Starting phenix.real_space_refine on Wed Mar 20 10:37:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agb_9616/03_2024/6agb_9616_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agb_9616/03_2024/6agb_9616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agb_9616/03_2024/6agb_9616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agb_9616/03_2024/6agb_9616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agb_9616/03_2024/6agb_9616_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agb_9616/03_2024/6agb_9616_neut.pdb" } resolution = 3.48 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= 0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 369 5.49 5 S 99 5.16 5 C 15766 2.51 5 N 4818 2.21 5 O 6137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 760": "NH1" <-> "NH2" Residue "B ARG 858": "NH1" <-> "NH2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "G TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "H ARG 7": "NH1" <-> "NH2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I ARG 237": "NH1" <-> "NH2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 83": "NH1" <-> "NH2" Residue "J TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 122": "NH1" <-> "NH2" Residue "K ARG 137": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27190 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 7861 Classifications: {'RNA': 369} Modifications used: {'rna2p_pur': 29, 'rna2p_pyr': 22, 'rna3p_pur': 159, 'rna3p_pyr': 159} Link IDs: {'rna2p': 51, 'rna3p': 317} Chain: "B" Number of atoms: 6389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6389 Classifications: {'peptide': 784} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 748} Chain breaks: 4 Chain: "C" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1435 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 14, 'TRANS': 160} Chain: "D" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1886 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1141 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "F" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1272 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "G" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain: "I" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain: "J" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2260 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain: "K" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1025 Unusual residues: {' ZN': 1} Classifications: {'peptide': 128, 'undetermined': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120, None: 1} Not linked: pdbres="SER K 144 " pdbres=" ZN K 201 " List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26766 SG CYS K 90 69.956 73.033 54.491 1.00 75.51 S ATOM 26963 SG CYS K 115 68.220 69.065 50.918 1.00 93.76 S ATOM 26973 SG CYS K 117 66.648 69.615 54.531 1.00 94.53 S Time building chain proxies: 13.82, per 1000 atoms: 0.51 Number of scatterers: 27190 At special positions: 0 Unit cell: (153.12, 121.44, 208.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 99 16.00 P 369 15.00 O 6137 8.00 N 4818 7.00 C 15766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 11.39 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 115 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 90 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 117 " 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 16 sheets defined 42.6% alpha, 16.8% beta 84 base pairs and 204 stacking pairs defined. Time for finding SS restraints: 9.41 Creating SS restraints... Processing helix chain 'B' and resid 58 through 85 removed outlier: 3.652A pdb=" N SER B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.890A pdb=" N LEU B 92 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.800A pdb=" N SER B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 145 through 166 removed outlier: 3.875A pdb=" N SER B 153 " --> pdb=" O LYS B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.529A pdb=" N THR B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.802A pdb=" N ILE B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.507A pdb=" N ARG B 249 " --> pdb=" O TRP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 307 through 318 removed outlier: 4.473A pdb=" N LYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 371 through 385 Processing helix chain 'B' and resid 407 through 416 Processing helix chain 'B' and resid 422 through 432 removed outlier: 3.663A pdb=" N GLU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.986A pdb=" N LYS B 468 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 469 " --> pdb=" O GLN B 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 465 through 469' Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.663A pdb=" N HIS B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.567A pdb=" N ILE B 487 " --> pdb=" O PRO B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 removed outlier: 3.803A pdb=" N ARG B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'B' and resid 564 through 571 removed outlier: 3.658A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B 571 " --> pdb=" O PRO B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 593 Processing