT: C 445 GLU cc_start: 0.6355 (mp0) cc_final: 0.6134 (mp0) REVERT: C 457 GLU cc_start: 0.5935 (mt-10) cc_final: 0.5500 (tm-30) REVERT: C 466 MET cc_start: 0.4073 (ttm) cc_final: 0.3481 (mmp) REVERT: C 593 LEU cc_start: 0.3285 (OUTLIER) cc_final: 0.3030 (mp) REVERT: C 599 HIS cc_start: 0.5804 (OUTLIER) cc_final: 0.5468 (t70) REVERT: C 604 GLU cc_start: 0.5568 (tt0) cc_final: 0.4994 (tm-30) REVERT: C 613 GLU cc_start: 0.6229 (tt0) cc_final: 0.5761 (mm-30) REVERT: C 660 MET cc_start: 0.2547 (mtp) cc_final: 0.2165 (mmm) REVERT: C 669 GLU cc_start: 0.5699 (tt0) cc_final: 0.5389 (mp0) REVERT: C 678 ARG cc_start: 0.1942 (ttp80) cc_final: 0.1289 (ttm-80) REVERT: D 11 GLU cc_start: 0.4827 (OUTLIER) cc_final: 0.3640 (mp0) REVERT: D 21 ARG cc_start: 0.5830 (mtp-110) cc_final: 0.5591 (ttm110) REVERT: D 22 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.5366 (ttt180) REVERT: D 34 GLU cc_start: 0.6491 (pt0) cc_final: 0.5906 (pp20) REVERT: D 105 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6152 (mp0) REVERT: D 108 GLN cc_start: 0.6442 (mt0) cc_final: 0.6078 (mm-40) REVERT: D 132 LYS cc_start: 0.4560 (OUTLIER) cc_final: 0.4304 (pttp) REVERT: D 133 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5908 (mt-10) REVERT: D 142 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6547 (mm-30) REVERT: D 170 ARG cc_start: 0.5911 (ptt180) cc_final: 0.5449 (ptm160) REVERT: D 204 ASP cc_start: 0.5714 (OUTLIER) cc_final: 0.5049 (p0) REVERT: E 26 LYS cc_start: 0.5891 (mttt) cc_final: 0.5248 (ttmt) REVERT: E 65 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.6003 (mt) REVERT: E 74 MET cc_start: 0.3234 (tmm) cc_final: 0.3026 (tmm) REVERT: E 126 ARG cc_start: 0.4877 (mtt-85) cc_final: 0.4056 (tpp-160) REVERT: E 135 GLN cc_start: 0.6209 (tt0) cc_final: 0.5809 (mm-40) REVERT: E 163 ARG cc_start: 0.3559 (OUTLIER) cc_final: 0.1850 (ttt180) REVERT: E 187 GLU cc_start: 0.5330 (mt-10) cc_final: 0.4909 (pt0) REVERT: F 54 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.6872 (tmmm) REVERT: F 152 LYS cc_start: 0.6376 (mtpp) cc_final: 0.6132 (mttt) REVERT: G 8 LYS cc_start: 0.6163 (OUTLIER) cc_final: 0.5652 (tmtt) REVERT: G 30 ARG cc_start: 0.7225 (mmm-85) cc_final: 0.6465 (tmm160) REVERT: G 155 LYS cc_start: 0.7465 (ttmm) cc_final: 0.7142 (ttpt) REVERT: H 60 GLU cc_start: 0.5426 (tt0) cc_final: 0.4906 (mt-10) REVERT: H 86 GLN cc_start: 0.4382 (OUTLIER) cc_final: 0.3721 (mp10) REVERT: H 111 ARG cc_start: 0.4777 (mtp85) cc_final: 0.4411 (mtm180) REVERT: I 34 ARG cc_start: 0.7140 (ttm170) cc_final: 0.6544 (ttt180) REVERT: I 110 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.6915 (mt0) REVERT: J 68 HIS cc_start: 0.5551 (m-70) cc_final: 0.4680 (p-80) REVERT: J 112 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.4647 (tt0) REVERT: L 17 GLU cc_start: 0.5631 (mp0) cc_final: 0.4994 (pm20) REVERT: L 32 LYS cc_start: 0.7004 (mmmt) cc_final: 0.6755 (mtpt) REVERT: L 36 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.7313 (p) REVERT: L 121 GLU cc_start: 0.6449 (mm-30) cc_final: 0.5975 (pt0) REVERT: M 17 ILE cc_start: 0.4178 (mp) cc_final: 