Starting phenix.real_space_refine on Tue Nov 19 03:26:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cec_16605/11_2024/8cec_16605.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cec_16605/11_2024/8cec_16605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cec_16605/11_2024/8cec_16605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cec_16605/11_2024/8cec_16605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cec_16605/11_2024/8cec_16605.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cec_16605/11_2024/8cec_16605.cif" } resolution = 3.57 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 179 residue(s): 1.49s 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': 110, 'rna2p_pyr': 75, 'rna3p_pur': 646, 'rna3p_pyr': 502} Link IDs: {'rna2p': 184, 'rna3p': 1148} 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: "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: "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: "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: "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: {'PTRANS': 5, '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: "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: "H" 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: "K" 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: "N" 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: "R" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 761 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "X" 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: "Y" 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: "a" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Time building chain proxies: 27.21, per 1000 atoms: 0.52 Number of scatterers: 51964 At special positions: 0 Unit cell: (188.8, 225.6, 204, 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 Y 24 " - pdb=" SG CYS Y 27 " distance=2.10 Simple disulfide: pdb=" SG CYS Y 27 " - pdb=" SG CYS Y 43 " distance=2.05 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: 11.32 Conformation dependent library (CDL) restraints added in 3.0 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: 95 helices and 34 sheets defined 42.5% alpha, 21.3% beta 421 base pairs and 788 stacking pairs defined. Time for finding SS restraints: 23.27 Creating SS restraints... Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 23 through 31 Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.621A pdb=" N LEU C 103 " --> pdb=" O PRO C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.585A pdb=" N LYS C 171 " --> pdb=" O LYS C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 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: 4.286A 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 493 removed outlier: 3.979A pdb=" N PHE C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 516 removed outlier: 4.002A pdb=" N LEU C 509 " --> pdb=" O HIS C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 531 Processing helix chain 'C' and resid 562 through 576 Processing helix chain 'C' and resid 582 through 624 Proline residue: C 594 - end of helix removed outlier: 3.580A pdb=" N ALA C 610 " --> pdb=" O ARG C 606 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 624 " --> pdb=" O ALA C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 660 No H-bonds generated for 'chain 'C' and resid 658 through 660' Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.850A pdb=" N ARG D 29 " --> pdb=" O LYS D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 63 removed outlier: 3.963A pdb=" N LYS D 48 " --> pdb=" O GLN D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.795A pdb=" N ARG D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 149 removed outlier: 3.503A pdb=" N GLN D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 179 Processing helix chain 'D' and resid 206 through 226 removed outlier: 3.613A pdb=" N MET D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 16 removed outlier: 4.102A pdb=" N LEU F 11 " --> pdb=" O PRO F 7 " (cutoff:3.500A) removed outlier: 3.723A 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 76 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: 3.734A 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 removed outlier: 3.646A pdb=" N SER F 154 " --> pdb=" O ILE F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 200 removed outlier: 3.968A pdb=" N ILE F 194 " --> pdb=" O ASN F 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 70 Processing helix chain 'G' and resid 108 through 119 Processing helix chain 'G' and resid 132 through 146 Processing helix chain 'G' and resid 149 through 158 removed outlier: 3.607A pdb=" N LEU G 156 " --> pdb=" O ASP G 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 19 Processing helix chain 'I' and resid 30 through 43 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 115 through 122 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 22 through 26 Processing helix chain 'L' and resid 127 through 131 Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.827A pdb=" N THR O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 77 Processing helix chain 'P' and resid 78 through 88 removed outlier: 3.525A pdb=" N GLN P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 41 Processing helix chain 'S' and resid 43 through 64 removed outlier: 3.505A pdb=" N THR S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR S 64 " --> pdb=" O LYS S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 84 removed outlier: 3.512A pdb=" N ARG S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 33 Processing helix chain 'T' and resid 68 through 82 removed outlier: 3.547A pdb=" N VAL T 72 " --> pdb=" O ASP T 68 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE T 81 " --> pdb=" O ARG T 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 22 Processing helix chain 'U' and resid 30 through 35 Processing helix chain 'U' and resid 36 through 38 No H-bonds generated for 'chain 'U' and resid 36 through 38' Processing helix chain 'U' and resid 46 through 51 Processing helix chain 'U' and resid 53 through 70 removed outlier: 3.613A pdb=" N LYS U 59 " --> pdb=" O LYS U 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 61 removed outlier: 4.085A pdb=" N SER V 60 " --> pdb=" O GLY V 56 " (cutoff:3.500A) removed outlier: 3.590A 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: 3.785A pdb=" N GLU V 78 " --> pdb=" O LYS V 74 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS V 79 " --> pdb=" O GLY V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 106 Processing helix chain 'H' and resid 6 through 12 Processing helix chain 'H' and resid 27 through 46 Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.840A pdb=" N GLY H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.524A pdb=" N GLY H 95 " --> pdb=" O ASN H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.532A pdb=" N GLU H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.746A pdb=" N LYS H 134 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 31 Processing helix chain 'K' and resid 35 through 55 removed outlier: 3.597A pdb=" N SER K 39 " --> pdb=" O LYS K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 70 Processing helix chain 'K' and resid 92 through 111 removed outlier: 3.519A pdb=" N THR K 97 " --> pdb=" O PRO K 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU K 110 " --> pdb=" O ASN K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 129 Processing helix chain 'K' and resid 133 through 148 Processing helix chain 'N' and resid 34 through 39 Processing helix chain 'N' and resid 41 through 55 Proline residue: N 51 - end of helix Processing helix chain 'N' and resid 71 through 91 removed outlier: 3.939A pdb=" N GLU N 89 " --> pdb=" O ARG N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 101 removed outlier: 3.710A pdb=" N ALA N 101 " --> pdb=" O THR N 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 33 removed outlier: 3.542A pdb=" N LYS R 24 " --> pdb=" O GLN R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 90 removed outlier: 3.543A pdb=" N MET R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 21 removed outlier: 3.739A pdb=" N TYR X 21 " --> pdb=" O ILE X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 37 Processing helix chain 'X' and resid 49 through 62 removed outlier: 3.803A pdb=" N LYS X 62 " --> pdb=" O ASP X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 82 removed outlier: 3.505A pdb=" N ASN X 76 " --> pdb=" O GLU X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 94 Processing helix chain 'Y' and resid 40 through 51 Processing helix chain 'a' and resid 12 through 25 removed outlier: 3.532A pdb=" N LYS a 18 " --> pdb=" O HIS a 14 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR a 25 " --> pdb=" O LYS a 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 45 Processing helix chain 'a' and resid 70 through 75 Processing sheet with id=AA1, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'C' and resid 96 through 98 removed outlier: 7.595A pdb=" N ILE C 111 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE C 132 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET C 113 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 164 through 166 removed outlier: 4.335A pdb=" N HIS C 178 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LYS C 179 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE C 201 " --> pdb=" O LYS C 179 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C 181 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 249 through 250 removed outlier: 3.720A pdb=" N GLU C 355 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 257 through 260 removed outlier: 6.388A 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 422 through 427 removed outlier: 7.146A pdb=" N GLU C 422 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE C 438 " --> pdb=" O GLU C 422 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS C 424 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL C 436 " --> pdb=" O LYS C 424 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU C 426 " --> pdb=" O LYS C 434 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 472 through 474 Processing sheet with id=AA9, first strand: chain 'C' and resid 630 through 639 removed outlier: 5.618A pdb=" N ILE C 635 " --> pdb=" O GLU C 646 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU C 646 " --> pdb=" O ILE C 635 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLU C 652 " --> pdb=" O ILE C 703 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N PHE C 705 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 654 " --> pdb=" O PHE C 705 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE C 707 " --> pdb=" O LEU C 654 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N HIS C 656 " --> pdb=" O ILE C 707 " (cutoff:3.500A) removed outlier: 12.841A pdb=" N GLY C 709 " --> pdb=" O HIS C 656 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C 702 " --> pdb=" O VAL C 696 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL C 696 " --> pdb=" O ASN C 702 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP C 704 " --> pdb=" O VAL C 694 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR C 690 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 665 through 668 Processing sheet with id=AB2, first strand: chain 'D' and resid 16 through 19 removed outlier: 5.870A pdb=" N PHE D 16 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE D 41 " --> pdb=" O PHE D 16 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N HIS D 18 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR D 33 " --> pdb=" O ILE D 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.545A pdb=" N TYR D 90 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU D 161 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE D 186 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE D 163 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE D 183 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE D 200 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY D 185 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=AB5, first strand: chain 'F' and resid 165 through 166 Processing sheet with id=AB6, first strand: chain 'G' and resid 12 through 24 removed outlier: 5.330A pdb=" N GLU G 13 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLY G 40 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU G 15 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL G 38 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR G 17 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 85 through 89 Processing sheet with id=AB8, first strand: chain 'I' and resid 24 through 28 removed outlier: 6.471A pdb=" N ILE I 59 " --> pdb=" O PHE I 51 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE I 51 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG I 61 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL I 