helix chain 'B' and resid 597 through 602 removed outlier: 3.793A pdb=" N TYR B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 627 Processing helix chain 'B' and resid 660 through 678 removed outlier: 3.847A pdb=" N LEU B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 718 removed outlier: 4.014A pdb=" N VAL B 706 " --> pdb=" O CYS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 798 Processing helix chain 'B' and resid 816 through 818 No H-bonds generated for 'chain 'B' and resid 816 through 818' Processing helix chain 'B' and resid 844 through 850 removed outlier: 3.722A pdb=" N GLN B 850 " --> pdb=" O ALA B 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 40 through 57 removed outlier: 4.155A pdb=" N GLN C 45 " --> pdb=" O PRO C 41 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N HIS C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.646A pdb=" N LEU C 105 " --> pdb=" O PRO C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.529A pdb=" N CYS C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 150 through 158 removed outlier: 4.917A pdb=" N GLN C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 removed outlier: 3.914A pdb=" N ASP D 10 " --> pdb=" O THR D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.632A pdb=" N ASN D 82 " --> pdb=" O TYR D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 82' Processing helix chain 'D' and resid 84 through 111 Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.665A pdb=" N HIS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 131 removed outlier: 3.642A pdb=" N GLU D 131 " --> pdb=" O PRO D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 155 Proline residue: D 141 - end of helix removed outlier: 4.012A pdb=" N GLU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU D 146 " --> pdb=" O MET D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 270 through 273 removed outlier: 3.958A pdb=" N MET D 273 " --> pdb=" O CYS D 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 273' Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'E' and resid 27 through 36 Processing helix chain 'E' and resid 44 through 60 Processing helix chain 'E' and resid 62 through 69 Processing helix chain 'E' and resid 92 through 102 Processing helix chain 'E' and resid 122 through 147 removed outlier: 3.915A pdb=" N ILE E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 removed outlier: 3.911A pdb=" N CYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 removed outlier: 3.648A pdb=" N LYS F 64 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.851A pdb=" N PHE F 98 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.541A pdb=" N ASN F 105 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN F 106 " --> pdb=" O ILE F 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 102 through 106' Processing helix chain 'G' and resid 40 through 59 removed outlier: 4.543A pdb=" N HIS G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 83 removed outlier: 3.866A pdb=" N GLN G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 27 removed outlier: 3.651A pdb=" N ASP H 24 " --> pdb=" O ASP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 45 removed outlier: 3.550A pdb=" N TRP H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 52 Processing helix chain 'H' and resid 73 through 82 removed outlier: 4.161A pdb=" N SER H 80 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 removed outlier: 3.807A pdb=" N ASP H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 37 removed outlier: 3.702A pdb=" N VAL I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY I 37 " --> pdb=" O LEU I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 76 removed outlier: 4.461A pdb=" N LEU I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.694A pdb=" N ALA I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 123 removed outlier: 3.643A pdb=" N THR I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.742A pdb=" N ILE I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 165 removed outlier: 3.746A pdb=" N LEU I 164 " --> pdb=" O GLY I 161 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG I 165 " --> pdb=" O TYR I 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 161 through 165' Processing helix chain 'I' and resid 167 through 185 removed outlier: 4.335A pdb=" N ARG I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG I 185 " --> pdb=" O ILE I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 201 removed outlier: 4.177A pdb=" N CYS I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 217 through 242 removed outlier: 4.540A pdb=" N ALA I 229 " --> pdb=" O MET I 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 36 removed outlier: 3.588A pdb=" N VAL J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU J 36 " --> pdb=" O THR J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 77 removed outlier: 3.982A pdb=" N ASP J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 104 removed outlier: 4.032A pdb=" N GLN J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 123 removed outlier: 3.746A pdb=" N LEU J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 removed outlier: 3.703A pdb=" N ILE J 146 " --> pdb=" O LYS