0.3857 (pt) REVERT: N 35 ARG cc_start: 0.7003 (mtt180) cc_final: 0.6234 (mtp-110) REVERT: O 38 ASN cc_start: 0.6607 (OUTLIER) cc_final: 0.6345 (m110) REVERT: P 8 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8116 (ptmt) REVERT: Q 6 GLN cc_start: 0.7709 (mp10) cc_final: 0.7216 (tt0) REVERT: Q 50 ASP cc_start: 0.8309 (p0) cc_final: 0.8043 (p0) REVERT: R 16 MET cc_start: 0.6639 (tpp) cc_final: 0.5826 (ptt) REVERT: R 52 TYR cc_start: 0.6164 (t80) cc_final: 0.5775 (t80) REVERT: S 14 ASN cc_start: 0.7576 (t0) cc_final: 0.7323 (m-40) REVERT: S 16 GLU cc_start: 0.7845 (mt-10) cc_final: 0.6726 (tm-30) REVERT: S 29 ARG cc_start: 0.6598 (mtt90) cc_final: 0.6215 (mtm110) REVERT: T 1 MET cc_start: 0.5370 (OUTLIER) cc_final: 0.4789 (ptp) REVERT: T 3 LYS cc_start: 0.6974 (mttt) cc_final: 0.6292 (tptt) REVERT: T 10 ILE cc_start: 0.6798 (mt) cc_final: 0.6369 (mm) REVERT: T 23 ILE cc_start: 0.4772 (OUTLIER) cc_final: 0.4517 (tt) REVERT: T 33 ASN cc_start: 0.5601 (m110) cc_final: 0.5314 (p0) REVERT: T 36 GLU cc_start: 0.5727 (pt0) cc_final: 0.5213 (pm20) REVERT: T 72 VAL cc_start: 0.6025 (t) cc_final: 0.5542 (m) REVERT: U 41 ARG cc_start: 0.5913 (mtp180) cc_final: 0.5400 (mtt-85) REVERT: U 47 ARG cc_start: 0.7074 (mtp85) cc_final: 0.5970 (mtm-85) REVERT: U 48 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5662 (mtt180) REVERT: V 19 GLU cc_start: 0.5314 (mt-10) cc_final: 0.4689 (mp0) REVERT: V 52 LEU cc_start: 0.2472 (OUTLIER) cc_final: 0.2264 (mm) REVERT: K 20 GLN cc_start: 0.6162 (mt0) cc_final: 0.5502 (tt0) REVERT: K 53 ARG cc_start: 0.5942 (mtm-85) cc_final: 0.5457 (ttm110) REVERT: K 57 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5214 (tmtm) outliers start: 138 outliers final: 103 residues processed: 400 average time/residue: 0.6771 time to fit residues: 446.5928 Evaluate side-chains 410 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 283 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 599 HIS Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 61 TRP Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain P residue 8 LYS Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 10.0000 chunk 382 optimal weight: 0.9990 chunk 348 optimal weight: 2.9990 chunk 371 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 291 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 336 optimal weight: 4.9990 chunk 351 optimal weight: 3.9990 chunk 370 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 HIS E 113 GLN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 55743 Z= 0.211 Angle : 0.637 9.191 81872 Z= 0.330 Chirality : 0.040 0.319 10277 Planarity : 0.005 0.052 5424 Dihedral : 23.887 175.307 24212 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.64 % Favored : 96.22 % Rotamer: Outliers : 4.79 % Allowed : 20.22 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 2884 helix: 0.63 (0.15), residues: 1171 sheet: -0.72 (0.23), residues: 473 loop : -1.22 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 200 HIS 0.007 0.001 HIS E 33 PHE 0.022 0.002 PHE T 26 TYR 0.020 0.002 TYR K 58 ARG 0.007 