49 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE I 63 " --> pdb=" O ARG I 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 76 through 79 Processing sheet with id=AC1, first strand: chain 'I' and resid 76 through 79 removed outlier: 5.238A pdb=" N VAL I 127 " --> pdb=" O SER I 107 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER I 107 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA I 129 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 27 through 29 removed outlier: 3.654A pdb=" N GLU L 34 " --> pdb=" O ASN L 29 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 43 through 53 removed outlier: 5.471A pdb=" N CYS L 47 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG L 69 " --> pdb=" O CYS L 47 " (cutoff:3.500A) removed outlier: 13.817A pdb=" N GLU L 75 " --> pdb=" O VAL L 106 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N TYR L 108 " --> pdb=" O GLU L 75 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR L 77 " --> pdb=" O TYR L 108 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE L 110 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TYR L 79 " --> pdb=" O ILE L 110 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 48 through 51 removed outlier: 5.818A pdb=" N THR P 36 " --> pdb=" O VAL P 22 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL P 22 " --> pdb=" O THR P 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Q' and resid 9 through 13 removed outlier: 7.558A pdb=" N ILE Q 60 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL Q 80 " --> pdb=" O ILE Q 60 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS Q 62 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 16.243A pdb=" N LYS Q 73 " --> pdb=" O SER Q 43 " (cutoff:3.500A) removed outlier: 13.503A pdb=" N LYS Q 45 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N PHE Q 75 " --> pdb=" O LYS Q 45 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS Q 47 " --> pdb=" O PHE Q 75 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU Q 77 " --> pdb=" O LYS Q 47 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS Q 49 " --> pdb=" O LEU Q 77 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLU Q 79 " --> pdb=" O HIS Q 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'T' and resid 36 through 42 removed outlier: 5.593A pdb=" N ILE T 37 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN T 66 " --> pdb=" O ILE T 37 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY T 39 " --> pdb=" O ASN T 64 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 36 through 42 removed outlier: 5.593A pdb=" N ILE T 37 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN T 66 " --> pdb=" O ILE T 37 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY T 39 " --> pdb=" O ASN T 64 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG T 87 " --> pdb=" O ILE T 9 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'V' and resid 43 through 48 removed outlier: 3.660A pdb=" N ILE V 22 " --> pdb=" O THR V 37 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY V 21 " --> pdb=" O GLU V 85 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR V 87 " --> pdb=" O GLY V 21 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA V 23 " --> pdb=" O THR V 87 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LYS V 89 " --> pdb=" O ALA V 23 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE V 25 " --> pdb=" O LYS V 89 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 20 through 21 removed outlier: 7.664A pdb=" N LYS H 21 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE H 56 " --> pdb=" O LYS H 21 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS H 68 " --> pdb=" O LYS H 53 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 147 through 152 removed outlier: 3.917A pdb=" N THR H 150 " --> pdb=" O TYR H 167 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 179 through 189 removed outlier: 5.995A pdb=" N ASP H 180 " --> pdb=" O ARG H 203 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 73 through 78 Processing sheet with id=AD4, first strand: chain 'N' and resid 6 through 12 Processing sheet with id=AD5, first strand: chain 'R' and resid 35 through 55 removed outlier: 5.035A pdb=" N VAL R 36 " --> pdb=" O VAL R 77 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL R 77 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLY R 38 " --> pdb=" O ASP R 75 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP R 75 " --> pdb=" O GLY R 38 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS R 71 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR R 44 " --> pdb=" O THR R 69 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR R 69 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS R 46 " --> pdb=" O MET R 67 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET R 67 " --> pdb=" O LYS R 46 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL R 48 " --> pdb=" O PHE R 65 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE R 65 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR R 50 " --> pdb=" O GLU R 63 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU R 63 " --> pdb=" O THR R 50 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU R 52 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER R 61 " --> pdb=" O LEU R 52 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA R 54 " --> pdb=" O LYS R 59 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS R 59 " --> pdb=" O ALA R 54 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS R 11 " --> pdb=" O ASP R 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 35 through 55 removed outlier: 5.035A pdb=" N VAL R 36 " --> pdb=" O VAL R 77 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL R 77 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLY R 38 " --> pdb=" O ASP R 75 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP R 75 " --> pdb=" O GLY R 38 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS R 71 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR R 44 " --> pdb=" O THR R 69 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR R 69 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS R 46 " --> pdb=" O MET R 67 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET R 67 " --> pdb=" O LYS R 46 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL R 48 " --> pdb=" O PHE R 65 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE R 65 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR R 50 " --> pdb=" O GLU R 63 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU R 63 " --> pdb=" O THR R 50 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU R 52 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER R 61 " --> pdb=" O LEU R 52 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA R 54 " --> pdb=" O LYS R 59 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS R 59 " --> pdb=" O ALA R 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'a' and resid 31 through 33 removed outlier: 6.301A pdb=" N VAL a 31 " --> pdb=" O ALA a 50 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR a 52 " --> pdb=" O VAL a 31 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N THR a 33 " --> pdb=" O TYR a 52 " (cutoff:3.500A) 1115 hydrogen bonds defined for protein. 3192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1048 hydrogen bonds 1666 hydrogen bond angles 0 basepair planarities 421 basepair parallelities 788 stacking parallelities Total time for adding SS restraints: 39.14 Time building geometry restraints manager: 13.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9781 1.34 - 1.47: 23805 1.47 - 1.60: 19746 1.60 - 1.73: 2278 1.73 - 1.86: 133 Bond restraints: 55743 Sorted by residual: bond pdb=" CA SER F 12 " pdb=" CB SER F 12 " ideal model delta sigma weight residual 1.530 1.447 0.083 1.56e-02 4.11e+03 2.80e+01 bond pdb=" CA SER F 18 " pdb=" CB SER F 18 " ideal model delta sigma weight residual 1.529 1.455 0.074 1.43e-02 4.89e+03 2.71e+01 bond pdb=" O5' C A1081 " pdb=" C5' C A1081 " ideal model delta sigma weight residual 1.420 1.492 -0.072 1.50e-02 4.44e+03 2.32e+01 bond pdb=" CD ARG D 110 " pdb=" NE ARG D 110 " ideal model delta sigma weight residual 1.458 1.393 0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" O3' C A 946 " pdb=" P A A 947 " ideal model delta sigma weight residual 1.607 1.675 -0.068 1.50e-02 4.44e+03 2.05e+01 ... (remaining 55738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 75639 2.91 - 5.81: 5855 5.81 - 8.72: 350 8.72 - 11.62: 21 11.62 - 14.53: 7 Bond angle restraints: 81872 Sorted by residual: angle pdb=" C HIS C 475 " pdb=" CA HIS C 475 " pdb=" CB HIS C 475 " ideal model delta sigma weight residual 110.62 125.15 -14.53 1.46e+00 4.69e-01 9.90e+01 angle pdb=" CA ASP F 95 " pdb=" CB ASP F 95 " pdb=" CG ASP F 95 " ideal model delta sigma weight residual 112.60 120.57 -7.97 1.00e+00 1.00e+00 6.35e+01 angle pdb=" CA HIS Q 49 " pdb=" CB HIS Q 49 " pdb=" CG HIS Q 49 " ideal model delta sigma weight residual 113.80 121.46 -7.66 1.00e+00 1.00e+00 5.87e+01 angle pdb=" O3' A B9002 " pdb=" P A B9003 " pdb=" O5' A B9003 " ideal model delta sigma weight residual 104.00 93.02 10.98 1.50e+00 4.44e-01 5.36e+01 angle pdb=" C PRO C 66 " pdb=" CA PRO C 66 " pdb=" CB PRO C 66 " ideal model delta sigma weight residual 111.56 123.52 -11.96 1.65e+00 3.67e-01 5.25e+01 ... (remaining 81867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 31974 35.95 - 71.91: 3039 71.91 - 107.86: 453 107.86 - 143.81: 27 143.81 - 179.77: 23 Dihedral angle restraints: 35516 sinusoidal: 27085 harmonic: 8431 Sorted by residual: dihedral pdb=" CA PRO D 130 " pdb=" C PRO D 130 " pdb=" N LYS D 131 " pdb=" CA LYS D 131 " ideal model delta harmonic sigma weight residual -180.00 -87.85 -92.15 0 5.00e+00 4.00e-02 3.40e+02 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 66.13 80.87 1 8.00e+00 1.56e-02 1.26e+02 dihedral pdb=" CA LYS P 45 " pdb=" C LYS P 45 " pdb=" N PRO P 46 " pdb=" CA PRO P 46 " ideal model delta harmonic sigma weight residual 180.00 129.86 50.14 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 35513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 8574 0.158 - 0.316: 1669 0.316 - 0.474: 28 0.474 - 0.632: 4 0.632 - 0.790: 2 Chirality restraints: 10277 Sorted by residual: chirality pdb=" CA LEU D 10 " pdb=" N LEU D 10 " pdb=" C LEU D 10 " pdb=" CB LEU D 10 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" P A A 94 " pdb=" OP1 A A 94 " pdb=" OP2 A A 94 " pdb=" O5' A A 94 " both_signs ideal model delta sigma weight residual True 2.41 -3.06 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P G A 8 " pdb=" OP1 G A 8 " pdb=" OP2 G A 8 " pdb=" O5' G A 8 " both_signs ideal model delta sigma weight residual True 2.41 -3.02 -0.61 2.00e-01 2.50e+01 9.28e+00 ... (remaining 10274 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 110 " -0.689 9.50e-02 1.11e+02 3.09e-01 5.98e+01 pdb=" NE ARG D 110 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG D 110 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG D 110 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 110 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 69 " 0.035 2.00e-02 2.50e+03 6.90e-02 4.76e+01 pdb=" C MET C 69 " -0.119 2.00e-02 2.50e+03 pdb=" O MET C 69 " 0.043 2.00e-02 2.50e+03 pdb=" N ASN C 70 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 200 " -0.092 2.00e-02 2.50e+03 4.24e-02 4.49e+01 pdb=" CG TRP H 200 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP H 200 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP H 200 " 0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP H 200 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 200 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP H 200 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 200 " -0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 200 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 200 " -0.023 2.00e-02 2.50e+03 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 4859 2.73 - 3.27: 49609 3.27 - 3.81: 106942 3.81 - 4.36: 135685 4.36 - 4.90: 185963 Nonbonded interactions: 483058 Sorted by model distance: nonbonded pdb=" O PRO C 66 " pdb=" N MET C 69 " model vdw 2.182 3.120 nonbonded pdb=" O LEU F 89 " pdb=" N SER F 92 " model vdw 2.184 3.120 nonbonded pdb=" OE2 GLU R 63 " pdb=" OH TYR Y 49 " model vdw 2.189 3.040 nonbonded pdb=" O PRO C 66 " pdb=" N ASN C 70 " model vdw 2.200 3.120 nonbonded pdb=" O2' A A 703 " pdb=" O5' A A 704 " model vdw 2.255 3.040 ... (remaining 483053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 2.040 Check model and map are aligned: 0.340 Set scattering table: 0.420 Process input model: 131.970 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 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 0.083 55743 Z= 0.607 Angle : 1.579 14.530 81872 Z= 0.990 Chirality : 0.112 0.790 10277 Planarity : 0.020 0.309 5424 Dihedral : 23.396 179.766 30066 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.10 % Favored : 93.17 % Rotamer: Outliers : 4.35 % Allowed : 5.31 % Favored : 90.35 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.36 % 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: -3.58 (0.13), residues: 2884 helix: -2.80 (0.11), residues: 1147 sheet: -2.27 (0.19), residues: 524 loop : -1.72 (0.16), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.010 TRP H 200 HIS 0.021 0.005 HIS Q 49 PHE 0.053 0.008 PHE D 162 TYR 0.090 0.009 TYR U 56 ARG 0.042 0.004 ARG F 13 *********************** 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 911 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 802 time to evaluate : 3.439 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 11 LEU cc_start: 0.4035 (OUTLIER) cc_final: 0.3777 (mt) REVERT: C 65 ILE cc_start: 0.1341 (OUTLIER) cc_final: 0.1135 (tt) REVERT: C 107 MET cc_start: 0.5023 (mtp) cc_final: 0.4239 (mmp) REVERT: C 139 ARG cc_start: 0.5171 (mtt180) cc_final: 0.4893 (mpt90) REVERT: C 171 LYS cc_start: 0.3658 (tttt) cc_final: 0.3055 (mmtt) REVERT: C 195 GLU cc_start: 0.4903 (mt-10) cc_final: 0.4670 (pt0) REVERT: C 197 GLU cc_start: 0.7417 (pt0) cc_final: 0.6820 (tm-30) REVERT: C 344 GLU cc_start: 0.4333 (tt0) cc_final: 0.4029 (tp30) REVERT: C 369 MET cc_start: 0.5895 (mmm) cc_final: 0.5559 (mmm) REVERT: C 377 ILE cc_start: 0.3915 (mt) cc_final: 0.3677 (mt) REVERT: C 395 MET cc_start: 0.4105 (ttp) cc_final: 0.3572 (ttt) REVERT: C 407 ARG cc_start: 0.6168 (ttt180) cc_final: 0.5753 (mtp180) REVERT: C 417 ASP cc_start: 0.5216 (t0) cc_final: 0.3910 (p0) REVERT: C 426 LEU cc_start: 0.5592 (mt) cc_final: 0.5281 (mp) REVERT: C 441 ARG cc_start: 0.5132 (mtm180) cc_final: 0.4776 (mtm-85) REVERT: C 449 GLU cc_start: 0.5874 (tt0) cc_final: 0.5574 (mm-30) REVERT: C 517 ARG cc_start: 0.4225 (ttm170) cc_final: 0.3981 (mmt-90) REVERT: C 529 MET cc_start: 0.6739 (ttm) cc_final: 0.6389 (ttm) REVERT: C 533 MET cc_start: 0.3669 (mmp) cc_final: 0.3363 (mmp) REVERT: C 551 GLU cc_start: 0.6061 (mt-10) cc_final: 0.5773 (tp30) REVERT: C 557 THR cc_start: 0.5738 (p) cc_final: 0.5304 (t) REVERT: C 638 VAL cc_start: 0.3655 (t) cc_final: 0.3331 (m) REVERT: C 651 ILE cc_start: 0.5956 (mt) cc_final: 0.5654 (mm) REVERT: C 710 MET cc_start: 0.1882 (mtp) cc_final: 0.1373 (mpp) REVERT: D 15 HIS cc_start: 0.6412 (OUTLIER) cc_final: 0.6146 (p90) REVERT: D 21 ARG cc_start: 0.4466 (mtp180) cc_final: 0.4013 (ttp-110) REVERT: D 27 MET cc_start: 0.5677 (mmm) cc_final: 0.5172 (mmm) REVERT: D 41 ILE cc_start: 0.6314 (mt) cc_final: 0.6112 (mt) REVERT: D 45 LYS cc_start: 0.6742 (mttt) cc_final: 0.6371 (tppt) REVERT: D 47 VAL cc_start: 0.7663 (t) cc_final: 0.7444 (m) REVERT: D 120 MET cc_start: 0.6077 (mtt) cc_final: 0.5753 (mtm) REVERT: D 155 LYS cc_start: 0.6959 (mttt) cc_final: 0.6753 (mmtm) REVERT: D 159 ASP cc_start: 0.5989 (m-30) cc_final: 0.5374 (t70) REVERT: D 170 ARG cc_start: 0.6779 (ptt180) cc_final: 0.6222 (mtt-85) REVERT: D 193 PRO cc_start: 0.7492 (Cg_endo) cc_final: 0.6980 (Cg_exo) REVERT: F 28 LYS cc_start: 0.6832 (mttt) cc_final: 0.6615 (tttm) REVERT: F 70 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.7201 (m) REVERT: F 91 ASP cc_start: 0.8041 (t70) cc_final: 0.7769 (t0) REVERT: F 122 ASP cc_start: 0.5424 (m-30) cc_final: 0.4533 (t70) REVERT: F 127 ASP cc_start: 0.6373 (p0) cc_final: 0.5923 (p0) REVERT: F 150 ILE cc_start: 0.4706 (pt) cc_final: 0.4480 (pt) REVERT: G 12 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6341 (mm-30) REVERT: G 13 GLU cc_start: 0.7582 (pt0) cc_final: 0.7341 (mp0) REVERT: G 19 ASN cc_start: 0.8084 (m-40) cc_final: 0.7847 (t0) REVERT: G 29 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7024 (mtm180) REVERT: G 32 ARG cc_start: 0.7531 (mtt90) cc_final: 0.7282 (mmm-85) REVERT: G 43 ASN cc_start: 0.7465 (m-40) cc_final: 0.6856 (t0) REVERT: G 79 THR cc_start: 0.7612 (p) cc_final: 0.7374 (p) REVERT: G 88 ARG cc_start: 0.7382 (mtt-85) cc_final: 0.6009 (ttp-110) REVERT: G 142 GLN cc_start: 0.7047 (tp40) cc_final: 0.6697 (tm-30) REVERT: G 159 LYS cc_start: 0.7060 (mttm) cc_final: 0.6791 (mttt) REVERT: I 26 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7764 (pt0) REVERT: I 48 ASP cc_start: 0.8090 (t70) cc_final: 0.7600 (m-30) REVERT: I 53 GLU cc_start: 0.6851 (mp0) cc_final: 0.6611 (mm-30) REVERT: I 78 LYS cc_start: 0.7578 (ttmm) cc_final: 0.7311 (tttt) REVERT: I 116 LYS cc_start: 0.7007 (mttp) cc_final: 0.6700 (ttpt) REVERT: L 2 PRO cc_start: 0.8384 (OUTLIER) cc_final: 0.7884 (Cg_endo) REVERT: L 33 LYS cc_start: 0.6593 (mmmt) cc_final: 0.6088 (mttm) REVERT: L 40 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8292 (p) REVERT: L 53 MET cc_start: 0.6972 (mtp) cc_final: 0.6359 (mtp) REVERT: L 57 LYS cc_start: 0.6916 (pttm) cc_final: 0.6462 (tptt) REVERT: L 58 PRO cc_start: 0.5643 (OUTLIER) cc_final: 0.5187 (Cg_exo) REVERT: L 59 ASN cc_start: 0.5412 (m-40) cc_final: 0.5154 (m-40) REVERT: L 64 LYS cc_start: 0.7338 (mptt) cc_final: 0.6995 (mmtt) REVERT: L 79 TYR cc_start: 0.6851 (t80) cc_final: 0.6640 (t80) REVERT: L 89 GLU cc_start: 0.8320 (tt0) cc_final: 0.7789 (mp0) REVERT: L 102 ASP cc_start: 0.6830 (p0) cc_final: 0.6580 (p0) REVERT: O 6 GLU cc_start: 0.6412 (pp20) cc_final: 0.5690 (pt0) REVERT: O 11 LEU cc_start: 0.8564 (mt) cc_final: 0.8214 (mt) REVERT: O 15 PHE cc_start: 0.7133 (m-80) cc_final: 0.6211 (m-80) REVERT: O 48 LYS cc_start: 0.6043 (OUTLIER) cc_final: 0.5750 (tppt) REVERT: O 64 ARG cc_start: 0.7412 (ttm110) cc_final: 0.6830 (ttt90) REVERT: O 71 ARG cc_start: 0.7488 (ttp-110) cc_final: 0.7082 (ttm-80) REVERT: O 88 ARG cc_start: 0.5780 (OUTLIER) cc_final: 0.4806 (mpp-170) REVERT: P 35 GLU cc_start: 0.8394 (tp30) cc_final: 0.8084 (tp30) REVERT: P 48 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7088 (mm-30) REVERT: P 50 LYS cc_start: 0.7658 (mtmt) cc_final: 0.7446 (ttpt) REVERT: P 53 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: P 61 GLN cc_start: 0.7947 (mt0) cc_final: 0.7407 (mm-40) REVERT: P 80 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6876 (mmm) REVERT: P 81 GLU cc_start: 0.8001 (tt0) cc_final: 0.7780 (tp30) REVERT: Q 6 GLN cc_start: 0.7472 (mp10) cc_final: 0.7039 (mp10) REVERT: Q 8 LYS cc_start: 0.7270 (mttm) cc_final: 0.6957 (mttp) REVERT: Q 10 TYR cc_start: 0.8103 (m-80) cc_final: 0.7820 (m-10) REVERT: Q 17 ASP cc_start: 0.6359 (p0) cc_final: 0.6117 (p0) REVERT: Q 28 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7008 (tp30) REVERT: Q 50 ASP cc_start: 0.5975 (p0) cc_final: 0.5157 (t0) REVERT: Q 65 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6709 (pt0) REVERT: Q 82 GLU cc_start: 0.8023 (tt0) cc_final: 0.7818 (tt0) REVERT: S 29 ARG cc_start: 0.6083 (mtt90) cc_final: 0.5694 (mtm110) REVERT: S 30 THR cc_start: 0.7542 (m) cc_final: 0.7305 (m) REVERT: S 34 GLN cc_start: 0.5704 (tp-100) cc_final: 0.5448 (mt0) REVERT: S 41 ASN cc_start: 0.7085 (t0) cc_final: 0.6867 (p0) REVERT: S 42 ASN cc_start: 0.7066 (m-40) cc_final: 0.6614 (t0) REVERT: S 59 ASP cc_start: 0.7999 (m-30) cc_final: 0.7520 (m-30) REVERT: T 5 GLU cc_start: 0.7747 (tt0) cc_final: 0.7328 (tm-30) REVERT: T 7 MET cc_start: 0.7890 (ttp) cc_final: 0.7374 (ttp) REVERT: T 46 ARG cc_start: 0.4041 (mtp85) cc_final: 0.3566 (mtp85) REVERT: T 77 ARG cc_start: 0.5372 (ttp80) cc_final: 0.5028 (mtm180) REVERT: T 78 LEU cc_start: 0.7144 (mt) cc_final: 0.6819 (mt) REVERT: T 80 LYS cc_start: 0.6218 (mtmt) cc_final: 0.6018 (tptm) REVERT: T 86 ILE cc_start: 0.5542 (pt) cc_final: 0.5309 (pt) REVERT: T 94 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.4863 (mm-30) REVERT: T 95 GLU cc_start: 0.4656 (OUTLIER) cc_final: 0.2438 (pm20) REVERT: U 25 HIS cc_start: 0.6939 (t70) cc_final: 0.6579 (t-170) REVERT: U 29 LYS cc_start: 0.6266 (mtmm) cc_final: 0.5643 (mttt) REVERT: U 44 ILE cc_start: 0.7825 (mt) cc_final: 0.7617 (mt) REVERT: U 48 ARG cc_start: 0.6293 (OUTLIER) cc_final: 0.5253 (ptp-170) REVERT: V 93 SER cc_start: 0.5148 (m) cc_final: 0.4912 (p) REVERT: V 107 LEU cc_start: 0.5446 (mt) cc_final: 0.5242 (mt) REVERT: H 35 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: H 40 GLU cc_start: 0.5933 (tt0) cc_final: 0.5712 (tp30) REVERT: H 48 ASP cc_start: 0.6162 (OUTLIER) cc_final: 0.5834 (p0) REVERT: H 56 ILE cc_start: 0.6775 (mt) cc_final: 0.6370 (tt) REVERT: H 88 LYS cc_start: 0.6759 (mttt) cc_final: 0.6518 (pttm) REVERT: H 104 GLU cc_start: 0.5404 (tt0) cc_final: 0.5111 (pm20) REVERT: H 107 ARG cc_start: 0.6722 (mtt180) cc_final: 0.6504 (mtm180) REVERT: H 133 GLN cc_start: 0.5411 (mt0) cc_final: 0.5172 (mm-40) REVERT: H 140 THR cc_start: 0.7450 (m) cc_final: 0.7221 (p) REVERT: H 165 GLU cc_start: 0.5623 (mm-30) cc_final: 0.5340 (mm-30) REVERT: H 167 TYR cc_start: 0.4738 (m-80) cc_final: 0.4470 (m-80) REVERT: H 175 HIS cc_start: 0.6093 (m-70) cc_final: 0.5568 (p90) REVERT: H 180 ASP cc_start: 0.6023 (t0) cc_final: 0.5734 (t0) REVERT: H 189 ASP cc_start: 0.4414 (m-30) cc_final: 0.4133 (t0) REVERT: K 4 LYS cc_start: 0.4481 (OUTLIER) cc_final: 0.3995 (mmtt) REVERT: K 17 ILE cc_start: 0.5139 (tp) cc_final: 0.4903 (mm) REVERT: K 18 TYR cc_start: 0.5525 (m-80) cc_final: 0.5007 (m-80) REVERT: K 22 LEU cc_start: 0.7217 (mt) cc_final: 0.6861 (tp) REVERT: K 33 ASP cc_start: 0.8123 (m-30) cc_final: 0.7903 (m-30) REVERT: K 66 LEU cc_start: 0.7049 (mt) cc_final: 0.6783 (tp) REVERT: K 75 VAL cc_start: 0.5100 (OUTLIER) cc_final: 0.4730 (m) REVERT: K 78 ARG cc_start: 0.2358 (tpp-160) cc_final: 0.1609 (ttm170) REVERT: K 86 GLN cc_start: 0.5357 (mt0) cc_final: 0.5038 (mm110) REVERT: K 92 ARG cc_start: 0.5301 (mtp-110) cc_final: 0.5026 (mtm110) REVERT: K 93 PRO cc_start: 0.6180 (Cg_exo) cc_final: 0.5886 (Cg_endo) REVERT: K 113 GLU cc_start: 0.4202 (tp30) cc_final: 0.3739 (mm-30) REVERT: K 116 MET cc_start: 0.5909 (tpt) cc_final: 0.4688 (tpp) REVERT: K 119 ARG cc_start: 0.5636 (mtm-85) cc_final: 0.5426 (mtt90) REVERT: K 130 ASN cc_start: 0.5910 (t0) cc_final: 0.5623 (m110) REVERT: K 138 ARG cc_start: 0.4729 (tmm160) cc_final: 0.4473 (ppt90) REVERT: N 46 GLU cc_start: 0.6167 (tt0) cc_final: 0.5733 (tm-30) REVERT: N 68 HIS cc_start: 0.7285 (m-70) cc_final: 0.6777 (p-80) REVERT: R 7 ARG cc_start: 0.2710 (ttm170) cc_final: 0.2464 (mmt-90) REVERT: R 42 LEU cc_start: 0.7994 (mt) cc_final: 0.7735 (tp) REVERT: R 45 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6220 (mm-30) REVERT: R 52 LEU cc_start: 0.8271 (mt) cc_final: 0.7970 (mp) REVERT: R 60 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6514 (p0) REVERT: X 35 LYS cc_start: 0.5712 (tttt) cc_final: 0.5193 (tptp) REVERT: X 55 LYS cc_start: 0.5420 (mtpp) cc_final: 0.5177 (tppt) REVERT: Y 17 LYS cc_start: 0.7269 (tttt) cc_final: 0.6846 (tptt) REVERT: Y 20 GLU cc_start: 0.6538 (mt-10) cc_final: 0.6068 (tp30) REVERT: Y 23 ARG cc_start: 0.5976 (mtp85) cc_final: 0.5198 (mtm180) REVERT: Y 25 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7256 (mm-30) REVERT: Y 26 ARG cc_start: 0.7425 (ttt-90) cc_final: 0.7219 (ttt90) REVERT: a 6 LYS cc_start: 0.6363 (pttt) cc_final: 0.5725 (mmtp) REVERT: a 15 LEU cc_start: 0.6255 (tp) cc_final: 0.5655 (tp) REVERT: a 16 MET cc_start: 0.4902 (tpp) cc_final: 0.4589 (tpp) REVERT: a 34 TRP cc_start: 0.6394 (m-90) cc_final: 0.5980 (m-90) REVERT: a 58 VAL cc_start: 0.7173 (OUTLIER) cc_final: 0.6806 (p) REVERT: a 79 THR cc_start: 0.5673 (m) cc_final: 0.5241 (p) REVERT: a 81 LYS cc_start: 0.5180 (OUTLIER) cc_final: 0.4613 (mmtm) outliers start: 109 outliers final: 18 residues processed: 869 average time/residue: 0.8343 time to fit residues: 1141.0738 Evaluate side-chains 497 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 456 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain L residue 2 PRO Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 58 PRO Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 80 MET Chi-restraints excluded: chain Q residue 7 ARG Chi-restraints excluded: chain Q residue 65 GLU Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain Y residue 27 CYS Chi-restraints excluded: chain Y residue 30 PRO Chi-restraints excluded: chain Y residue 54 PRO Chi-restraints excluded: chain a residue 56 LYS Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 81 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 0.9990 chunk 313 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 324 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 241 optimal weight: 0.7980 chunk 375 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN C 172 ASN C 292 HIS C 333 ASN ** D 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN D 94 GLN I 18 ASN L 5 ASN O 18 HIS O 28 GLN O 40 ASN O 46 HIS O 72 ASN P 72 ASN S 20 HIS T 66 GLN H 99 HIS H 136 GLN N 5 GLN N 81 HIS R 56 HIS R 82 GLN X 104 ASN a 14 HIS a 57 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 55743 Z= 0.190 Angle : 0.717 24.486 81872 Z= 0.381 Chirality : 0.044 0.443 10277 Planarity : 0.005 0.077 5424 Dihedral : 23.970 179.958 24246 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.46 % Favored : 97.16 % Rotamer: Outliers : 3.51 % Allowed : 11.37 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.14 % 