J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.537A pdb=" N ARG J 165 " --> pdb=" O TYR J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 184 removed outlier: 4.079A pdb=" N GLN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER J 179 " --> pdb=" O SER J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 removed outlier: 3.660A pdb=" N GLU J 200 " --> pdb=" O SER J 197 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 197 through 201' Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 217 through 227 Processing helix chain 'J' and resid 227 through 241 removed outlier: 3.702A pdb=" N VAL J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY J 236 " --> pdb=" O VAL J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 55 removed outlier: 3.985A pdb=" N ALA K 54 " --> pdb=" O ALA K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 77 removed outlier: 3.849A pdb=" N ALA K 63 " --> pdb=" O HIS K 59 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG K 64 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.549A pdb=" N LYS K 86 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 216 through 217 removed outlier: 4.038A pdb=" N GLY B 216 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B 393 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 295 " --> pdb=" O CYS B 394 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER B 340 " --> pdb=" O PRO B 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.847A pdb=" N HIS B 251 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 450 removed outlier: 3.672A pdb=" N VAL B 546 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER B 400 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 762 through 769 removed outlier: 4.835A pdb=" N GLY B 836 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 837 " --> pdb=" O THR B 828 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 828 " --> pdb=" O MET B 837 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 839 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER B 826 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N PHE B 841 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 824 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASP B 843 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY B 822 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 781 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE B 823 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA B 779 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 856 " --> pdb=" O TYR B 782 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 18 through 19 removed outlier: 4.001A pdb=" N THR K 19 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN C 17 " --> pdb=" O THR K 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'D' and resid 197 through 199 removed outlier: 7.950A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 207 through 211 Processing sheet with id=AA9, first strand: chain 'E' and resid 73 through 78 removed outlier: 3.559A pdb=" N GLN E 73 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE E 85 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE E 77 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR E 83 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS E 118 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU E 12 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E 14 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL E 114 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.332A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.332A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 15 through 17 removed outlier: 6.540A pdb=" N ILE G 33 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N MET G 68 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 55 through 61 removed outlier: 8.809A pdb=" N TYR H 55 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ASN H 70 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE H 57 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ARG H 68 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N HIS H 59 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR H 66 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR H 11 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLU H 102 " --> pdb=" O TYR H 11 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LYS H 13 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.605A pdb=" N VAL I 3 " --> pdb=" O HIS I 40 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA I 42 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU I 5 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN I 44 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL I 7 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR I 46 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE I 41 " --> pdb=" O TYR I 81 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG I 83 " --> pdb=" O ILE I 41 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE I 43 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR I 85 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE I 45 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE I 87 " --> pdb=" O PHE I 45 