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 305 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 LYS cc_start: 0.3578 (mmtt) cc_final: 0.3152 (ttpt) REVERT: C 101 ASN cc_start: 0.3415 (OUTLIER) cc_final: 0.3110 (p0) REVERT: C 103 LEU cc_start: 0.3691 (OUTLIER) cc_final: 0.3102 (pp) REVERT: C 131 ARG cc_start: 0.4742 (ttt180) cc_final: 0.3143 (ttt90) REVERT: C 141 VAL cc_start: 0.5346 (OUTLIER) cc_final: 0.4738 (p) REVERT: C 171 LYS cc_start: 0.4789 (tttt) cc_final: 0.4560 (ttpp) REVERT: C 218 LYS cc_start: 0.5768 (tttt) cc_final: 0.4945 (tppt) REVERT: C 230 MET cc_start: 0.2970 (mmm) cc_final: 0.2669 (mtp) REVERT: C 277 ASP cc_start: 0.4676 (m-30) cc_final: 0.4159 (t0) REVERT: C 346 THR cc_start: 0.5534 (m) cc_final: 0.5189 (p) REVERT: C 430 GLU cc_start: 0.3760 (mp0) cc_final: 0.3187 (tt0) REVERT: C 445 GLU cc_start: 0.6372 (mp0) cc_final: 0.6076 (mp0) REVERT: C 457 GLU cc_start: 0.5914 (mt-10) cc_final: 0.5505 (tm-30) REVERT: C 466 MET cc_start: 0.4252 (ttm) cc_final: 0.3613 (mmp) REVERT: C 593 LEU cc_start: 0.3223 (OUTLIER) cc_final: 0.2942 (mp) REVERT: C 599 HIS cc_start: 0.5847 (OUTLIER) cc_final: 0.5486 (t70) REVERT: C 604 GLU cc_start: 0.5472 (tt0) cc_final: 0.4936 (tm-30) REVERT: C 613 GLU cc_start: 0.6207 (tt0) cc_final: 0.5707 (mm-30) REVERT: C 660 MET cc_start: 0.2631 (mtp) cc_final: 0.1891 (mmm) REVERT: C 669 GLU cc_start: 0.5711 (tt0) cc_final: 0.5394 (mp0) REVERT: C 678 ARG cc_start: 0.2056 (ttp80) cc_final: 0.1405 (ttm-80) REVERT: D 11 GLU cc_start: 0.4635 (OUTLIER) cc_final: 0.3512 (mp0) REVERT: D 22 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5419 (ttt180) REVERT: D 34 GLU cc_start: 0.6564 (pt0) cc_final: 0.5940 (pp20) REVERT: D 105 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6201 (mp0) REVERT: D 108 GLN cc_start: 0.6489 (mt0) cc_final: 0.6120 (mm-40) REVERT: D 132 LYS cc_start: 0.4654 (OUTLIER) cc_final: 0.4174 (mmtt) REVERT: D 133 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5993 (mt-10) REVERT: D 142 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6519 (mm-30) REVERT: D 170 ARG cc_start: 0.5781 (ptt180) cc_final: 0.5320 (ptm160) REVERT: D 204 ASP cc_start: 0.5662 (OUTLIER) cc_final: 0.5045 (p0) REVERT: E 26 LYS cc_start: 0.5944 (mttt) cc_final: 0.5289 (ttmt) REVERT: E 65 ILE cc_start: 0.6445 (OUTLIER) cc_final: 0.5958 (mt) REVERT: E 74 MET cc_start: 0.3235 (tmm) cc_final: 0.2980 (tmm) REVERT: E 87 ARG cc_start: 0.5142 (mtp-110) cc_final: 0.4690 (mtt180) REVERT: E 103 LEU cc_start: 0.4708 (mm) cc_final: 0.4229 (mt) REVERT: E 126 ARG cc_start: 0.4979 (mtt-85) cc_final: 0.4102 (tpp-160) REVERT: E 135 GLN cc_start: 0.6113 (tt0) cc_final: 0.5734 (mm-40) REVERT: E 163 ARG cc_start: 0.3617 (OUTLIER) cc_final: 0.1796 (ttt180) REVERT: E 187 GLU cc_start: 0.5369 (mt-10) cc_final: 0.4931 (pt0) REVERT: E 205 GLU cc_start: 0.6713 (mt-10) cc_final: 0.5938 (pt0) REVERT: F 54 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.6750 (tmmm) REVERT: F 152 LYS cc_start: 0.6443 (mtpp) cc_final: 0.6190 (mttt) REVERT: G 8 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5714 (tmtt) REVERT: G 30 ARG cc_start: 