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: -0.79 (0.15), residues: 2884 helix: 0.28 (0.14), residues: 1165 sheet: -1.28 (0.21), residues: 503 loop : -0.83 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 200 HIS 0.009 0.001 HIS a 14 PHE 0.026 0.002 PHE C 39 TYR 0.025 0.002 TYR a 52 ARG 0.009 0.001 ARG D 110 *********************** 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 590 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 502 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.4799 (mtp) cc_final: 0.3767 (mmp) REVERT: C 139 ARG cc_start: 0.4912 (mtt180) cc_final: 0.4653 (mpt90) REVERT: C 153 VAL cc_start: 0.6727 (m) cc_final: 0.6328 (p) REVERT: C 171 LYS cc_start: 0.3271 (tttt) cc_final: 0.2894 (mmtt) REVERT: C 197 GLU cc_start: 0.7442 (pt0) cc_final: 0.6840 (tm-30) REVERT: C 417 ASP cc_start: 0.5535 (t0) cc_final: 0.4194 (p0) REVERT: C 461 GLU cc_start: 0.6616 (tp30) cc_final: 0.6377 (tp30) REVERT: C 464 HIS cc_start: 0.4888 (t70) cc_final: 0.4678 (t70) REVERT: C 503 ASN cc_start: 0.6291 (m-40) cc_final: 0.5809 (p0) REVERT: C 517 ARG cc_start: 0.4072 (ttm170) cc_final: 0.3796 (mmt-90) REVERT: C 551 GLU cc_start: 0.5824 (mt-10) cc_final: 0.5522 (tp30) REVERT: C 623 MET cc_start: 0.5029 (mmm) cc_final: 0.3522 (tpp) REVERT: C 638 VAL cc_start: 0.3456 (t) cc_final: 0.2584 (t) REVERT: C 710 MET cc_start: 0.1382 (mtp) cc_final: 0.0987 (mpp) REVERT: D 21 ARG cc_start: 0.4467 (mtp180) cc_final: 0.4125 (ttp-110) REVERT: D 45 LYS cc_start: 0.6680 (mttt) cc_final: 0.6382 (tppt) REVERT: D 159 ASP cc_start: 0.5854 (m-30) cc_final: 0.5207 (t70) REVERT: D 170 ARG cc_start: 0.6953 (ptt180) cc_final: 0.6381 (mtt180) REVERT: D 193 PRO cc_start: 0.7301 (Cg_endo) cc_final: 0.7024 (Cg_exo) REVERT: F 101 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7435 (tp) REVERT: F 109 GLN cc_start: 0.7404 (tt0) cc_final: 0.6976 (tp40) REVERT: F 122 ASP cc_start: 0.5536 (m-30) cc_final: 0.4490 (t70) REVERT: F 134 LYS cc_start: 0.7417 (mtmt) cc_final: 0.6806 (mmtt) REVERT: F 163 GLU cc_start: 0.7621 (mp0) cc_final: 0.7385 (mm-30) REVERT: F 188 GLU cc_start: 0.6411 (mp0) cc_final: 0.6175 (tp30) REVERT: G 12 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6079 (mm-30) REVERT: G 39 VAL cc_start: 0.8747 (m) cc_final: 0.8417 (t) REVERT: G 43 ASN cc_start: 0.7131 (m-40) cc_final: 0.6740 (t0) REVERT: G 88 ARG cc_start: 0.6987 (mtt-85) cc_final: 0.5605 (ttp-110) REVERT: G 152 ASP cc_start: 0.6540 (m-30) cc_final: 0.6201 (p0) REVERT: I 26 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7620 (pt0) REVERT: I 51 PHE cc_start: 0.7993 (m-80) cc_final: 0.7469 (m-10) REVERT: I 53 GLU cc_start: 0.7030 (mp0) cc_final: 0.6770 (tp30) REVERT: I 68 GLN cc_start: 0.3585 (OUTLIER) cc_final: 0.3334 (mm-40) REVERT: I 70 ASN cc_start: 0.5971 (OUTLIER) cc_final: 0.5484 (t0) REVERT: I 71 GLU cc_start: 0.7367 (tt0) cc_final: 0.6814 (pt0) REVERT: I 78 LYS cc_start: 0.7275 (ttmm) cc_final: 0.7031 (tttt) REVERT: I 116 LYS cc_start: 0.6799 (mttp) cc_final: 0.6482 (ttpt) REVERT: L 17 GLU cc_start: 0.6877 (pt0) cc_final: 0.6430 (mt-10) REVERT: L 33 LYS cc_start: 0.6607 (mmmt) cc_final: 0.6187 (mttm) REVERT: L 34 GLU cc_start: 0.7893 (tp30) cc_final: 0.7457 (mt-10) REVERT: L 57 LYS cc_start: 0.6896 (pttm) cc_final: 0.6431 (tptt) REVERT: L 89 GLU cc_start: 0.8114 (tt0) cc_final: 0.7654 (mp0) REVERT: O 26 GLU cc_start: 0.8110 (mp0) cc_final: 0.7803 (mp0) REVERT: O 48 LYS cc_start: 0.6140 (OUTLIER) cc_final: 0.5732 (tppt) REVERT: O 64 ARG cc_start: 0.7751 (ttm110) cc_final: 0.6957 (ttt90) REVERT: O 71 ARG cc_start: 0.7194 (ttp-110) cc_final: 0.6723 (ttt90) REVERT: P 35 GLU cc_start: 0.8191 (tp30) cc_final: 0.7888 (tp30) REVERT: P 48 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7210 (mm-30) REVERT: P 50 LYS cc_start: 0.7711 (mtmt) cc_final: 0.7478 (ttpp) REVERT: P 53 GLU cc_start: 0.7636 (tt0) cc_final: 0.7068 (mp0) REVERT: P 61 GLN cc_start: 0.7782 (mt0) cc_final: 0.7251 (mm-40) REVERT: P 81 GLU cc_start: 0.7402 (tt0) cc_final: 0.7125 (tm-30) REVERT: Q 6 GLN cc_start: 0.7479 (mp10) cc_final: 0.7062 (mp10) REVERT: Q 20 ASP cc_start: 0.7258 (m-30) cc_final: 0.6854 (t0) REVERT: Q 50 ASP cc_start: 0.5554 (p0) cc_final: 0.4613 (t0) REVERT: S 34 GLN cc_start: 0.5673 (tp-100) cc_final: 0.5433 (mt0) REVERT: S 42 ASN cc_start: 0.6690 (m-40) cc_final: 0.6267 (t0) REVERT: S 59 ASP cc_start: 0.7934 (m-30) cc_final: 0.7519 (m-30) REVERT: S 69 LYS cc_start: 0.6329 (mtmm) cc_final: 0.5744 (mptt) REVERT: T 51 GLU cc_start: 0.6421 (pm20) cc_final: 0.5705 (tp30) REVERT: T 60 TYR cc_start: 0.7042 (m-80) cc_final: 0.6827 (m-80) REVERT: T 94 GLU cc_start: 0.6088 (OUTLIER) cc_final: 0.4786 (tp30) REVERT: T 95 GLU cc_start: 0.4480 (OUTLIER) cc_final: 0.2382 (pm20) REVERT: U 31 VAL cc_start: 0.6336 (t) cc_final: 0.6069 (m) REVERT: U 45 LEU cc_start: 0.8142 (mt) cc_final: 0.7876 (mt) REVERT: U 48 ARG cc_start: 0.6099 (OUTLIER) cc_final: 0.4972 (ptp-170) REVERT: V 89 LYS cc_start: 0.3970 (mttt) cc_final: 0.3406 (tmtt) REVERT: H 17 ASP cc_start: 0.7673 (m-30) cc_final: 0.6696 (p0) REVERT: H 18 TRP cc_start: 0.5853 (m-90) cc_final: 0.5217 (m-90) REVERT: H 35 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6587 (m-30) REVERT: H 40 GLU cc_start: 0.5975 (tt0) cc_final: 0.5501 (tp30) REVERT: H 56 ILE cc_start: 0.6948 (mt) cc_final: 0.6420 (tt) REVERT: H 62 ARG cc_start: 0.5913 (mtt180) cc_final: 0.5540 (ptt-90) REVERT: H 104 GLU cc_start: 0.5468 (tt0) cc_final: 0.5151 (pm20) REVERT: H 115 VAL cc_start: 0.6103 (t) cc_final: 0.5836 (m) REVERT: H 131 ARG cc_start: 0.6354 (ttt180) cc_final: 0.5982 (tpp-160) REVERT: H 140 THR cc_start: 0.7227 (m) cc_final: 0.6905 (p) REVERT: H 175 HIS cc_start: 0.6197 (m-70) cc_final: 0.5801 (p-80) REVERT: H 180 ASP cc_start: 0.5888 (t0) cc_final: 0.5676 (t0) REVERT: H 189 ASP cc_start: 0.4539 (m-30) cc_final: 0.4168 (t0) REVERT: K 4 LYS cc_start: 0.4459 (OUTLIER) cc_final: 0.3991 (mmtt) REVERT: K 17 ILE cc_start: 0.5155 (tp) cc_final: 0.4833 (mm) REVERT: K 44 TYR cc_start: 0.5397 (m-10) cc_final: 0.4891 (m-10) REVERT: K 66 LEU cc_start: 0.6840 (mt) cc_final: 0.6604 (mt) REVERT: K 69 ILE cc_start: 0.6372 (mt) cc_final: 0.6163 (pt) REVERT: K 78 ARG cc_start: 0.1900 (tpp-160) cc_final: 0.1484 (ttp-170) REVERT: K 87 VAL cc_start: 0.3894 (t) cc_final: 0.3475 (p) REVERT: K 99 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6139 (mm) REVERT: K 113 GLU cc_start: 0.5886 (tp30) cc_final: 0.5464 (tp30) REVERT: K 116 MET cc_start: 0.5648 (tpt) cc_final: 0.4757 (tpp) REVERT: K 119 ARG cc_start: 0.5595 (mtm-85) cc_final: 0.5384 (mtt90) REVERT: K 130 ASN cc_start: 0.5923 (t0) cc_final: 0.5235 (t0) REVERT: N 15 SER cc_start: 0.7854 (t) cc_final: 0.7561 (p) REVERT: N 46 GLU cc_start: 0.6084 (tt0) cc_final: 0.5675 (tm-30) REVERT: R 7 ARG cc_start: 0.2657 (ttm170) cc_final: 0.2401 (mmt180) REVERT: R 14 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6304 (t70) REVERT: R 52 LEU cc_start: 0.8355 (mt) cc_final: 0.8089 (mp) REVERT: R 60 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6677 (p0) REVERT: X 35 LYS cc_start: 0.5690 (tttt) cc_final: 0.5231 (tptp) REVERT: X 72 GLU cc_start: 0.6364 (tt0) cc_final: 0.5991 (mm-30) REVERT: Y 23 ARG cc_start: 0.5785 (mtp85) cc_final: 0.5178 (mtm180) REVERT: a 6 LYS cc_start: 0.6023 (pttt) cc_final: 0.5618 (mmtp) REVERT: a 15 LEU cc_start: 0.6339 (tp) cc_final: 0.5724 (tp) REVERT: a 16 MET cc_start: 0.5009 (tpp) cc_final: 0.4663 (tpp) REVERT: a 34 TRP cc_start: 0.6515 (m-90) cc_final: 0.5747 (m-90) REVERT: a 58 VAL cc_start: 0.6842 (OUTLIER) cc_final: 0.6595 (p) REVERT: a 79 THR cc_start: 0.5213 (m) cc_final: 0.4806 (p) REVERT: a 81 LYS cc_start: 0.5430 (OUTLIER) cc_final: 0.4765 (mmtm) outliers start: 88 outliers final: 37 residues processed: 566 average time/residue: 0.7061 time to fit residues: 650.9586 Evaluate side-chains 424 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 372 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 23 TRP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 82 GLN Chi-restraints excluded: chain Y residue 27 CYS Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 56 LYS Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 81 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 312 optimal weight: 0.9990 chunk 256 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 376 optimal weight: 2.9990 chunk 406 optimal weight: 0.9980 chunk 335 optimal weight: 5.9990 chunk 373 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 302 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 HIS D 15 HIS O 28 GLN O 40 ASN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 33 ASN V 42 ASN H 175 HIS K 64 GLN K 86 GLN ** R 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 GLN a 23 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 55743 Z= 0.264 Angle : 0.725 11.406 81872 Z= 0.378 Chirality : 0.044 0.457 10277 Planarity : 0.006 0.073 5424 Dihedral : 24.023 178.549 24197 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.40 % Favored : 96.32 % Rotamer: Outliers : 4.31 % Allowed : 13.44 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.07 % 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: -0.21 (0.15), residues: 2884 helix: 0.75 (0.14), residues: 1167 sheet: -0.76 (0.22), residues: 514 loop : -0.61 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 200 HIS 0.010 0.002 HIS S 20 PHE 0.044 0.003 PHE C 463 TYR 0.025 0.003 TYR F 99 ARG 0.010 0.001 ARG D 110 *********************** 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 536 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 428 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.4291 (mtp) cc_final: 0.3282 (mmp) REVERT: C 139 ARG cc_start: 0.5149 (mtt180) cc_final: 0.4880 (mpt90) REVERT: C 153 VAL cc_start: 0.6503 (m) cc_final: 0.6132 (p) REVERT: C 171 LYS cc_start: 0.3247 (tttt) cc_final: 0.2782 (mmtt) REVERT: C 232 GLN cc_start: 0.4292 (tt0) cc_final: 0.3326 (mm-40) REVERT: C 417 ASP cc_start: 0.5688 (t0) cc_final: 0.4380 (p0) REVERT: C 503 ASN cc_start: 0.6560 (m-40) cc_final: 0.6176 (p0) REVERT: C 531 ARG cc_start: 0.6671 (ptt180) cc_final: 0.6234 (mtt180) REVERT: C 551 GLU cc_start: 0.5665 (mt-10) cc_final: 0.5350 (tp30) REVERT: C 598 GLU cc_start: 0.5610 (tt0) cc_final: 0.5021 (tp30) REVERT: C 623 MET cc_start: 0.4925 (mmm) cc_final: 0.3425 (tpp) REVERT: C 710 MET cc_start: 0.0702 (mtp) cc_final: 0.0478 (mpp) REVERT: D 21 ARG cc_start: 0.4639 (mtp180) cc_final: 0.4216 (ttp-110) REVERT: D 27 MET cc_start: 0.5242 (mmm) cc_final: 0.4881 (mmm) REVERT: D 45 LYS cc_start: 0.6945 (mttt) cc_final: 0.6481 (tppt) REVERT: D 90 TYR cc_start: 0.5155 (m-80) cc_final: 0.4953 (m-80) REVERT: D 134 VAL cc_start: 0.6531 (OUTLIER) cc_final: 0.6281 (m) REVERT: D 159 ASP cc_start: 0.5863 (m-30) cc_final: 0.5238 (t70) REVERT: D 170 ARG cc_start: 0.6951 (ptt180) cc_final: 0.6159 (mtt-85) REVERT: F 103 LEU cc_start: 0.7672 (mp) cc_final: 0.7434 (mp) REVERT: F 122 ASP cc_start: 0.5746 (m-30) cc_final: 0.5406 (m-30) REVERT: F 163 GLU cc_start: 0.7584 (mp0) cc_final: 0.7374 (mp0) REVERT: G 43 ASN cc_start: 0.6939 (m-40) cc_final: 0.6525 (t0) REVERT: G 88 ARG cc_start: 0.7119 (mtt-85) cc_final: 0.5873 (ttp-110) REVERT: I 26 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7653 (pt0) REVERT: I 51 PHE cc_start: 0.7950 (m-80) cc_final: 0.7358 (m-10) REVERT: I 68 GLN cc_start: 0.3152 (OUTLIER) cc_final: 0.2943 (mm-40) REVERT: I 71 GLU cc_start: 0.7281 (tt0) cc_final: 0.6712 (pt0) REVERT: L 17 GLU cc_start: 0.6809 (pt0) cc_final: 0.6356 (mt-10) REVERT: L 33 LYS cc_start: 0.6597 (mmmt) cc_final: 0.6177 (mttm) REVERT: L 34 GLU cc_start: 0.8043 (tp30) cc_final: 0.7651 (mt-10) REVERT: L 57 LYS cc_start: 0.7076 (pttm) cc_final: 0.6646 (tptt) REVERT: L 89 GLU cc_start: 0.7903 (tt0) cc_final: 0.7134 (mp0) REVERT: O 48 LYS cc_start: 0.5879 (OUTLIER) cc_final: 0.5666 (tppt) REVERT: O 64 ARG cc_start: 0.7619 (ttm110) cc_final: 0.6778 (tpt170) REVERT: O 71 ARG cc_start: 0.7227 (ttp-110) cc_final: 0.6573 (ttt90) REVERT: O 88 ARG cc_start: 0.5479 (mmp80) cc_final: 0.4744 (mpp-170) REVERT: P 35 GLU cc_start: 0.8251 (tp30) cc_final: 0.8019 (tp30) REVERT: P 48 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7129 (mm-30) REVERT: P 50 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7522 (ttpt) REVERT: P 53 GLU cc_start: 0.7531 (tt0) cc_final: 0.7049 (mp0) REVERT: Q 6 GLN cc_start: 0.7575 (mp10) cc_final: 0.7232 (mp10) REVERT: Q 10 TYR cc_start: 0.7958 (m-10) cc_final: 0.7625 (m-10) REVERT: Q 20 ASP cc_start: 0.7247 (m-30) cc_final: 0.6900 (t0) REVERT: Q 32 LYS cc_start: 0.6220 (OUTLIER) cc_final: 0.6011 (mtpp) REVERT: Q 50 ASP cc_start: 0.5300 (p0) cc_final: 0.4473 (t0) REVERT: S 34 GLN cc_start: 0.5717 (tp-100) cc_final: 0.5502 (mt0) REVERT: S 42 ASN cc_start: 0.6696 (m-40) cc_final: 0.6314 (t0) REVERT: S 53 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6591 (tm-30) REVERT: S 59 ASP cc_start: 0.7916 (m-30) cc_final: 0.7674 (m-30) REVERT: T 5 GLU cc_start: 0.7580 (tt0) cc_final: 0.7049 (tm-30) REVERT: T 46 ARG cc_start: 0.3899 (mtp85) cc_final: 0.3565 (mtp85) REVERT: T 51 GLU cc_start: 0.6686 (pm20) cc_final: 0.5950 (tp30) REVERT: T 72 VAL cc_start: 0.5948 (t) cc_final: 0.5689 (m) REVERT: T 80 LYS cc_start: 0.6093 (tptp) cc_final: 0.5781 (mmmt) REVERT: T 94 GLU cc_start: 0.5539 (mt-10) cc_final: 0.4099 (tp30) REVERT: T 95 GLU cc_start: 0.4375 (OUTLIER) cc_final: 0.2201 (pm20) REVERT: U 29 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6685 (mttm) REVERT: U 30 ASP cc_start: 0.7595 (t70) cc_final: 0.7358 (t0) REVERT: U 48 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.4685 (ptp-170) REVERT: U 69 GLN cc_start: 0.6256 (tt0) cc_final: 0.5913 (mm110) REVERT: V 89 LYS cc_start: 0.3875 (mttt) cc_final: 0.3332 (tmtt) REVERT: H 18 TRP cc_start: 0.6176 (m-90) cc_final: 0.5345 (m-90) REVERT: H 35 ASP cc_start: 0.7180 (m-30) cc_final: 0.6836 (m-30) REVERT: H 40 GLU cc_start: 0.5981 (tt0) cc_final: 0.5551 (tp30) REVERT: H 56 ILE cc_start: 0.6594 (mt) cc_final: 0.6035 (tt) REVERT: H 62 ARG cc_start: 0.6065 (mtt180) cc_final: 0.5639 (ptt-90) REVERT: H 104 GLU cc_start: 0.5342 (tt0) cc_final: 0.5105 (pm20) REVERT: K 4 LYS cc_start: 0.4486 (OUTLIER) cc_final: 0.4154 (tppt) REVERT: K 33 ASP cc_start: 0.7755 (m-30) cc_final: 0.7439 (m-30) REVERT: K 44 TYR cc_start: 0.5247 (m-10) cc_final: 0.4797 (m-10) REVERT: K 69 ILE cc_start: 0.6252 (mt) cc_final: 0.6016 (pt) REVERT: K 78 ARG cc_start: 0.2461 (tpp-160) cc_final: 0.1611 (ttm170) REVERT: K 99 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.6066 (mm) REVERT: K 116 MET cc_start: 0.5579 (tpt) cc_final: 0.5009 (tpp) REVERT: N 12 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.5826 (ttp-170) REVERT: N 15 SER cc_start: 0.7896 (t) cc_final: 0.7561 (p) REVERT: N 46 GLU cc_start: 0.6188 (tt0) cc_final: 0.5916 (tm-30) REVERT: R 6 ILE cc_start: 0.5290 (mt) cc_final: 0.4769 (mp) REVERT: R 7 ARG cc_start: 0.3028 (ttm170) cc_final: 0.2813 (mmt-90) REVERT: R 60 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7510 (p0) REVERT: R 88 MET cc_start: 0.4276 (mpp) cc_final: 0.3510 (ppp) REVERT: X 35 LYS cc_start: 0.5490 (tttt) cc_final: 0.5032 (tptp) REVERT: X 72 GLU cc_start: 0.6432 (tt0) cc_final: 0.6158 (mm-30) REVERT: Y 17 LYS cc_start: 0.7004 (tttt) cc_final: 0.6792 (tppt) REVERT: Y 23 ARG cc_start: 0.5960 (mtp85) cc_final: 0.5391 (mtm180) REVERT: a 6 LYS cc_start: 0.6131 (pttt) cc_final: 0.5738 (mmtp) REVERT: a 12 ASP cc_start: 0.3979 (OUTLIER) cc_final: 0.3577 (m-30) REVERT: a 15 LEU cc_start: 0.6378 (tp) cc_final: 0.5615 (tp) REVERT: a 58 VAL cc_start: 0.6792 (OUTLIER) cc_final: 0.6565 (p) REVERT: a 79 THR cc_start: 0.4855 (m) cc_final: 0.4522 (p) REVERT: a 81 LYS cc_start: 0.5861 (OUTLIER) cc_final: 0.5168 (mmtm) outliers start: 108 outliers final: 56 residues processed: 513 average time/residue: 0.6778 time to fit residues: 577.2218 Evaluate side-chains 417 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 347 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 68 GLN Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 32 LYS Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 27 CYS Chi-restraints excluded: chain a residue 12 ASP Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 56 LYS Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 81 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 195 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 252 optimal weight: 0.0570 chunk 377 optimal weight: 9.9990 chunk 400 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 358 optimal weight: 0.0870 chunk 107 optimal weight: 10.0000 overall best weight: 1.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 GLN C 178 HIS ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 HIS D 77 GLN G 70 ASN I 68 GLN O 13 ASN O 28 GLN H 118 ASN K 40 GLN N 68 HIS Y 19 GLN a 43 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 55743 Z= 0.161 Angle : 0.602 8.755 81872 Z= 0.317 Chirality : 0.039 0.390 10277 Planarity : 0.005 0.074 5424 Dihedral : 23.892 179.910 24186 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.57 % Favored : 97.16 % Rotamer: Outliers : 3.15 % Allowed : 16.43 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.26 (0.15), residues: 2884 helix: 1.26 (0.15), residues: 1168 sheet: -0.63 (0.22), residues: 507 loop : -0.44 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 200 HIS 0.027 0.001 HIS D 15 PHE 0.024 0.002 PHE D 32 TYR 0.018 0.002 TYR R 58 ARG 0.008 0.001 ARG V 95 *********************** 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 461 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 382 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.4441 (mtp) cc_final: 0.3174 (mmp) REVERT: C 139 ARG cc_start: 0.5162 (mtt180) cc_final: 0.4874 (mpt90) REVERT: C 171 LYS cc_start: 0.3079 (tttt) cc_final: 0.2682 (mmtt) REVERT: C 232 GLN cc_start: 0.4317 (tt0) cc_final: 0.3319 (mm-40) REVERT: C 503 ASN cc_start: 0.6534 (m-40) cc_final: 0.6163 (p0) REVERT: C 507 ARG cc_start: 0.5366 (tpp80) cc_final: 0.5109 (ptm160) REVERT: C 531 ARG cc_start: 0.6758 (ptt180) cc_final: 0.6357 (mtm-85) REVERT: C 551 GLU cc_start: 0.5711 (mt-10) cc_final: 0.5400 (tp30) REVERT: C 598 GLU cc_start: 0.5524 (tt0) cc_final: 0.4975 (tp30) REVERT: C 623 MET cc_start: 0.5055 (mmm) cc_final: 0.3514 (tpt) REVERT: C 650 THR cc_start: 0.7300 (p) cc_final: 0.6668 (t) REVERT: C 710 MET cc_start: 0.0720 (mtp) cc_final: 0.0339 (mpp) REVERT: D 21 ARG cc_start: 0.4467 (mtp180) cc_final: 0.4075 (ttp-110) REVERT: D 45 LYS cc_start: 0.6925 (mttt) cc_final: 0.6505 (tppt) REVERT: D 82 GLU cc_start: 0.5354 (mt-10) cc_final: 0.5084 (tm-30) REVERT: D 134 VAL cc_start: 0.6463 (OUTLIER) cc_final: 0.6146 (p) REVERT: D 136 GLN cc_start: 0.5569 (pt0) cc_final: 0.5298 (tt0) REVERT: D 159 ASP cc_start: 0.5904 (m-30) cc_final: 0.5298 (t0) REVERT: D 170 ARG cc_start: 0.6891 (ptt180) cc_final: 0.6193 (mtt-85) REVERT: F 101 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7421 (tp) REVERT: F 122 ASP cc_start: 0.5875 (m-30) cc_final: 0.5455 (m-30) REVERT: G 43 ASN cc_start: 0.7004 (m-40) cc_final: 0.6586 (t0) REVERT: G 66 ASP cc_start: 0.7712 (t0) cc_final: 0.7403 (t0) REVERT: G 88 ARG cc_start: 0.6995 (mtt-85) cc_final: 0.5772 (ttp-110) REVERT: I 26 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7601 (pt0) REVERT: I 51 PHE cc_start: 0.7949 (m-80) cc_final: 0.7401 (m-10) REVERT: L 17 GLU cc_start: 0.6823 (pt0) cc_final: 0.6356 (mt-10) REVERT: L 33 LYS cc_start: 0.6609 (mmmt) cc_final: 0.6208 (mttm) REVERT: L 34 GLU cc_start: 0.7969 (tp30) cc_final: 0.7564 (mt-10) REVERT: L 57 LYS cc_start: 0.7180 (pttm) cc_final: 0.6787 (tptt) REVERT: L 89 GLU cc_start: 0.7658 (tt0) cc_final: 0.7184 (mp0) REVERT: O 16 LYS cc_start: 0.6870 (pttt) cc_final: 0.6293 (ptmt) REVERT: O 26 GLU cc_start: 0.8089 (mp0) cc_final: 0.7818 (mp0) REVERT: O 48 LYS cc_start: 0.5870 (OUTLIER) cc_final: 0.5595 (tppt) REVERT: O 64 ARG cc_start: 0.7634 (ttm110) cc_final: 0.6791 (tmt-80) REVERT: O 71 ARG cc_start: 0.7046 (ttp-110) cc_final: 0.6418 (ttt90) REVERT: O 88 ARG cc_start: 0.5521 (mmp80) cc_final: 0.4909 (mpp-170) REVERT: P 35 GLU cc_start: 0.8230 (tp30) cc_final: 0.7991 (tp30) REVERT: P 48 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7063 (mm-30) REVERT: P 50 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7731 (mmmt) REVERT: P 53 GLU cc_start: 0.7586 (tt0) cc_final: 0.7092 (mp0) REVERT: P 71 ARG cc_start: 0.6207 (tmt-80) cc_final: 0.5956 (tmt-80) REVERT: Q 6 GLN cc_start: 0.7626 (mp10) cc_final: 0.7256 (mp10) REVERT: Q 20 ASP cc_start: 0.7205 (m-30) cc_final: 0.6796 (t0) REVERT: Q 50 ASP cc_start: 0.5255 (p0) cc_final: 0.4630 (t0) REVERT: S 34 GLN cc_start: 0.5732 (tp-100) cc_final: 0.5491 (mt0) REVERT: S 42 ASN cc_start: 0.6587 (m-40) cc_final: 0.6179 (t0) REVERT: S 53 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6801 (tm-30) REVERT: S 59 ASP cc_start: 0.7878 (m-30) cc_final: 0.7628 (m-30) REVERT: T 7 MET cc_start: 0.7725 (ttp) cc_final: 0.7340 (ttp) REVERT: T 51 GLU cc_start: 0.6626 (pm20) cc_final: 0.5913 (tp30) REVERT: T 60 TYR cc_start: 0.6875 (m-80) cc_final: 0.6614 (m-80) REVERT: T 72 VAL cc_start: 0.5927 (t) cc_final: 0.5696 (m) REVERT: T 80 LYS cc_start: 0.6035 (tptp) cc_final: 0.5766 (mmmt) REVERT: T 94 GLU cc_start: 0.5405 (mt-10) cc_final: 0.3978 (tp30) REVERT: T 95 GLU cc_start: 0.4048 (OUTLIER) cc_final: 0.2032 (pm20) REVERT: U 48 ARG cc_start: 0.5980 (OUTLIER) cc_final: 0.4762 (ptp-170) REVERT: U 69 GLN cc_start: 0.6270 (tt0) cc_final: 0.5950 (mm110) REVERT: V 55 ARG cc_start: 0.4061 (mtp-110) cc_final: 0.3336 (tmt170) REVERT: H 18 TRP cc_start: 0.6205 (m-90) cc_final: 0.5412 (m-90) REVERT: H 35 ASP cc_start: 0.7201 (m-30) cc_final: 0.6877 (m-30) REVERT: H 40 GLU cc_start: 0.6033 (tt0) cc_final: 0.5625 (tp30) REVERT: H 56 ILE cc_start: 0.6638 (mt) cc_final: 0.6097 (tt) REVERT: H 62 ARG cc_start: 0.6165 (mtt180) cc_final: 0.5626 (ptt-90) REVERT: H 104 GLU cc_start: 0.5180 (tt0) cc_final: 0.4866 (pm20) REVERT: H 163 ARG cc_start: 0.5647 (ptt90) cc_final: 0.5297 (ptt-90) REVERT: K 4 LYS cc_start: 0.4409 (OUTLIER) cc_final: 0.4047 (tppt) REVERT: K 33 ASP cc_start: 0.7740 (m-30) cc_final: 0.7462 (m-30) REVERT: K 44 TYR cc_start: 0.5264 (m-10) cc_final: 0.4835 (m-10) REVERT: K 69 ILE cc_start: 0.6282 (mt) cc_final: 0.6039 (pt) REVERT: K 78 ARG cc_start: 0.2452 (tpp-160) cc_final: 0.1856 (ttp-170) REVERT: K 116 MET cc_start: 0.5750 (tpt) cc_final: 0.5230 (tpp) REVERT: N 15 SER cc_start: 0.7888 (t) cc_final: 0.7555 (p) REVERT: N 46 GLU cc_start: 0.6206 (tt0) cc_final: 0.5944 (tm-30) REVERT: R 6 ILE cc_start: 0.5173 (mt) cc_final: 0.4676 (mp) REVERT: R 7 ARG cc_start: 0.3000 (ttm170) cc_final: 0.2711 (mpt180) REVERT: R 60 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7631 (p0) REVERT: R 88 MET cc_start: 0.4427 (mpp) cc_final: 0.3375 (ppp) REVERT: X 35 LYS cc_start: 0.5753 (tttt) cc_final: 0.5266 (tptp) REVERT: X 72 GLU cc_start: 0.6440 (tt0) cc_final: 0.6160 (mm-30) REVERT: Y 23 ARG cc_start: 0.5954 (mtp85) cc_final: 0.5426 (mtm180) REVERT: a 6 LYS cc_start: 0.6019 (pttt) cc_final: 0.5673 (mmtp) REVERT: a 15 LEU cc_start: 0.6368 (tp) cc_final: 0.5819 (tp) REVERT: a 34 TRP cc_start: 0.6341 (m-90) cc_final: 0.5049 (m-90) REVERT: a 79 THR cc_start: 0.4766 (m) cc_final: 0.4490 (p) REVERT: a 81 LYS cc_start: 0.5856 (OUTLIER) cc_final: 0.5239 (mmtm) outliers start: 79 outliers final: 45 residues processed: 443 average time/residue: 0.7225 time to fit residues: 525.1765 Evaluate side-chains 394 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 341 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 27 CYS Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 56 LYS Chi-restraints excluded: chain a residue 81 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 333 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 341 optimal weight: 0.3980 chunk 276 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 359 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 292 HIS C 462 HIS ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 HIS O 28 GLN O 38 ASN O 46 HIS U 69 GLN V 66 GLN K 19 ASN K 86 GLN X 104 ASN a 69 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 55743 Z= 0.379 Angle : 0.829 11.305 81872 Z= 0.420 Chirality : 0.048 0.385 10277 Planarity : 0.007 0.093 5424 Dihedral : 24.225 179.928 24177 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.16 % Favored : 95.60 % Rotamer: Outliers : 4.27 % Allowed : 16.95 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.07 % 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: -0.45 (0.15), residues: 2884 helix: 0.40 (0.14), residues: 1165 sheet: -0.70 (0.22), residues: 517 loop : -0.67 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP H 200 HIS 0.011 0.002 HIS S 20 PHE 0.032 0.003 PHE D 32 TYR 0.029 0.003 TYR C 293 ARG 0.011 0.001 ARG D 110 *********************** 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 478 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 371 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.4388 (mtp) cc_final: 0.3993 (mtm) REVERT: C 232 GLN cc_start: 0.4554 (tt0) cc_final: 0.3621 (mp10) REVERT: C 503 ASN cc_start: 0.6474 (m-40) cc_final: 0.6168 (p0) REVERT: C 504 ILE cc_start: 0.5341 (OUTLIER) cc_final: 0.5112 (pt) REVERT: C 507 ARG cc_start: 0.5438 (tpp80) cc_final: 0.5146 (ptm160) REVERT: C 551 GLU cc_start: 0.5879 (mt-10) cc_final: 0.5554 (tp30) REVERT: C 598 GLU cc_start: 0.5789 (tt0) cc_final: 0.5242 (tp30) REVERT: C 623 MET cc_start: 0.4863 (mmm) cc_final: 0.3440 (tpp) REVERT: C 666 ARG cc_start: 0.3998 (ttt180) cc_final: 0.3022 (mtm180) REVERT: C 710 MET cc_start: 0.0801 (mtp) cc_final: 0.0266 (mpp) REVERT: D 21 ARG cc_start: 0.4484 (mtp180) cc_final: 0.4060 (ptt90) REVERT: D 45 LYS cc_start: 0.6902 (mttt) cc_final: 0.6470 (tppt) REVERT: D 136 GLN cc_start: 0.5549 (pt0) cc_final: 0.5337 (tt0) REVERT: D 159 ASP cc_start: 0.5864 (m-30) cc_final: 0.5177 (t0) REVERT: D 170 ARG cc_start: 0.7002 (ptt180) cc_final: 0.6183 (mtt-85) REVERT: F 122 ASP cc_start: 