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL I 47 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N ILE I 106 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER I 82 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA I 108 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE I 84 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU I 110 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU I 86 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL I 107 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR I 130 " --> pdb=" O VAL I 107 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ALA I 109 " --> pdb=" O THR I 130 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU I 156 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY I 192 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE I 158 " --> pdb=" O GLY I 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 3 through 8 removed outlier: 4.313A pdb=" N VAL J 3 " --> pdb=" O HIS J 40 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA J 42 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU J 5 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASN J 44 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL J 7 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR J 46 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE J 41 " --> pdb=" O TYR J 81 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ARG J 83 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE J 43 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR J 85 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE J 45 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE J 87 " --> pdb=" O PHE J 45 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL J 47 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N ILE J 106 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER J 82 " --> pdb=" O ILE J 106 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA J 108 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE J 84 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL J 107 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N THR J 130 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ALA J 109 " --> pdb=" O THR J 130 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU J 156 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLY J 192 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE J 158 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 102 through 105 removed outlier: 3.528A pdb=" N LYS K 102 " --> pdb=" O MET K 114 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 219 hydrogen bonds 422 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 204 stacking parallelities Total time for adding SS restraints: 12.15 Time building geometry restraints manager: 12.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5628 1.33 - 1.45: 8247 1.45 - 1.58: 13706 1.58 - 1.70: 737 1.70 - 1.82: 150 Bond restraints: 28468 Sorted by residual: bond pdb=" C ILE C 108 " pdb=" N PRO C 109 " ideal model delta sigma weight residual 1.337 1.388 -0.051 1.11e-02 8.12e+03 2.13e+01 bond pdb=" C PHE B 598 " pdb=" N PRO B 599 " ideal model delta sigma weight residual 1.336 1.380 -0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" C PRO K 24 " pdb=" N PRO K 25 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.45e+00 bond pdb=" N GLN B 331 " pdb=" CA GLN B 331 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.34e+00 bond pdb=" C ASP C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.24e+00 ... (remaining 28463 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.46: 2609 106.46 - 113.81: 16732 113.81 - 121.16: 13368 121.16 - 128.52: 7017 128.52 - 135.87: 502 Bond angle restraints: 40228 Sorted by residual: angle pdb=" N ILE I 112 " pdb=" CA ILE I 112 " pdb=" C ILE I 112 " ideal model delta sigma weight residual 113.10 105.97 7.13 9.70e-01 1.06e+00 5.40e+01 angle pdb=" C VAL B 361 " pdb=" N GLN B 362 " pdb=" CA GLN B 362 " ideal model delta sigma weight residual 121.54 131.50 -9.96 1.91e+00 2.74e-01 2.72e+01 angle pdb=" N ASN D 215 " pdb=" CA ASN D 215 " pdb=" C ASN D 215 " ideal model delta sigma weight residual 111.14 106.00 5.14 1.08e+00 8.57e-01 2.26e+01 angle pdb=" N VAL H 111 " pdb=" CA VAL H 111 " pdb=" C VAL H 111 " ideal model delta sigma weight residual 108.82 103.02 5.80 1.22e+00 6.72e-01 2.26e+01 angle pdb=" C3' U A 266 " pdb=" O3' U A 266 " pdb=" P U A 267 " ideal model delta sigma weight residual 120.20 127.25 -7.05 1.50e+00 4.44e-01 2.21e+01 ... (remaining 40223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 16809 34.97 - 69.93: 965 69.93 - 104.90: 114 104.90 - 139.87: 2 139.87 - 174.84: 9 Dihedral angle restraints: 17899 sinusoidal: 10844 harmonic: 7055 Sorted by residual: dihedral pdb=" C4' A A 191 " pdb=" C3' A A 191 " pdb=" C2' A A 191 " pdb=" C1' A A 191 " ideal model delta sinusoidal sigma weight residual -35.00 35.90 -70.90 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" O4' A A 191 " pdb=" C2' A A 191 " pdb=" C1' A A 191 " pdb=" C3' A A 191 " ideal model delta sinusoidal sigma weight residual -35.00 33.56 -68.56 1 8.00e+00 1.56e-02 9.52e+01 dihedral pdb=" O4' U A 329 " pdb=" C1' U A 329 " pdb=" N1 U A 329 " pdb=" C2 