0.7234 (mmm-85) cc_final: 0.6481 (tmm160) REVERT: G 155 LYS cc_start: 0.7464 (ttmm) cc_final: 0.7077 (ttpt) REVERT: H 16 PRO cc_start: 0.5544 (Cg_endo) cc_final: 0.5330 (Cg_exo) REVERT: H 30 MET cc_start: 0.5945 (OUTLIER) cc_final: 0.5292 (mpp) REVERT: H 60 GLU cc_start: 0.5367 (tt0) cc_final: 0.4845 (mt-10) REVERT: H 70 MET cc_start: 0.5222 (mtt) cc_final: 0.4869 (mtm) REVERT: H 103 TRP cc_start: 0.5631 (m-10) cc_final: 0.5229 (m100) REVERT: H 111 ARG cc_start: 0.4818 (mtp85) cc_final: 0.4481 (mtm180) REVERT: H 139 GLU cc_start: 0.5021 (OUTLIER) cc_final: 0.4524 (tp30) REVERT: I 34 ARG cc_start: 0.7175 (ttm170) cc_final: 0.6581 (ttt180) REVERT: I 55 SER cc_start: 0.5603 (p) cc_final: 0.5317 (m) REVERT: I 110 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.6896 (mt0) REVERT: J 66 ASN cc_start: 0.5944 (t0) cc_final: 0.5623 (t0) REVERT: J 68 HIS cc_start: 0.5571 (m-70) cc_final: 0.4655 (p-80) REVERT: J 112 GLU cc_start: 0.5622 (OUTLIER) cc_final: 0.4711 (tt0) REVERT: L 17 GLU cc_start: 0.5607 (mp0) cc_final: 0.5260 (tp30) REVERT: L 32 LYS cc_start: 0.6992 (mmmt) cc_final: 0.6746 (mtpt) REVERT: L 36 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7296 (p) REVERT: L 121 GLU cc_start: 0.6393 (mm-30) cc_final: 0.5926 (pt0) REVERT: M 17 ILE cc_start: 0.4063 (mp) cc_final: 0.3735 (pt) REVERT: N 35 ARG cc_start: 0.7049 (mtt180) cc_final: 0.6327 (mtp-110) REVERT: O 38 ASN cc_start: 0.6474 (OUTLIER) cc_final: 0.6272 (m-40) REVERT: P 8 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8117 (ptmt) REVERT: Q 6 GLN cc_start: 0.7776 (mp10) cc_final: 0.7213 (tt0) REVERT: Q 50 ASP cc_start: 0.8298 (p0) cc_final: 0.8047 (p0) REVERT: R 16 MET cc_start: 0.6624 (tpp) cc_final: 0.5806 (ptt) REVERT: R 52 TYR cc_start: 0.6152 (t80) cc_final: 0.5843 (t80) REVERT: S 14 ASN cc_start: 0.7583 (t0) cc_final: 0.7230 (m110) REVERT: S 29 ARG cc_start: 0.6600 (mtt90) cc_final: 0.6217 (mtm110) REVERT: S 30 THR cc_start: 0.7318 (t) cc_final: 0.7105 (p) REVERT: S 34 GLN cc_start: 0.6503 (tp-100) cc_final: 0.6215 (tt0) REVERT: T 1 MET cc_start: 0.5247 (OUTLIER) cc_final: 0.4722 (ptp) REVERT: T 3 LYS cc_start: 0.7047 (mttt) cc_final: 0.6365 (tptt) REVERT: T 10 ILE cc_start: 0.6801 (mt) cc_final: 0.6368 (mm) REVERT: T 23 ILE cc_start: 0.4560 (OUTLIER) cc_final: 0.4324 (tt) REVERT: T 36 GLU cc_start: 0.5729 (pt0) cc_final: 0.5229 (pm20) REVERT: T 72 VAL cc_start: 0.5880 (t) cc_final: 0.5314 (m) REVERT: U 41 ARG cc_start: 0.5938 (mtp180) cc_final: 0.5437 (mtt-85) REVERT: U 47 ARG cc_start: 0.7007 (mtp85) cc_final: 0.5889 (mtm-85) REVERT: U 48 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.5659 (mtt180) REVERT: V 19 GLU cc_start: 0.5329 (mt-10) cc_final: 0.4688 (mp0) REVERT: K 20 GLN cc_start: 0.6135 (mt0) cc_final: 0.5468 (tt0) REVERT: K 53 ARG cc_start: 0.5835 (mtm-85) cc_final: 0.5421 (ttm110) REVERT: K 57 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5089 (tmtm) REVERT: K 88 MET cc_start: 0.4195 (mpp) cc_final: 0.3956 (mpp) outliers start: 120 outliers final: 89 residues processed: 395 average time/residue: 0.6849 time to fit residues: 447.9922 