0.6548 (m-30) cc_final: 0.6276 (m-30) REVERT: G 43 ASN cc_start: 0.7217 (m-40) cc_final: 0.6639 (t0) REVERT: G 88 ARG cc_start: 0.7216 (mtt-85) cc_final: 0.6074 (ttp-110) REVERT: I 26 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7669 (pt0) REVERT: L 17 GLU cc_start: 0.6832 (pt0) cc_final: 0.6263 (mt-10) REVERT: L 33 LYS cc_start: 0.6703 (mmmt) cc_final: 0.6130 (mttm) REVERT: L 34 GLU cc_start: 0.8063 (tp30) cc_final: 0.7687 (mt-10) REVERT: L 53 MET cc_start: 0.6506 (mtp) cc_final: 0.5723 (mtp) REVERT: L 57 LYS cc_start: 0.7388 (pttm) cc_final: 0.7065 (tptt) REVERT: L 89 GLU cc_start: 0.7603 (tt0) cc_final: 0.7215 (mp0) REVERT: O 64 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7041 (ttt90) REVERT: O 71 ARG cc_start: 0.7213 (ttp-110) cc_final: 0.6707 (ttt90) REVERT: O 88 ARG cc_start: 0.5395 (mmp80) cc_final: 0.4622 (mpt180) REVERT: P 48 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7076 (mm-30) REVERT: P 50 LYS cc_start: 0.8154 (mtmt) cc_final: 0.7727 (ttpp) REVERT: P 53 GLU cc_start: 0.7499 (tt0) cc_final: 0.6950 (mp0) REVERT: Q 6 GLN cc_start: 0.7533 (mp10) cc_final: 0.7032 (mp10) REVERT: Q 20 ASP cc_start: 0.7122 (m-30) cc_final: 0.6902 (t0) REVERT: Q 50 ASP cc_start: 0.5199 (p0) cc_final: 0.4374 (t0) REVERT: Q 57 ILE cc_start: 0.6659 (OUTLIER) cc_final: 0.6272 (mt) REVERT: S 34 GLN cc_start: 0.5827 (tp-100) cc_final: 0.5445 (mt0) REVERT: S 42 ASN cc_start: 0.6506 (m-40) cc_final: 0.6226 (t0) REVERT: S 53 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6957 (tm-30) REVERT: T 51 GLU cc_start: 0.6799 (pm20) cc_final: 0.6031 (tp30) REVERT: T 72 VAL cc_start: 0.5939 (t) cc_final: 0.5619 (m) REVERT: T 80 LYS cc_start: 0.6058 (tptp) cc_final: 0.5800 (mmmt) REVERT: T 94 GLU cc_start: 0.5162 (mt-10) cc_final: 0.3886 (tp30) REVERT: T 95 GLU cc_start: 0.4263 (OUTLIER) cc_final: 0.2099 (pm20) REVERT: U 30 ASP cc_start: 0.7505 (t70) cc_final: 0.7213 (t0) REVERT: U 34 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7123 (tp) REVERT: U 48 ARG cc_start: 0.5814 (OUTLIER) cc_final: 0.4277 (ptp-170) REVERT: H 18 TRP cc_start: 0.6206 (m-90) cc_final: 0.5468 (m-90) REVERT: H 35 ASP cc_start: 0.7138 (m-30) cc_final: 0.6734 (m-30) REVERT: H 62 ARG cc_start: 0.6171 (mtt180) cc_final: 0.5900 (mtp85) REVERT: H 104 GLU cc_start: 0.5047 (tt0) cc_final: 0.4593 (pm20) REVERT: H 163 ARG cc_start: 0.5589 (ptt90) cc_final: 0.5268 (ptt-90) REVERT: H 175 HIS cc_start: 0.5968 (OUTLIER) cc_final: 0.5594 (p-80) REVERT: K 69 ILE cc_start: 0.6291 (mt) cc_final: 0.6041 (pt) REVERT: K 78 ARG cc_start: 0.2903 (tpp-160) cc_final: 0.1676 (ttp-170) REVERT: K 116 MET cc_start: 0.5591 (tpt) cc_final: 0.5187 (tpp) REVERT: R 6 ILE cc_start: 0.5586 (mt) cc_final: 0.5208 (mp) REVERT: R 88 MET cc_start: 0.4289 (mpp) cc_final: 0.3250 (ppp) REVERT: X 16 VAL cc_start: 0.5462 (m) cc_final: 0.5236 (t) REVERT: X 35 LYS cc_start: 0.5557 (tttt) cc_final: 0.5115 (tptp) REVERT: X 71 ARG cc_start: 0.5898 (mtm110) cc_final: 0.5512 (ttp-110) REVERT: Y 23 ARG cc_start: 0.6055 (mtp85) cc_final: 0.5439 (mtm180) REVERT: a 6 LYS cc_start: 0.6059 (pttt) cc_final: 0.5672 (mmtp) REVERT: a 7 LYS cc_start: 0.6568 (mttm) cc_final: 0.5431 (pttm) REVERT: a 12 ASP cc_start: 0.4051 (OUTLIER) cc_final: 0.3596 (m-30) REVERT: a 15 LEU cc_start: 0.6360 (tp) cc_final: 0.5754 (tp) REVERT: a 79 THR cc_start: 0.4498 (m) cc_final: 0.4213 (p) outliers start: 107 outliers final: 74 residues processed: 454 average time/residue: 0.6954 time to fit residues: 519.9547 Evaluate side-chains 419 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 338 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 44 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 175 HIS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain K residue 19 ASN Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 83 ILE Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 27 CYS Chi-restraints excluded: chain a residue 12 ASP Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 56 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 134 optimal weight: 0.0070 chunk 360 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 400 optimal weight: 10.0000 chunk 332 optimal weight: 0.8980 chunk 185 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 overall best weight: 3.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 ASN C 404 GLN C 464 HIS ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS ** a 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 55743 Z= 0.231 Angle : 0.669 12.067 81872 Z= 0.346 Chirality : 0.041 0.345 10277 Planarity : 0.005 0.083 5424 Dihedral : 24.084 178.175 24167 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.36 % Favored : 96.39 % Rotamer: Outliers : 4.15 % Allowed : 17.87 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.20 (0.15), residues: 2884 helix: 0.70 (0.15), residues: 1172 sheet: -0.60 (0.23), residues: 502 loop : -0.63 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 200 HIS 0.025 0.002 HIS D 15 PHE 0.023 0.002 PHE D 32 TYR 0.025 0.002 TYR K 18 ARG 0.009 0.001 ARG D 110 *********************** 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 465 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 361 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.4278 (mtp) cc_final: 0.4062 (mtm) REVERT: C 232 GLN cc_start: 0.4468 (tt0) cc_final: 0.3576 (mp10) REVERT: C 420 PHE cc_start: 0.5520 (m-10) cc_final: 0.5307 (m-10) REVERT: C 503 ASN cc_start: 0.6549 (m-40) cc_final: 0.6271 (p0) REVERT: C 507 ARG cc_start: 0.5406 (tpp80) cc_final: 0.5118 (ptm160) REVERT: C 531 ARG cc_start: 0.6820 (ptt180) cc_final: 0.6372 (mtm-85) REVERT: C 551 GLU cc_start: 0.5753 (mt-10) cc_final: 0.5491 (tp30) REVERT: C 598 GLU cc_start: 0.5819 (tt0) cc_final: 0.5234 (tp30) REVERT: C 623 MET cc_start: 0.4906 (mmm) cc_final: 0.3473 (tpt) REVERT: C 643 MET cc_start: 0.4364 (OUTLIER) cc_final: 0.4114 (mmt) REVERT: C 650 THR cc_start: 0.7381 (p) cc_final: 0.6789 (t) REVERT: C 666 ARG cc_start: 0.3705 (ttt180) cc_final: 0.2822 (mtm180) REVERT: C 710 MET cc_start: 0.0966 (mtp) cc_final: 0.0412 (mpp) REVERT: D 21 ARG cc_start: 0.4489 (mtp180) cc_final: 0.3926 (ttp-110) REVERT: D 45 LYS cc_start: 0.6855 (mttt) cc_final: 0.6448 (tppt) REVERT: D 136 GLN cc_start: 0.5594 (pt0) cc_final: 0.5301 (tt0) REVERT: D 159 ASP cc_start: 0.5983 (m-30) cc_final: 0.5296 (t0) REVERT: D 170 ARG cc_start: 0.6979 (ptt180) cc_final: 0.6177 (mtt-85) REVERT: G 14 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7608 (ttt180) REVERT: G 43 ASN cc_start: 0.7125 (m-40) cc_final: 0.6580 (t0) REVERT: G 66 ASP cc_start: 0.7744 (t0) cc_final: 0.7374 (t0) REVERT: I 26 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7666 (pt0) REVERT: L 17 GLU cc_start: 0.6875 (pt0) cc_final: 0.6344 (mt-10) REVERT: L 33 LYS cc_start: 0.6695 (mmmt) cc_final: 0.6180 (mttm) REVERT: L 34 GLU cc_start: 0.7981 (tp30) cc_final: 0.7616 (mt-10) REVERT: L 49 ARG cc_start: 0.5215 (ttp-110) cc_final: 0.4817 (tpt170) REVERT: L 53 MET cc_start: 0.6414 (mtp) cc_final: 0.5722 (mtp) REVERT: L 57 LYS cc_start: 0.7382 (pttm) cc_final: 0.7051 (tptt) REVERT: L 89 GLU cc_start: 0.7519 (tt0) cc_final: 0.7131 (mp0) REVERT: O 47 LYS cc_start: 0.6267 (mtmp) cc_final: 0.5770 (mmmt) REVERT: O 64 ARG cc_start: 0.7780 (ttm110) cc_final: 0.6969 (ttt90) REVERT: O 71 ARG cc_start: 0.7148 (ttp-110) cc_final: 0.6631 (ttt90) REVERT: O 88 ARG cc_start: 0.5395 (mmp80) cc_final: 0.4658 (mpt180) REVERT: P 48 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7147 (mm-30) REVERT: P 50 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7801 (ttpp) REVERT: P 53 GLU cc_start: 0.7542 (tt0) cc_final: 0.6989 (mp0) REVERT: Q 6 GLN cc_start: 0.7617 (mp10) cc_final: 0.7080 (mp10) REVERT: Q 20 ASP cc_start: 0.7175 (m-30) cc_final: 0.6943 (t0) REVERT: Q 50 ASP cc_start: 0.5243 (p0) cc_final: 0.4635 (t0) REVERT: Q 57 ILE cc_start: 0.6642 (OUTLIER) cc_final: 0.6236 (mt) REVERT: S 34 GLN cc_start: 0.5938 (tp-100) cc_final: 0.5524 (mt0) REVERT: S 42 ASN cc_start: 0.6493 (m-40) cc_final: 0.6147 (t0) REVERT: S 53 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6870 (tm-30) REVERT: T 51 GLU cc_start: 0.6929 (pm20) cc_final: 0.6180 (tp30) REVERT: T 72 VAL cc_start: 0.6042 (t) cc_final: 0.5759 (m) REVERT: T 80 LYS cc_start: 0.5932 (tptp) cc_final: 0.5725 (mmmt) REVERT: T 94 GLU cc_start: 0.4933 (mt-10) cc_final: 0.3851 (tp30) REVERT: U 48 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.4486 (ptp-170) REVERT: U 69 GLN cc_start: 0.6225 (tt0) cc_final: 0.5797 (mm110) REVERT: V 55 ARG cc_start: 0.4106 (mtp-110) cc_final: 0.3412 (tmt170) REVERT: H 18 TRP cc_start: 0.6071 (m-90) cc_final: 0.5422 (m-90) REVERT: H 35 ASP cc_start: 0.7121 (m-30) cc_final: 0.6736 (m-30) REVERT: H 62 ARG cc_start: 0.6198 (mtt180) cc_final: 0.5647 (ptt-90) REVERT: H 104 GLU cc_start: 0.4799 (tt0) cc_final: 0.4239 (pm20) REVERT: H 163 ARG cc_start: 0.5611 (ptt90) cc_final: 0.5294 (ptt-90) REVERT: H 175 HIS cc_start: 0.5827 (OUTLIER) cc_final: 0.5531 (p-80) REVERT: K 22 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6499 (tp) REVERT: K 78 ARG cc_start: 0.3172 (tpp-160) cc_final: 0.1901 (ttp-170) REVERT: K 116 MET cc_start: 0.5492 (tpt) cc_final: 0.5067 (tpp) REVERT: R 63 GLU cc_start: 0.7631 (tt0) cc_final: 0.7231 (mm-30) REVERT: R 88 MET cc_start: 0.4321 (mpp) cc_final: 0.3247 (ppp) REVERT: X 16 VAL cc_start: 0.5384 (OUTLIER) cc_final: 0.5154 (t) REVERT: X 35 LYS cc_start: 0.5668 (tttt) cc_final: 0.5183 (tptp) REVERT: X 71 ARG cc_start: 0.5893 (mtm110) cc_final: 0.5535 (ttp-110) REVERT: Y 23 ARG cc_start: 0.5970 (mtp85) cc_final: 0.5484 (mtm180) REVERT: a 6 LYS cc_start: 0.6120 (pttt) cc_final: 0.5717 (mmtp) REVERT: a 7 LYS cc_start: 0.6480 (mttm) cc_final: 0.5314 (pttm) REVERT: a 15 LEU cc_start: 0.6327 (tp) cc_final: 0.5860 (tp) REVERT: a 79 THR cc_start: 0.4566 (m) cc_final: 0.4307 (p) outliers start: 104 outliers final: 79 residues processed: 437 average time/residue: 0.6936 time to fit residues: 503.2945 Evaluate side-chains 425 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 339 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 464 HIS Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain C residue 643 MET Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 152 LYS Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 14 ARG Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 31 LYS Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 110 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 175 HIS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain K residue 19 ASN Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 27 CYS Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 56 LYS Chi-restraints excluded: chain a residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 386 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 228 optimal weight: 6.9990 chunk 292 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 337 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 399 optimal weight: 7.9990 chunk 249 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 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 178 HIS ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 HIS O 28 GLN K 19 ASN X 32 GLN X 104 ASN ** a 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 55743 Z= 0.213 Angle : 0.646 11.457 81872 Z= 0.334 Chirality : 0.040 0.355 10277 Planarity : 0.005 0.084 5424 Dihedral : 24.017 178.298 24164 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.81 % Favored : 95.94 % Rotamer: Outliers : 4.07 % Allowed : 18.63 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.10 (0.15), residues: 2884 helix: 0.85 (0.15), residues: 1169 sheet: -0.53 (0.22), residues: 500 loop : -0.67 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 465 HIS 0.035 0.002 HIS C 464 PHE 0.037 0.002 PHE C 463 TYR 0.017 0.002 TYR R 58 ARG 0.008 0.001 ARG C 410 *********************** 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 456 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 354 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.4294 (mtp) cc_final: 0.3981 (mtm) REVERT: C 150 PHE cc_start: 0.4373 (OUTLIER) cc_final: 0.4137 (p90) REVERT: C 232 GLN cc_start: 0.4376 (tt0) cc_final: 0.3558 (mp10) REVERT: C 245 LEU cc_start: 0.4068 (OUTLIER) cc_final: 0.3482 (mt) REVERT: C 420 PHE cc_start: 0.5415 (m-10) cc_final: 0.5198 (m-10) REVERT: C 503 ASN cc_start: 0.6563 (m-40) cc_final: 0.6282 (p0) REVERT: C 507 ARG cc_start: 0.5317 (tpp80) cc_final: 0.5038 (ptm160) REVERT: C 531 ARG cc_start: 0.6867 (ptt180) cc_final: 0.6436 (mtt90) REVERT: C 551 GLU cc_start: 0.5853 (mt-10) cc_final: 0.5553 (tp30) REVERT: C 598 GLU cc_start: 0.5843 (tt0) cc_final: 0.5276 (tp30) REVERT: C 623 MET cc_start: 0.4913 (mmm) cc_final: 0.3501 (tpt) REVERT: C 650 THR cc_start: 0.7363 (p) cc_final: 0.6796 (t) REVERT: C 666 ARG cc_start: 0.3736 (ttt180) cc_final: 0.2786 (mtm180) REVERT: C 710 MET cc_start: 0.1143 (mtp) cc_final: -0.0076 (mpp) REVERT: D 21 ARG cc_start: 0.4490 (mtp180) cc_final: 0.3838 (ttp-110) REVERT: D 45 LYS cc_start: 0.6815 (mttt) cc_final: 0.6426 (tppt) REVERT: D 136 GLN cc_start: 0.5523 (pt0) cc_final: 0.5197 (tt0) REVERT: D 159 ASP cc_start: 0.6016 (m-30) cc_final: 0.5330 (t0) REVERT: D 170 ARG cc_start: 0.7008 (ptt180) cc_final: 0.6200 (mtt-85) REVERT: G 14 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7593 (ttt180) REVERT: G 43 ASN cc_start: 0.7173 (m-40) cc_final: 0.6614 (t0) REVERT: G 131 ASN cc_start: 0.7993 (p0) cc_final: 0.7641 (p0) REVERT: I 26 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7654 (pt0) REVERT: L 17 GLU cc_start: 0.6857 (pt0) cc_final: 0.6329 (mt-10) REVERT: L 33 LYS cc_start: 0.6702 (mmmt) cc_final: 0.6179 (mttm) REVERT: L 34 GLU cc_start: 0.7980 (tp30) cc_final: 0.7631 (mt-10) REVERT: L 53 MET cc_start: 0.6442 (mtp) cc_final: 0.5751 (mtp) REVERT: L 57 LYS cc_start: 0.7341 (pttm) cc_final: 0.7021 (tptt) REVERT: L 89 GLU cc_start: 0.7459 (tt0) cc_final: 0.7073 (mp0) REVERT: O 47 LYS cc_start: 0.6264 (mtmp) cc_final: 0.5783 (mmmt) REVERT: O 64 ARG cc_start: 0.7718 (ttm110) cc_final: 0.6913 (ttt90) REVERT: O 71 ARG cc_start: 0.7074 (ttp-110) cc_final: 0.6506 (ttt90) REVERT: O 88 ARG cc_start: 0.5327 (mmp80) cc_final: 0.4653 (mpt180) REVERT: P 48 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7145 (mm-30) REVERT: P 50 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7728 (ttpp) REVERT: P 53 GLU cc_start: 0.7576 (tt0) cc_final: 0.7003 (mp0) REVERT: P 71 ARG cc_start: 0.6275 (tmt-80) cc_final: 0.5963 (tmt-80) REVERT: Q 6 GLN cc_start: 0.7617 (mp10) cc_final: 0.7092 (mp10) REVERT: Q 20 ASP cc_start: 0.7155 (m-30) cc_final: 0.6935 (t0) REVERT: Q 50 ASP cc_start: 0.5185 (p0) cc_final: 0.4358 (t0) REVERT: Q 57 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.6210 (mt) REVERT: S 34 GLN cc_start: 0.5899 (tp-100) cc_final: 0.5478 (mt0) REVERT: S 42 ASN cc_start: 0.6497 (m-40) cc_final: 0.6168 (t0) REVERT: S 53 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6870 (tm-30) REVERT: T 51 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6213 (tp30) REVERT: T 72 VAL cc_start: 0.6051 (t) cc_final: 0.5782 (m) REVERT: T 94 GLU cc_start: 0.4976 (mt-10) cc_final: 0.3845 (tp30) REVERT: U 30 ASP cc_start: 0.7548 (t70) cc_final: 0.7263 (t0) REVERT: U 69 GLN cc_start: 0.6314 (tt0) cc_final: 0.5812 (mm110) REVERT: V 55 ARG cc_start: 0.4148 (mtp-110) cc_final: 0.3480 (tpt170) REVERT: H 18 TRP cc_start: 0.6086 (m-90) cc_final: 0.4793 (m-90) REVERT: H 35 ASP cc_start: 0.7130 (m-30) cc_final: 0.6777 (m-30) REVERT: H 62 ARG cc_start: 0.6309 (mtt180) cc_final: 0.5994 (mtp85) REVERT: H 104 GLU cc_start: 0.4673 (tt0) cc_final: 0.4094 (pm20) REVERT: H 163 ARG cc_start: 0.5501 (ptt90) cc_final: 0.5191 (ptt-90) REVERT: H 175 HIS cc_start: 0.5763 (OUTLIER) cc_final: 0.5450 (p-80) REVERT: K 78 ARG cc_start: 0.3221 (tpp-160) cc_final: 0.1890 (ttp-170) REVERT: K 116 MET cc_start: 0.5522 (tpt) cc_final: 0.5083 (tpp) REVERT: R 63 GLU cc_start: 0.7603 (tt0) cc_final: 0.7214 (mm-30) REVERT: R 88 MET cc_start: 0.4259 (mpp) cc_final: 0.3174 (ppp) REVERT: X 16 VAL cc_start: 0.5473 (OUTLIER) cc_final: 0.5213 (t) REVERT: X 35 LYS cc_start: 0.5632 (tttt) cc_final: 0.5142 (tptp) REVERT: X 71 ARG cc_start: 0.5916 (mtm110) cc_final: 0.5541 (ttp-110) REVERT: Y 23 ARG cc_start: 0.5921 (mtp85) cc_final: 0.5455 (mtm180) REVERT: a 6 LYS cc_start: 0.6086 (pttt) cc_final: 0.5665 (mmtp) REVERT: a 7 LYS cc_start: 0.6532 (mttm) cc_final: 0.5325 (pttm) REVERT: a 15 LEU cc_start: 0.6341 (tp) cc_final: 0.5928 (tp) REVERT: a 79 THR cc_start: 0.4464 (m) cc_final: 0.4231 (p) REVERT: a 81 LYS cc_start: 0.6045 (OUTLIER) cc_final: 0.5283 (mtmm) outliers start: 102 outliers final: 77 residues processed: 430 average time/residue: 0.6731 time to fit residues: 480.0960 Evaluate side-chains 417 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 332 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain C residue 643 MET Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 14 ARG Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 31 LYS Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 44 ILE Chi-restraints excluded: chain V residue 110 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 175 HIS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain K residue 19 ASN Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 27 CYS Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 56 LYS Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 81 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 246 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 271 optimal weight: 0.2980 chunk 197 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN C 149 ASN C 219 HIS ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 HIS ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN N 5 GLN N 32 ASN Y 19 GLN ** a 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 55743 Z= 0.263 Angle : 0.699 12.355 81872 Z= 0.357 Chirality : 0.042 0.361 10277 Planarity : 0.005 0.086 5424 Dihedral : 24.077 176.945 24160 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.13 % Favored : 95.63 % Rotamer: Outliers : 4.35 % Allowed : 19.07 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.30 (0.15), residues: 2884 helix: 0.70 (0.15), residues: 1167 sheet: -0.73 (0.22), residues: 508 loop : -0.74 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 200 HIS 0.039 0.002 HIS D 15 PHE 0.026 0.002 PHE D 16 TYR 0.027 0.002 TYR K 18 ARG 0.008 0.001 ARG C 410 *********************** 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 458 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 349 time to evaluate : 3.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.4063 (mtp) cc_final: 0.3766 (mtm) REVERT: C 150 PHE cc_start: 0.4533 (OUTLIER) cc_final: 0.4269 (p90) REVERT: C 232 GLN cc_start: 0.4424 (tt0) cc_final: 0.3624 (mp10) REVERT: C 245 LEU cc_start: 0.4112 (OUTLIER) cc_final: 0.3543 (mt) REVERT: C 420 PHE cc_start: 0.5359 (m-80) cc_final: 0.5122 (m-10) REVERT: C 503 ASN cc_start: 0.6612 (m-40) cc_final: 0.6346 (p0) REVERT: C 507 ARG cc_start: 0.5254 (tpp80) cc_final: 0.4992 (ptm160) REVERT: C 531 ARG cc_start: 0.6847 (ptt180) cc_final: 0.6408 (mtp180) REVERT: C 598 GLU cc_start: 0.5870 (tt0) cc_final: 0.5363 (tp30) REVERT: C 623 MET cc_start: 0.4885 (mmm) cc_final: 0.3523 (tpp) REVERT: C 643 MET cc_start: 0.4189 (OUTLIER) cc_final: 0.3447 (mmt) REVERT: C 650 THR cc_start: 0.7422 (p) cc_final: 0.6841 (t) REVERT: C 652 GLU cc_start: 0.4237 (tt0) cc_final: 0.3401 (tp30) REVERT: C 666 ARG cc_start: 0.3735 (ttt180) cc_final: 0.2810 (mtm180) REVERT: C 710 MET cc_start: 0.1332 (mtp) cc_final: 0.0231 (mpp) REVERT: D 21 ARG cc_start: 0.4456 (mtp180) cc_final: 0.3805 (ttp-110) REVERT: D 45 LYS cc_start: 0.6805 (mttt) cc_final: 0.6409 (tppt) REVERT: D 136 GLN cc_start: 0.5428 (pt0) cc_final: 0.5197 (tt0) REVERT: D 159 ASP cc_start: 0.6164 (m-30) cc_final: 0.5445 (t0) REVERT: D 170 ARG cc_start: 0.7051 (ptt180) cc_final: 0.6219 (mtt-85) REVERT: G 14 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7559 (ttt180) REVERT: G 30 ARG cc_start: 0.6890 (mmm-85) cc_final: 0.6201 (mtt180) REVERT: G 43 ASN cc_start: 0.7223 (m-40) cc_final: 0.6643 (t0) REVERT: G 131 ASN cc_start: 0.7984 (p0) cc_final: 0.7635 (p0) REVERT: I 26 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7678 (pt0) REVERT: I 51 PHE cc_start: 0.7848 (m-80) cc_final: 0.7433 (m-80) REVERT: L 33 LYS cc_start: 0.6602 (mmmt) cc_final: 0.6060 (mttm) REVERT: L 34 GLU cc_start: 0.8008 (tp30) cc_final: 0.7656 (mt-10) REVERT: L 53 MET cc_start: 0.6580 (mtp) cc_final: 0.5823 (mtp) REVERT: L 57 LYS cc_start: 0.7375 (pttm) cc_final: 0.7078 (tptt) REVERT: L 89 GLU cc_start: 0.7454 (tt0) cc_final: 0.7079 (mp0) REVERT: O 47 LYS cc_start: 0.6366 (mtmp) cc_final: 0.5819 (mmmt) REVERT: O 64 ARG cc_start: 0.7684 (ttm110) cc_final: 0.6867 (ttt90) REVERT: O 71 ARG cc_start: 0.7077 (ttp-110) cc_final: 0.6543 (ttt90) REVERT: O 88 ARG cc_start: 0.5217 (mmp80) cc_final: 0.4644 (mpt180) REVERT: P 48 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7137 (mm-30) REVERT: P 50 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7725 (ttpp) REVERT: P 53 GLU cc_start: 0.7573 (tt0) cc_final: 0.6995 (mp0) REVERT: Q 6 GLN cc_start: 0.7610 (mp10) cc_final: 0.7052 (mp10) REVERT: Q 50 ASP cc_start: 0.5189 (p0) cc_final: 0.4381 (t0) REVERT: Q 57 ILE cc_start: 0.6709 (OUTLIER) cc_final: 0.6294 (mt) REVERT: S 34 GLN cc_start: 0.5930 (tp-100) cc_final: 0.5486 (mt0) REVERT: S 42 ASN cc_start: 0.6599 (m-40) cc_final: 0.6320 (t0) REVERT: S 53 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6949 (tm-30) REVERT: T 51 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6567 (pm20) REVERT: T 72 VAL cc_start: 0.6026 (t) cc_final: 0.5733 (m) REVERT: T 94 GLU cc_start: 0.5040 (mt-10) cc_final: 0.3870 (tp30) REVERT: U 30 ASP cc_start: 0.7550 (t70) cc_final: 0.7219 (t0) REVERT: U 69 GLN cc_start: 0.6216 (tt0) cc_final: 0.5797 (mm110) REVERT: V 55 ARG cc_start: 0.4187 (mtp-110) cc_final: 0.3562 (tpt170) REVERT: H 18 TRP cc_start: 0.6097 (m-90) cc_final: 0.5542 (m-90) REVERT: H 35 ASP cc_start: 0.7101 (m-30) cc_final: 0.6768 (m-30) REVERT: H 62 ARG cc_start: 0.6288 (mtt180) cc_final: 0.5989 (mtp85) REVERT: H 104 GLU cc_start: 0.4770 (tt0) cc_final: 0.4178 (pm20) REVERT: H 163 ARG cc_start: 0.5539 (ptt90) cc_final: 0.5205 (ptt-90) REVERT: H 175 HIS cc_start: 0.5951 (OUTLIER) cc_final: 0.5562 (p-80) REVERT: K 22 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6513 (tp) REVERT: K 33 ASP cc_start: 0.7603 (m-30) cc_final: 0.7365 (t0) REVERT: K 78 ARG cc_start: 0.3484 (tpp-160) cc_final: 0.2046 (ttp-170) REVERT: K 116 MET cc_start: 0.5518 (tpt) cc_final: 0.5132 (tpp) REVERT: R 88 MET cc_start: 0.4213 (mpp) cc_final: 0.2936 (ppp) REVERT: X 16 VAL cc_start: 0.5467 (OUTLIER) cc_final: 0.5236 (t) REVERT: X 35 LYS cc_start: 0.5583 (tttt) cc_final: 0.5101 (tptp) REVERT: X 71 ARG cc_start: 0.5927 (mtm110) cc_final: 0.5566 (ttp-110) REVERT: Y 23 ARG cc_start: 0.5908 (mtp85) cc_final: 0.5452 (mtm180) REVERT: a 6 LYS cc_start: 0.6105 (pttt) cc_final: 0.5676 (mmtp) REVERT: a 7 LYS cc_start: 0.6519 (mttm) cc_final: 0.5304 (pttm) REVERT: a 15 LEU cc_start: 0.6391 (tp) cc_final: 0.5968 (tp) REVERT: a 36 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.5743 (mtp180) REVERT: a 79 THR cc_start: 0.4546 (m) cc_final: 0.4266 (p) outliers start: 109 outliers final: 82 residues processed: 428 average time/residue: 0.6723 time to fit residues: 479.5729 Evaluate side-chains 423 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 331 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 643 MET Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 14 ARG Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 31 LYS Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 44 ILE Chi-restraints excluded: chain V residue 110 THR Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 175 HIS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 130 ASN Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 27 CYS Chi-restraints excluded: chain a residue 36 ARG Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 56 LYS Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 9.9990 chunk 382 optimal weight: 6.9990 chunk 348 optimal weight: 0.8980 chunk 371 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 336 optimal weight: 6.9990 chunk 351 optimal weight: 8.9990 chunk 370 optimal weight: 6.