U A 329 " ideal model delta sinusoidal sigma weight residual 200.00 43.12 156.88 1 1.50e+01 4.44e-03 8.19e+01 ... (remaining 17896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4422 0.076 - 0.152: 383 0.152 - 0.227: 43 0.227 - 0.303: 2 0.303 - 0.379: 2 Chirality restraints: 4852 Sorted by residual: chirality pdb=" C3' A A 367 " pdb=" C4' A A 367 " pdb=" O3' A A 367 " pdb=" C2' A A 367 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C3' G A 179 " pdb=" C4' G A 179 " pdb=" O3' G A 179 " pdb=" C2' G A 179 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' U A 266 " pdb=" C4' U A 266 " pdb=" O3' U A 266 " pdb=" C2' U A 266 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 4849 not shown) Planarity restraints: 3725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 728 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.62e+00 pdb=" N PRO B 729 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 729 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 729 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 44 " 0.018 2.00e-02 2.50e+03 1.79e-02 7.99e+00 pdb=" CG TRP C 44 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP C 44 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 44 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 44 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 44 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 44 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 44 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 44 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 44 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 543 " -0.045 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO B 544 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 544 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 544 " -0.038 5.00e-02 4.00e+02 ... (remaining 3722 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 93 2.48 - 3.09: 15839 3.09 - 3.69: 42272 3.69 - 4.30: 61659 4.30 - 4.90: 93355 Nonbonded interactions: 213218 Sorted by model distance: nonbonded pdb=" O2' A A 191 " pdb=" OP1 C A 192 " model vdw 1.877 2.440 nonbonded pdb=" O2' C A 151 " pdb=" OP1 U A 190 " model vdw 1.911 2.440 nonbonded pdb=" O2' G A 96 " pdb=" O2 U A 158 " model vdw 2.251 2.440 nonbonded pdb=" O LEU J 238 " pdb=" OG SER J 242 " model vdw 2.266 2.440 nonbonded pdb=" O2' U A 363 " pdb=" O CYS D 222 " model vdw 2.272 2.440 ... (remaining 213213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.240 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 81.140 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 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:2.800 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 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 : 0.003 0.072 28468 Z= 0.210 Angle : 0.838 12.614 40228 Z= 0.487 Chirality : 0.044 0.379 4852 Planarity : 0.006 0.078 3725 Dihedral : 18.493 174.837 13315 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 0.18 % Allowed : 3.20 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.53 (0.14), residues: 2372 helix: -2.63 (0.12), residues: 896 sheet: -0.72 (0.24), residues: 426 loop : -2.70 (0.16), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP C 44 HIS 0.006 0.001 HIS B 273 PHE 0.030 0.002 PHE K 34 TYR 0.029 0.002 TYR B 597 ARG 0.008 0.001 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 926 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.7554 (t160) cc_final: 0.7334 (t0) REVERT: B 146 GLN cc_start: 0.8079 (pt0) cc_final: 0.7530 (pt0) REVERT: B 217 VAL cc_start: 0.7608 (t) cc_final: 0.7302 (m) REVERT: B 311 LYS cc_start: 0.7498 (ttpt) cc_final: 0.6899 (mmtt) REVERT: B 342 ASN cc_start: 0.7845 (t0) cc_final: 0.7634 (t0) REVERT: B 452 ASP cc_start: 0.7214 (t0) cc_final: 0.5147 (t70) REVERT: B 588 GLN cc_start: 0.8278 (tt0) cc_final: 0.7956 (tt0) REVERT: C 19 TYR cc_start: 0.8022 (m-80) cc_final: 0.7685 (m-10) REVERT: C 91 LEU cc_start: 0.8290 (tp) cc_final: 0.8059 (tp) REVERT: C 97 ASP cc_start: 0.7371 (t0) cc_final: 0.6370 (t70) REVERT: C 103 VAL cc_start: 0.7941 (t) cc_final: 0.7669 (t) REVERT: C 118 THR cc_start: 0.6400 (m) cc_final: 0.6158 (m) REVERT: D 199 ILE cc_start: 0.8045 (mp) cc_final: 0.7776 (mt) REVERT: E 57 SER cc_start: 0.7418 (m) cc_final: 0.7014 (p) REVERT: G 41 TYR cc_start: 0.8703 (t80) cc_final: 0.8368 (t80) REVERT: G 76 LEU cc_start: 0.8774 (mt) cc_final: 0.8102 (mp) REVERT: G 98 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7080 (tp30) REVERT: H 39 ASN cc_start: 0.8017 (m110) cc_final: 0.7663 (m-40) REVERT: H 55 TYR cc_start: 0.7847 (p90) cc_final: 0.7645 (p90) REVERT: H 120 LYS cc_start: 0.7962 (tttt) cc_final: 0.7585 (tptp) REVERT: I 157 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7132 (tm-30) REVERT: I 159 VAL cc_start: 0.9195 (t) cc_final: 0.8872 (t) REVERT: J 191 ILE cc_start: 0.9206 (pt) cc_final: 0.8986 (pt) REVERT: K 134 TYR cc_start: 0.8083 (t80) cc_final: 0.7763 (t80) outliers start: 4 outliers final: 0 residues processed: 929 average time/residue: 0.4544 time to fit residues: 620.0615 Evaluate side-chains 492 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 0.6980 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 247 