Evaluate side-chains 408 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 294 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 599 HIS Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain P residue 8 LYS Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 3.9990 chunk 393 optimal weight: 10.0000 chunk 239 optimal weight: 0.0060 chunk 186 optimal weight: 0.9980 chunk 273 optimal weight: 1.9990 chunk 412 optimal weight: 7.9990 chunk 379 optimal weight: 1.9990 chunk 328 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 253 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 HIS ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 33 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 55743 Z= 0.148 Angle : 0.570 10.678 81872 Z= 0.296 Chirality : 0.036 0.273 10277 Planarity : 0.004 0.049 5424 Dihedral : 23.699 176.755 24212 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.57 % Rotamer: Outliers : 3.51 % Allowed : 21.54 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 2884 helix: 1.01 (0.15), residues: 1176 sheet: -0.48 (0.23), residues: 498 loop : -1.01 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 200 HIS 0.007 0.001 HIS E 33 PHE 0.034 0.001 PHE C 556 TYR 0.021 0.001 TYR C 575 ARG 0.007 0.000 ARG H 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 328 time to evaluate : 3.569 Fit side-chains revert: symmetry clash REVERT: C 68 LYS cc_start: 0.3500 (mmtt) cc_final: 0.3087 (ttpt) REVERT: C 69 MET cc_start: 0.2849 (OUTLIER) cc_final: 0.2487 (mmp) REVERT: C 101 ASN cc_start: 0.3625 (OUTLIER) cc_final: 0.3312 (p0) REVERT: C 103 LEU cc_start: 0.3857 (OUTLIER) cc_final: 0.3311 (pp) REVERT: C 141 VAL cc_start: 0.5395 (OUTLIER) cc_final: 0.4789 (p) REVERT: C 171 LYS cc_start: 0.4955 (tttt) cc_final: 0.4676 (ttpp) REVERT: C 218 LYS cc_start: 0.5777 (tttt) cc_final: 0.4934 (tppt) REVERT: C 230 MET cc_start: 0.2962 (mmm) cc_final: 0.2643 (mtp) REVERT: C 277 ASP cc_start: 0.4666 (m-30) cc_final: 0.4198 (t0) REVERT: C 346 THR cc_start: 0.5561 (m) cc_final: 0.5159 (p) REVERT: C 430 GLU cc_start: 0.3895 (mp0) cc_final: 0.3360 (tt0) REVERT: C 445 GLU cc_start: 0.6460 (mp0) cc_final: 0.6182 (mp0) REVERT: C 447 LEU cc_start: 0.4575 (OUTLIER) cc_final: 0.4182 (tp) REVERT: C 457 GLU cc_start: 0.5998 (mt-10) cc_final: 0.5582 (tm-30) REVERT: C 466 MET cc_start: 0.4193 (ttm) cc_final: 0.3443 (mmp) REVERT: C 468 VAL cc_start: 0.2796 (OUTLIER) cc_final: 0.2552 (t) REVERT: C 514 ASP cc_start: 0.5912 (m-30) cc_final: 0.5676 (p0) REVERT: C 531 ARG cc_start: 0.4389 (mtt180) cc_final: 0.4033 (mmt180) REVERT: C 593 LEU cc_start: 0.3163 (OUTLIER) cc_final: 0.2791 (mp) REVERT: C 599 HIS cc_start: 0.5878 (OUTLIER) cc_final: 0.5499 (t70) REVERT: C 604 GLU cc_start: 0.5431 (tt0) cc_final: 0.4885 (tm-30) REVERT: C 613 GLU cc_start: 0.6152 (tt0) cc_final: 0.5664 (mm-30) REVERT: C 660 MET cc_start: 0.2615 (mtp) cc_final: 0.1747 (mmm) REVERT: C 669 GLU cc_start: 0.5662 (tt0) cc_final: 0.5326 (mp0) REVERT: C 678 ARG cc_start: 0.2057 (ttp80) cc_final: 0.1507 (ttm-80) REVERT: C 710 MET cc_start: 0.2012 (tmm) cc_final: 0.0848 (mpp) REVERT: D 11 GLU cc_start: 0.4433 (OUTLIER) cc_final: 0.2396 (mt-10) REVERT: D 22 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.5389 (ttt180) REVERT: D 105 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6223 (mp0) REVERT: D 108 GLN cc_start: 0.6446 (mt0) cc_final: 0.6068 (mm-40) REVERT: D 132 LYS cc_start: 0.4730 (OUTLIER) cc_final: 0.4237 (mmtt) REVERT: D 133 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6099 (mp0) REVERT: D 142 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6504 (mm-30) REVERT: D 159 ASP cc_start: 0.6785 (m-30) cc_final: 0.5989 (t70) REVERT: D 170 ARG cc_start: 0.5722 (ptt180) cc_final: 0.5291 (ptm160) REVERT: D 204 ASP cc_start: 0.5634 (OUTLIER) cc_final: 0.5058 (p0) REVERT: E 26 LYS cc_start: 0.5948 (mttt) cc_final: 0.4867 (tptt) REVERT: E 65 ILE cc_start: 0.6379 (mm) cc_final: 0.5920 (mt) REVERT: E 74 MET cc_start: 0.3311 (tmm) cc_final: 0.3056 (tmm) REVERT: E 87 ARG cc_start: 0.5197 (mtp-110) cc_final: 0.4754 (mtt180) REVERT: E 103 LEU cc_start: 0.4812 (mm) cc_final: 0.4348 (mt) REVERT: E 105 ILE cc_start: 0.3577 (mt) cc_final: 0.3262 (mt) REVERT: E 126 ARG cc_start: 0.4833 (mtt-85) cc_final: 0.3992 (tpp-160) REVERT: E 135 GLN cc_start: 0.6125 (tt0) cc_final: 0.5775 (mm-40) REVERT: E 163 ARG cc_start: 0.3481 (ppt170) cc_final: 0.1646 (ttt180) REVERT: E 175 HIS cc_start: 0.7033 (m170) cc_final: 0.6567 (m90) REVERT: E 187 GLU cc_start: 0.5480 (mt-10) cc_final: 0.4932 (pt0) REVERT: E 205 GLU cc_start: 0.6655 (mt-10) cc_final: 0.5857 (mm-30) REVERT: F 54 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.6624 (tmmm) REVERT: G 8 LYS cc_start: 0.6282 (OUTLIER) cc_final: 0.5807 (tmtt) REVERT: G 30 ARG cc_start: 0.7200 (mmm-85) cc_final: 0.6542 (tmm160) REVERT: G 155 LYS cc_start: 0.7457 (ttmm) cc_final: 0.7072 (ttpt) REVERT: H 60 GLU cc_start: 0.5333 (tt0) cc_final: 0.4850 (mt-10) REVERT: H 70 MET cc_start: 0.5294 (mtt) cc_final: 0.4966 (mtm) REVERT: H 103 TRP cc_start: 0.5671 (m-10) cc_final: 0.5293 (m100) REVERT: H 111 ARG cc_start: 0.4960 (mtp85) cc_final: 0.4498 (mtm180) REVERT: H 117 GLU cc_start: 0.4489 (OUTLIER) cc_final: 0.4056 (mp0) REVERT: H 144 MET cc_start: 0.4265 (mtm) cc_final: 0.4039 (mmm) REVERT: I 34 ARG cc_start: 0.7178 (ttm170) cc_final: 0.6478 (ttt180) REVERT: I 38 GLU cc_start: 0.7821 (tt0) cc_final: 0.7470 (mm-30) REVERT: I 54 ASP cc_start: 0.7506 (m-30) cc_final: 0.6827 (p0) REVERT: I 55 SER cc_start: 0.5643 (p) cc_final: 0.5146 (m) REVERT: I 110 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.6871 (mt0) REVERT: J 66 ASN cc_start: 0.5796 (t0) cc_final: 0.5509 (t0) REVERT: J 68 HIS cc_start: 0.5503 (m-70) cc_final: 0.4600 (p-80) REVERT: J 100 ARG cc_start: 0.6066 (OUTLIER) cc_final: 0.5489 (tpt-90) REVERT: J 112 GLU cc_start: 0.5216 (OUTLIER) cc_final: 0.4548 (tt0) REVERT: L 17 GLU cc_start: 0.5695 (mp0) cc_final: 0.5341 (tp30) REVERT: L 32 LYS cc_start: 0.6993 (mmmt) cc_final: 0.6751 (mtpt) REVERT: L 36 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7428 (p) REVERT: L 53 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6560 (ttm) REVERT: L 69 