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN C 464 HIS ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 HIS ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 32 ASN X 32 GLN ** a 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 55743 Z= 0.253 Angle : 0.693 13.735 81872 Z= 0.353 Chirality : 0.041 0.362 10277 Planarity : 0.005 0.087 5424 Dihedral : 24.094 177.176 24160 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.37 % Favored : 95.39 % Rotamer: Outliers : 4.07 % Allowed : 19.63 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.37 (0.15), residues: 2884 helix: 0.68 (0.15), residues: 1166 sheet: -0.70 (0.22), residues: 501 loop : -0.86 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 200 HIS 0.009 0.002 HIS D 15 PHE 0.024 0.002 PHE D 32 TYR 0.020 0.002 TYR O 78 ARG 0.008 0.001 ARG C 410 *********************** 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 446 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 344 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.3869 (mtp) cc_final: 0.3076 (mmp) REVERT: C 232 GLN cc_start: 0.4411 (tt0) cc_final: 0.3658 (mp10) REVERT: C 245 LEU cc_start: 0.4172 (OUTLIER) cc_final: 0.3613 (mt) REVERT: C 420 PHE cc_start: 0.5519 (m-80) cc_final: 0.5263 (m-10) REVERT: C 461 GLU cc_start: 0.6562 (tp30) cc_final: 0.6230 (pt0) REVERT: C 503 ASN cc_start: 0.6544 (m-40) cc_final: 0.6267 (p0) REVERT: C 531 ARG cc_start: 0.6832 (ptt180) cc_final: 0.6478 (mtp180) REVERT: C 598 GLU cc_start: 0.5837 (tt0) cc_final: 0.5325 (tp30) REVERT: C 623 MET cc_start: 0.4881 (mmm) cc_final: 0.3554 (tpp) REVERT: C 643 MET cc_start: 0.4197 (OUTLIER) cc_final: 0.3418 (mmt) REVERT: C 652 GLU cc_start: 0.4144 (tt0) cc_final: 0.3345 (tp30) REVERT: C 666 ARG cc_start: 0.3853 (ttt180) cc_final: 0.2890 (mtm180) REVERT: C 710 MET cc_start: 0.1250 (mtp) cc_final: 0.0234 (mpp) REVERT: D 21 ARG cc_start: 0.4475 (mtp180) cc_final: 0.3861 (ttp-110) REVERT: D 45 LYS cc_start: 0.6809 (mttt) cc_final: 0.6433 (tppt) REVERT: D 136 GLN cc_start: 0.5446 (pt0) cc_final: 0.5195 (tt0) REVERT: D 159 ASP cc_start: 0.6127 (m-30) cc_final: 0.5419 (t0) REVERT: D 170 ARG cc_start: 0.7051 (ptt180) cc_final: 0.6209 (mtt-85) REVERT: G 14 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7579 (ttt180) REVERT: G 30 ARG cc_start: 0.6954 (mmm-85) cc_final: 0.6301 (mtt180) REVERT: G 43 ASN cc_start: 0.7282 (m-40) cc_final: 0.6677 (t0) REVERT: G 131 ASN cc_start: 0.7877 (p0) cc_final: 0.7518 (p0) REVERT: I 26 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7679 (pt0) REVERT: I 51 PHE cc_start: 0.7838 (m-80) cc_final: 0.7417 (m-80) REVERT: L 33 LYS cc_start: 0.6586 (mmmt) cc_final: 0.6043 (mttm) REVERT: L 34 GLU cc_start: 0.8023 (tp30) cc_final: 0.7683 (mt-10) REVERT: L 53 MET cc_start: 0.6523 (mtp) cc_final: 0.5682 (mtp) REVERT: L 57 LYS cc_start: 0.7397 (pttm) cc_final: 0.7091 (tptt) REVERT: L 89 GLU cc_start: 0.7472 (tt0) cc_final: 0.7098 (mp0) REVERT: O 47 LYS cc_start: 0.6422 (mtmp) cc_final: 0.5869 (mmmt) REVERT: O 64 ARG cc_start: 0.7631 (ttm110) cc_final: 0.6809 (ttt90) REVERT: O 71 ARG cc_start: 0.7158 (ttp-110) cc_final: 0.6555 (ttt90) REVERT: P 48 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7141 (mm-30) REVERT: P 50 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7724 (ttpp) REVERT: P 53 GLU cc_start: 0.7463 (tt0) cc_final: 0.6941 (mp0) REVERT: Q 6 GLN cc_start: 0.7634 (mp10) cc_final: 0.7188 (mm-40) REVERT: Q 50 ASP cc_start: 0.5142 (p0) cc_final: 0.4315 (t0) REVERT: Q 57 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6255 (mt) REVERT: S 34 GLN cc_start: 0.5936 (tp-100) cc_final: 0.5483 (mt0) REVERT: S 42 ASN cc_start: 0.6542 (m-40) cc_final: 0.6277 (t0) REVERT: S 53 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6939 (tm-30) REVERT: T 51 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6630 (pm20) REVERT: T 72 VAL cc_start: 0.6104 (t) cc_final: 0.5817 (m) REVERT: T 94 GLU cc_start: 0.5054 (mt-10) cc_final: 0.3858 (tp30) REVERT: U 30 ASP cc_start: 0.7550 (t70) cc_final: 0.7262 (t0) REVERT: U 34 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7109 (tp) REVERT: U 69 GLN cc_start: 0.6232 (tt0) cc_final: 0.5802 (mm110) REVERT: V 55 ARG cc_start: 0.4195 (mtp-110) cc_final: 0.3562 (tpt170) REVERT: H 18 TRP cc_start: 0.6093 (m-90) cc_final: 0.5715 (m-90) REVERT: H 35 ASP cc_start: 0.7057 (m-30) cc_final: 0.6739 (m-30) REVERT: H 62 ARG cc_start: 0.6262 (mtt180) cc_final: 0.6004 (mtp85) REVERT: H 104 GLU cc_start: 0.4793 (tt0) cc_final: 0.4166 (pm20) REVERT: H 163 ARG cc_start: 0.5453 (ptt90) cc_final: 0.5194 (ptt-90) REVERT: H 175 HIS cc_start: 0.5822 (OUTLIER) cc_final: 0.5447 (p90) REVERT: K 22 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6559 (tp) REVERT: K 33 ASP cc_start: 0.7662 (m-30) cc_final: 0.7423 (t0) REVERT: K 78 ARG cc_start: 0.3513 (tpp-160) cc_final: 0.2041 (ttp-170) REVERT: R 63 GLU cc_start: 0.7480 (tt0) cc_final: 0.7054 (mm-30) REVERT: R 88 MET cc_start: 0.4189 (mpp) cc_final: 0.2902 (ppp) REVERT: X 16 VAL cc_start: 0.5480 (OUTLIER) cc_final: 0.5220 (t) REVERT: X 35 LYS cc_start: 0.5589 (tttt) cc_final: 0.5037 (tptp) REVERT: X 71 ARG cc_start: 0.5950 (mtm110) cc_final: 0.5589 (ttp-110) REVERT: Y 23 ARG cc_start: 0.5930 (mtp85) cc_final: 0.5481 (mtm180) REVERT: a 6 LYS cc_start: 0.6125 (pttt) cc_final: 0.5744 (mmtp) REVERT: a 15 LEU cc_start: 0.6398 (tp) cc_final: 0.6074 (tp) REVERT: a 36 ARG cc_start: 0.6031 (OUTLIER) cc_final: 0.5722 (mtp180) REVERT: a 79 THR cc_start: 0.4571 (m) cc_final: 0.4295 (p) outliers start: 102 outliers final: 84 residues processed: 422 average time/residue: 0.6829 time to fit residues: 479.5917 Evaluate side-chains 421 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 327 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 464 HIS Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 643 MET Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 14 ARG Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 20 ASP Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 31 LYS Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 44 ILE Chi-restraints excluded: chain V residue 110 THR Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 175 HIS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 27 CYS Chi-restraints excluded: chain a residue 12 ASP Chi-restraints excluded: chain a residue 36 ARG Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 56 LYS Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 8.9990 chunk 393 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 412 optimal weight: 4.9990 chunk 379 optimal weight: 4.9990 chunk 328 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN C 375 ASN ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.5515 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= 0.209 Angle : 0.651 12.656 81872 Z= 0.333 Chirality : 0.040 0.359 10277 Planarity : 0.005 0.088 5424 Dihedral : 24.048 177.800 24160 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.06 % Favored : 95.74 % Rotamer: Outliers : 4.03 % Allowed : 19.66 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.22 (0.15), residues: 2884 helix: 0.81 (0.15), residues: 1168 sheet: -0.63 (0.23), residues: 496 loop : -0.78 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 465 HIS 0.016 0.001 HIS C 464 PHE 0.024 0.002 PHE D 32 TYR 0.021 0.002 TYR O 78 ARG 0.007 0.001 ARG H 45 ********************** 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 442 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 341 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.4353 (mtp) cc_final: 0.3449 (mmp) REVERT: C 232 GLN cc_start: 0.4397 (tt0) cc_final: 0.3656 (mp10) REVERT: C 245 LEU cc_start: 0.4159 (OUTLIER) cc_final: 0.3598 (mt) REVERT: C 420 PHE cc_start: 0.5575 (m-80) cc_final: 0.5280 (m-10) REVERT: C 461 GLU cc_start: 0.6608 (tp30) cc_final: 0.6141 (pt0) REVERT: C 462 HIS cc_start: 0.6728 (t70) cc_final: 0.6524 (t70) REVERT: C 503 ASN cc_start: 0.6549 (m-40) cc_final: 0.6252 (p0) REVERT: C 531 ARG cc_start: 0.6763 (ptt180) cc_final: 0.6429 (mtp180) REVERT: C 598 GLU cc_start: 0.5907 (tt0) cc_final: 0.5425 (tp30) REVERT: C 623 MET cc_start: 0.4956 (mmm) cc_final: 0.3625 (tpp) REVERT: C 643 MET cc_start: 0.4347 (OUTLIER) cc_final: 0.3540 (mmt) REVERT: C 650 THR cc_start: 0.7355 (p) cc_final: 0.6849 (t) REVERT: C 652 GLU cc_start: 0.4121 (tt0) cc_final: 0.3330 (tp30) REVERT: C 666 ARG cc_start: 0.3840 (ttt180) cc_final: 0.2883 (mtm180) REVERT: C 710 MET cc_start: 0.1104 (mtp) cc_final: -0.0125 (mpp) REVERT: D 21 ARG cc_start: 0.4545 (mtp180) cc_final: 0.3899 (ttp-110) REVERT: D 45 LYS cc_start: 0.6785 (mttt) cc_final: 0.6453 (tppt) REVERT: D 136 GLN cc_start: 0.5456 (pt0) cc_final: 0.5202 (tt0) REVERT: D 159 ASP cc_start: 0.6179 (m-30) cc_final: 0.5456 (t0) REVERT: D 170 ARG cc_start: 0.7010 (ptt180) cc_final: 0.6173 (mtt-85) REVERT: D 212 LEU cc_start: 0.6135 (mp) cc_final: 0.5816 (tp) REVERT: G 14 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7591 (ttt180) REVERT: G 30 ARG cc_start: 0.6940 (mmm-85) cc_final: 0.6293 (mtt180) REVERT: G 43 ASN cc_start: 0.7242 (m-40) cc_final: 0.6669 (t0) REVERT: G 131 ASN cc_start: 0.7592 (p0) cc_final: 0.7171 (p0) REVERT: I 26 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7677 (pt0) REVERT: I 51 PHE cc_start: 0.7818 (m-80) cc_final: 0.7414 (m-80) REVERT: L 33 LYS cc_start: 0.6578 (mmmt) cc_final: 0.6041 (mttm) REVERT: L 34 GLU cc_start: 0.7949 (tp30) cc_final: 0.7620 (mt-10) REVERT: L 53 MET cc_start: 0.6521 (mtp) cc_final: 0.5869 (mtp) REVERT: L 57 LYS cc_start: 0.7386 (pttm) cc_final: 0.7095 (tptt) REVERT: L 103 LEU cc_start: 0.7396 (mt) cc_final: 0.7069 (mp) REVERT: O 47 LYS cc_start: 0.6402 (mtmp) cc_final: 0.5844 (mmmt) REVERT: O 64 ARG cc_start: 0.7644 (ttm110) cc_final: 0.6839 (ttt90) REVERT: O 71 ARG cc_start: 0.7081 (ttp-110) cc_final: 0.6529 (ttt90) REVERT: P 48 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7129 (mm-30) REVERT: P 50 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7695 (ttpp) REVERT: P 53 GLU cc_start: 0.7497 (tt0) cc_final: 0.6961 (mp0) REVERT: Q 6 GLN cc_start: 0.7637 (mp10) cc_final: 0.7180 (mm-40) REVERT: Q 50 ASP cc_start: 0.5166 (p0) cc_final: 0.4325 (t0) REVERT: Q 57 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6232 (mt) REVERT: S 34 GLN cc_start: 0.5984 (tp-100) cc_final: 0.5530 (mt0) REVERT: S 42 ASN cc_start: 0.6461 (m-40) cc_final: 0.6198 (t0) REVERT: S 53 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6936 (tm-30) REVERT: T 51 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6603 (pm20) REVERT: T 72 VAL cc_start: 0.6129 (t) cc_final: 0.5843 (m) REVERT: T 94 GLU cc_start: 0.5066 (mt-10) cc_final: 0.4017 (tp30) REVERT: U 30 ASP cc_start: 0.7557 (t70) cc_final: 0.7253 (t0) REVERT: U 34 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7081 (tp) REVERT: U 69 GLN cc_start: 0.6243 (tt0) cc_final: 0.5803 (mm110) REVERT: V 55 ARG cc_start: 0.4133 (mtp-110) cc_final: 0.3558 (tpt170) REVERT: H 18 TRP cc_start: 0.6044 (m-90) cc_final: 0.4871 (m-90) REVERT: H 35 ASP cc_start: 0.7031 (m-30) cc_final: 0.6682 (m-30) REVERT: H 62 ARG cc_start: 0.6280 (mtt180) cc_final: 0.6006 (mtp85) REVERT: H 104 GLU cc_start: 0.4770 (tt0) cc_final: 0.4148 (pm20) REVERT: H 163 ARG cc_start: 0.5410 (ptt90) cc_final: 0.5141 (ptt-90) REVERT: H 175 HIS cc_start: 0.5820 (OUTLIER) cc_final: 0.5437 (p-80) REVERT: K 22 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6537 (tp) REVERT: K 33 ASP cc_start: 0.7611 (m-30) cc_final: 0.7409 (t0) REVERT: K 78 ARG cc_start: 0.3530 (tpp-160) cc_final: 0.2058 (ttp-170) REVERT: K 116 MET cc_start: 0.4651 (tpp) cc_final: 0.4252 (tpp) REVERT: R 60 ASP cc_start: 0.8133 (p0) cc_final: 0.7877 (p0) REVERT: R 63 GLU cc_start: 0.7491 (tt0) cc_final: 0.7075 (mm-30) REVERT: R 88 MET cc_start: 0.4165 (mpp) cc_final: 0.2873 (ppp) REVERT: X 35 LYS cc_start: 0.5626 (tttt) cc_final: 0.5047 (tptp) REVERT: X 71 ARG cc_start: 0.5969 (mtm110) cc_final: 0.5595 (ttp-110) REVERT: Y 23 ARG cc_start: 0.5976 (mtp85) cc_final: 0.5488 (mtm180) REVERT: a 6 LYS cc_start: 0.6113 (pttt) cc_final: 0.5789 (mmtm) REVERT: a 15 LEU cc_start: 0.6331 (tp) cc_final: 0.5974 (tp) REVERT: a 79 THR cc_start: 0.4631 (m) cc_final: 0.4355 (p) outliers start: 101 outliers final: 81 residues processed: 418 average time/residue: 0.6801 time to fit residues: 473.7587 Evaluate side-chains 420 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 331 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain C residue 643 MET Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 14 ARG Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 112 ARG Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 20 ASP Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 31 LYS Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 110 THR Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 175 HIS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 27 CYS Chi-restraints excluded: chain a residue 12 ASP Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 56 LYS Chi-restraints excluded: chain a residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 260 optimal weight: 0.9990 chunk 349 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 302 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 328 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 337 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN C 464 HIS ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN ** a 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.089655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.081391 restraints weight = 197694.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.081657 restraints weight = 381427.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.081854 restraints weight = 154466.919| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 55743 Z= 0.234 Angle : 0.672 13.180 81872 Z= 0.342 Chirality : 0.040 0.353 10277 Planarity : 0.005 0.089 5424 Dihedral : 24.061 178.653 24160 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.26 % Favored : 95.53 % Rotamer: Outliers : 4.07 % Allowed : 19.55 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.33 (0.15), residues: 2884 helix: 0.73 (0.15), residues: 1165 sheet: -0.62 (0.22), residues: 494 loop : -0.89 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 200 HIS 0.015 0.001 HIS C 464 PHE 0.024 0.002 PHE D 32 TYR 0.023 0.002 TYR X 86 ARG 0.006 0.001 ARG H 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10342.58 seconds wall clock time: 212 minutes 19.05 seconds (12739.05 seconds total)