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 90 GLN B 146 GLN ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 251 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 463 ASN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN B 505 ASN ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 HIS B 665 GLN B 675 GLN B 677 ASN B 704 ASN B 803 ASN B 808 HIS C 25 ASN C 40 GLN C 48 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN D 197 GLN E 50 GLN E 69 ASN E 139 ASN F 8 ASN F 37 ASN F 54 ASN F 76 GLN F 87 HIS G 28 GLN ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 ASN I 12 ASN I 34 HIS I 49 HIS I 143 HIS I 151 ASN ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 203 ASN J 95 GLN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN K 33 HIS K 42 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28468 Z= 0.295 Angle : 0.692 13.345 40228 Z= 0.355 Chirality : 0.039 0.292 4852 Planarity : 0.006 0.065 3725 Dihedral : 21.089 175.075 8400 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 4.07 % Allowed : 14.34 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.16), residues: 2372 helix: -0.69 (0.16), residues: 927 sheet: -0.58 (0.24), residues: 455 loop : -2.07 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 256 HIS 0.011 0.002 HIS F 87 PHE 0.028 0.003 PHE J 104 TYR 0.022 0.002 TYR D 130 ARG 0.010 0.001 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 551 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8011 (t0) cc_final: 0.7399 (t0) REVERT: B 166 MET cc_start: 0.7798 (ptm) cc_final: 0.7593 (ptm) REVERT: B 201 ASN cc_start: 0.7119 (t0) cc_final: 0.6831 (t0) REVERT: B 225 LYS cc_start: 0.6969 (mtmt) cc_final: 0.6667 (mtmt) REVERT: B 311 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7121 (mmtt) REVERT: B 370 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.5976 (pp) REVERT: B 461 LYS cc_start: 0.7973 (tptp) cc_final: 0.7584 (ttmm) REVERT: B 463 ASN cc_start: 0.6631 (OUTLIER) cc_final: 0.6159 (m-40) REVERT: B 588 GLN cc_start: 0.8856 (tt0) cc_final: 0.8643 (tt0) REVERT: B 650 SER cc_start: 0.7213 (p) cc_final: 0.6998 (p) REVERT: B 665 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7749 (pp30) REVERT: B 803 ASN cc_start: 0.8699 (t160) cc_final: 0.8482 (t0) REVERT: C 47 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7080 (tp) REVERT: C 123 GLN cc_start: 0.6483 (tm-30) cc_final: 0.6089 (tm-30) REVERT: C 147 ASP cc_start: 0.6462 (p0) cc_final: 0.5932 (p0) REVERT: D 210 MET cc_start: 0.8503 (mtm) cc_final: 0.8289 (mtt) REVERT: D 248 ILE cc_start: 0.8366 (pt) cc_final: 0.7969 (pt) REVERT: E 8 TYR cc_start: 0.7962 (m-80) cc_final: 0.7690 (m-80) REVERT: E 57 SER cc_start: 0.7882 (m) cc_final: 0.7662 (p) REVERT: F 68 MET cc_start: 0.7134 (ppp) cc_final: 0.6807 (ppp) REVERT: F 133 LEU cc_start: 0.6721 (mp) cc_final: 0.6480 (mp) REVERT: G 98 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7065 (tp30) REVERT: I 5 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7533 (pp) REVERT: I 21 GLN cc_start: 0.8525 (mp10) cc_final: 0.8230 (mp10) REVERT: I 79 LYS cc_start: 0.7179 (pmmt) cc_final: 0.6367 (ptpp) REVERT: I 157 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7404 (tm-30) REVERT: K 35 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.8268 (m90) REVERT: K 134 TYR cc_start: 0.8607 (t80) cc_final: 0.8349 (t80) outliers start: 89 outliers final: 54 residues processed: 613 average time/residue: 0.4003 time to fit residues: 379.8732 Evaluate side-chains 462 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 402 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 35 HIS Chi-restraints excluded: chain K residue 143 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 247 optimal weight: 3.9990 chunk 267 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN E 59 ASN F 21 GLN F 45 GLN F 52 ASN G 87 ASN H 27 HIS ** I 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 HIS I 172 GLN J 213 ASN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 ASN J 261 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 28468 Z= 0.320 Angle : 0.698 12.495 40228 Z= 0.356 Chirality : 0.041 0.222 4852 Planarity : 0.006 0.088 3725 Dihedral : 20.913 175.498 8400 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.53 % Allowed : 16.81 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.17), residues: 2372 helix: 0.06 (0.17), residues: 931 sheet: -0.46 (0.24), residues: 451 loop : -1.81 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 9 HIS 0.046 0.002 HIS I 49 PHE 0.031 0.003 PHE B 657 TYR 0.023 0.002 TYR B 865 ARG 0.009 0.001 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 443 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8086 (t0) cc_final: 0.7613 (t0) REVERT: B 225 LYS cc_start: 0.7677 (mtmt) cc_final: 0.7463 (mtmt) REVERT: B 311 LYS cc_start: 0.7709 (ttpt) cc_final: 0.7137 (mmtt) REVERT: B 462 LEU cc_start: 0.6791 (tp) cc_final: 0.6335 (tt) REVERT: B 588 GLN cc_start: 0.8878 (tt0) cc_final: 0.8580 (tt0) REVERT: B 632 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8203 (ptt90) REVERT: B 650 SER cc_start: 0.7406 (p) cc_final: 0.7137 (p) REVERT: B 655 ASP cc_start: 0.7839 (t70) cc_final: 0.7478 (t0) REVERT: B 714 