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7109 (tmt170) REVERT: L 121 GLU cc_start: 0.6371 (mm-30) cc_final: 0.5876 (pt0) REVERT: N 35 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6283 (mtp-110) REVERT: Q 6 GLN cc_start: 0.7733 (mp10) cc_final: 0.7185 (tt0) REVERT: Q 50 ASP cc_start: 0.8254 (p0) cc_final: 0.7997 (p0) REVERT: R 16 MET cc_start: 0.6684 (tpp) cc_final: 0.5819 (ptt) REVERT: R 52 TYR cc_start: 0.6114 (t80) cc_final: 0.5729 (t80) REVERT: S 29 ARG cc_start: 0.6622 (mtt90) cc_final: 0.6198 (mtm110) REVERT: S 34 GLN cc_start: 0.6549 (tp-100) cc_final: 0.6252 (tt0) REVERT: T 1 MET cc_start: 0.5128 (OUTLIER) cc_final: 0.4438 (ptp) REVERT: T 3 LYS cc_start: 0.7134 (mttt) cc_final: 0.6387 (tptt) REVERT: T 10 ILE cc_start: 0.6777 (mt) cc_final: 0.6343 (mm) REVERT: T 23 ILE cc_start: 0.4598 (OUTLIER) cc_final: 0.4329 (tt) REVERT: T 33 ASN cc_start: 0.5672 (m110) cc_final: 0.5289 (p0) REVERT: T 36 GLU cc_start: 0.5677 (pt0) cc_final: 0.5191 (pm20) REVERT: T 72 VAL cc_start: 0.5739 (t) cc_final: 0.5131 (m) REVERT: T 84 ASP cc_start: 0.4564 (m-30) cc_final: 0.4222 (t0) REVERT: U 41 ARG cc_start: 0.5927 (mtp180) cc_final: 0.5428 (mtt-85) REVERT: U 47 ARG cc_start: 0.6955 (mtp85) cc_final: 0.5755 (mtm-85) REVERT: U 48 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.5707 (mtt180) REVERT: K 20 GLN cc_start: 0.6089 (mt0) cc_final: 0.5413 (tt0) REVERT: K 53 ARG cc_start: 0.5814 (mtm-85) cc_final: 0.5215 (ttm110) REVERT: K 57 LYS cc_start: 0.6289 (OUTLIER) cc_final: 0.5910 (tptt) REVERT: K 88 MET cc_start: 0.4101 (mpp) cc_final: 0.3886 (mpp) outliers start: 88 outliers final: 50 residues processed: 393 average time/residue: 0.6966 time to fit residues: 444.5957 Evaluate side-chains 377 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 302 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 599 HIS Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 260 optimal weight: 10.0000 chunk 349 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 302 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 HIS ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.125052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.119218 restraints weight = 107907.804| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 0.55 r_work: 0.3817 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 1.80 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 55743 Z= 0.483 Angle : 0.893 10.536 81872 Z= 0.445 Chirality : 0.051 0.421 10277 Planarity : 0.007 0.146 5424 Dihedral : 24.079 175.210 24206 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.24 % Favored : 94.63 % Rotamer: Outliers : 4.11 % Allowed : 21.34 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 2884 helix: 0.13 (0.14), residues: 1183 sheet: -0.68 (0.23), residues: 460 loop : -1.45 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 200 HIS 0.010 0.002 HIS J 38 PHE 0.031 0.003 PHE C 641 TYR 0.037 0.003 TYR K 58 ARG 0.014 0.001 ARG E 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12138.56 seconds wall clock time: 223 minutes 1.62 seconds (13381.62 seconds total)