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7627 (tt0) REVERT: B 757 PHE cc_start: 0.7166 (t80) cc_final: 0.6952 (t80) REVERT: D 126 HIS cc_start: 0.7063 (t-90) cc_final: 0.6586 (t-90) REVERT: D 277 ILE cc_start: 0.7328 (mm) cc_final: 0.6865 (mm) REVERT: F 65 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8231 (mt0) REVERT: F 68 MET cc_start: 0.7245 (ppp) cc_final: 0.5101 (mmp) REVERT: F 133 LEU cc_start: 0.7332 (mp) cc_final: 0.7116 (mp) REVERT: G 102 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7216 (mt-10) REVERT: H 15 SER cc_start: 0.8370 (t) cc_final: 0.7863 (p) REVERT: H 36 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8317 (tp40) REVERT: H 39 ASN cc_start: 0.8966 (m110) cc_final: 0.8276 (m110) REVERT: H 73 ASP cc_start: 0.8131 (p0) cc_final: 0.7605 (p0) REVERT: I 5 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8005 (pp) REVERT: I 79 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7623 (ptpp) REVERT: I 157 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7791 (tt0) REVERT: I 186 SER cc_start: 0.8804 (m) cc_final: 0.8511 (t) REVERT: J 212 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8170 (mtmm) REVERT: J 279 MET cc_start: 0.8466 (mtp) cc_final: 0.8139 (mtp) outliers start: 121 outliers final: 87 residues processed: 528 average time/residue: 0.3728 time to fit residues: 309.9103 Evaluate side-chains 443 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 353 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 272 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 143 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 0.0970 chunk 186 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 262 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN B 803 ASN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN D 197 GLN E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 ASN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS J 213 ASN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28468 Z= 0.174 Angle : 0.573 10.273 40228 Z= 0.291 Chirality : 0.037 0.205 4852 Planarity : 0.004 0.085 3725 Dihedral : 20.831 175.415 8400 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.43 % Allowed : 19.32 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.86 (0.17), residues: 2372 helix: 0.53 (0.17), residues: 942 sheet: -0.42 (0.24), residues: 451 loop : -1.72 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 9 HIS 0.008 0.001 HIS I 49 PHE 0.031 0.002 PHE B 740 TYR 0.016 0.002 TYR J 160 ARG 0.005 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 387 time to evaluate : 2.439 Fit side-chains revert: symmetry clash REVERT: B 79 ASN cc_start: 0.7961 (t0) cc_final: 0.7600 (t0) REVERT: B 201 ASN cc_start: 0.7115 (t0) cc_final: 0.6858 (t0) REVERT: B 311 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7263 (mmtt) REVERT: B 389 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8202 (pp) REVERT: B 588 GLN cc_start: 0.8786 (tt0) cc_final: 0.8521 (tt0) REVERT: B 632 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7984 (ptt90) REVERT: B 650 SER cc_start: 0.7147 (p) cc_final: 0.6878 (p) REVERT: B 655 ASP cc_start: 0.7701 (t70) cc_final: 0.7397 (t0) REVERT: C 29 ASN cc_start: 0.7875 (p0) cc_final: 0.6982 (p0) REVERT: C 72 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7609 (t80) REVERT: C 104 LEU cc_start: 0.8757 (pp) cc_final: 0.8183 (tp) REVERT: D 216 ILE cc_start: 0.6263 (mm) cc_final: 0.6027 (mt) REVERT: D 233 GLU cc_start: 0.8350 (mp0) cc_final: 0.7928 (mp0) REVERT: D 277 ILE cc_start: 0.7363 (mm) cc_final: 0.6999 (mm) REVERT: E 8 TYR cc_start: 0.8052 (m-80) cc_final: 0.7742 (m-80) REVERT: F 65 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8255 (mt0) REVERT: F 68 MET cc_start: 0.7272 (ppp) cc_final: 0.5048 (mmp) REVERT: F 82 PHE cc_start: 0.8440 (p90) cc_final: 0.8117 (p90) REVERT: F 132 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.6209 (mtp85) REVERT: G 28 GLN cc_start: 0.8869 (tt0) cc_final: 0.8648 (mt0) REVERT: G 41 TYR cc_start: 0.9195 (t80) cc_final: 0.8943 (t80) REVERT: G 68 MET cc_start: 0.8697 (ptm) cc_final: 0.8349 (ptt) REVERT: H 36 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8225 (tp40) REVERT: H 73 ASP cc_start: 0.8165 (p0) cc_final: 0.7762 (p0) REVERT: H 120 LYS cc_start: 0.7102 (tttp) cc_final: 0.6478 (ttpt) REVERT: I 157 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7802 (tt0) REVERT: I 186 SER cc_start: 0.8705 (m) cc_final: 0.8452 (t) REVERT: J 87 ILE cc_start: 0.8997 (mp) cc_final: 0.8706 (tt) REVERT: J 212 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8228 (ttpp) REVERT: J 222 SER cc_start: 0.7468 (m) cc_final: 0.6969 (p) outliers start: 97 outliers final: 64 residues processed: 452 average time/residue: 0.3889 time to fit residues: 282.3299 Evaluate side-chains 425 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 357 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 272 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 143 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 108 optimal weight: 0.0050 chunk 224 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 134 optimal weight: 0.0370 chunk 235 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 437 HIS ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN D 197 GLN E 59 ASN E 139 ASN G 85 GLN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28468 Z= 0.200 Angle : 0.567 10.208 40228 Z= 0.289 Chirality : 0.037 0.202 4852 Planarity : 0.004 0.083 3725 Dihedral : 20.706 175.038 8400 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.07 % Allowed : 19.64 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2372 helix: 0.78 (0.17), residues: 944 sheet: -0.33 (0.25), residues: 436 loop : -1.67 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 9 HIS 0.009 0.001 HIS B 437 PHE 0.034 0.002 PHE B 740 TYR 0.023 0.002 TYR K 134 ARG 0.006 0.001 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 380 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8053 (t0) cc_final: 0.7683 (t0) REVERT: B 311 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7269 (mmtt) REVERT: B 389 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8152 (pp) REVERT: B 632 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8332 (ptt90) REVERT: B 650 SER cc_start: 0.7142 (p) cc_final: 0.6854 (p) REVERT: B 655 ASP cc_start: 0.7583 (t70) cc_final: 0.7288 (t0) REVERT: B 774 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.8419 (p-80) REVERT: C 29 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7425 (p0) REVERT: D 1 MET cc_start: 0.7799 (ptm) cc_final: 0.7592 (ppp) REVERT: D 142 MET cc_start: 0.7152 (ttm) cc_final: 0.6848 (ttm) REVERT: D 277 ILE cc_start: 0.7660 (mm) cc_final: 0.7343 (mm) REVERT: E 8 TYR cc_start: 0.8139 (m-80) cc_final: 0.7765 (m-80) REVERT: F 65 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8384 (mt0) REVERT: F 68 MET cc_start: 0.6985 (ppp) cc_final: 0.5399 (mmp) REVERT: F 82 PHE cc_start: 0.8414 (p90) cc_final: 0.8101 (p90) REVERT: F 132 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6976 (mtm110) REVERT: G 28 GLN cc_start: 0.8948 (tt0) cc_final: 0.8711 (mt0) REVERT: G 41 TYR cc_start: 0.9216 (t80) cc_final: 0.9009 (t80) REVERT: G 68 MET cc_start: 0.8747 (ptm) cc_final: 0.8403 (ptt) REVERT: H 62 ASP cc_start: 0.5453 (p0) cc_final: 0.5203 (p0) REVERT: I 157 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7547 (tm-30) REVERT: J 191 ILE cc_start: 0.9061 (pt) cc_final: 0.8441 (mt) REVERT: J 212 LYS cc_start: 0.8383 (mmmt) cc_final: 0.8167 (ttpp) REVERT: J 222 SER cc_start: 0.7345 (m) cc_final: 0.6857 (p) REVERT: K 42 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8445 (mt0) REVERT: K 134 TYR cc_start: 0.8470 (t80) cc_final: 0.8179 (t80) outliers start: 111 outliers final: 76 residues processed: 449 average time/residue: 0.3677 time to fit residues: 263.7903 Evaluate side-chains 424 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 342 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 143 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 154 optimal weight: 0.0370 chunk 64 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.7172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28468 Z= 0.188 Angle : 0.564 10.569 40228 Z= 0.285 Chirality : 0.037 0.198 4852 Planarity : 0.004 0.078 3725 Dihedral : 20.675 174.809 8400 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.93 % Allowed : 20.47 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2372 helix: 0.90 (0.17), residues: 952 sheet: -0.32 (0.25), residues: 433 loop : -1.62 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 9 HIS 0.006 0.001 HIS B 437 PHE 0.032 0.002 PHE B 740 TYR 0.017 0.002 TYR D 108 ARG 0.006 0.000 ARG K 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 353 time to evaluate : 2.518 Fit side-chains revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8120 (t0) cc_final: 0.7818 (t0) REVERT: B 180 HIS cc_start: 0.6288 (m-70) cc_final: 0.5907 (m-70) REVERT: B 389 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8342 (pp) REVERT: B 632 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8455 (ptt90) REVERT: B 650 SER cc_start: 0.7196 (p) cc_final: 0.6874 (p) REVERT: B 655 ASP cc_start: 0.7747 (t70) cc_final: 0.7496 (t0) REVERT: C 29 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.7215 (p0) REVERT: D 1 MET cc_start: 0.7786 (ptm) cc_final: 0.7529 (ppp) REVERT: D 126 HIS cc_start: 0.7212 (m-70) cc_final: 0.6957 (m90) REVERT: D 142 MET cc_start: 0.7115 (ttm) cc_final: 0.6857 (ttm) REVERT: D 220 ILE cc_start: 0.9069 (mm) cc_final: 0.8700 (mt) REVERT: D 248 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8565 (pt) REVERT: D 277 ILE cc_start: 0.7719 (mm) cc_final: 0.7414 (mm) REVERT: E 8 TYR cc_start: 0.8184 (m-80) cc_final: 0.7771 (m-80) REVERT: F 65 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7531 (mt0) REVERT: F 82 PHE cc_start: 0.8417 (p90) cc_final: 0.8023 (p90) REVERT: G 28 GLN cc_start: 0.8970 (tt0) cc_final: 0.8705 (mt0) REVERT: G 41 TYR cc_start: 0.9178 (t80) cc_final: 0.8971 (t80) REVERT: G 68 MET cc_start: 0.8736 (ptm) cc_final: 0.8419 (ptt) REVERT: H 44 ARG cc_start: 0.7403 (tpp-160) cc_final: 0.6824 (mmm160) REVERT: H 62 ASP cc_start: 0.5668 (p0) cc_final: 0.5424 (p0) REVERT: I 71 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7629 (tm-30) REVERT: I 157 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7544 (tm-30) REVERT: J 87 ILE cc_start: 0.8834 (mp) cc_final: 0.8561 (tt) REVERT: J 191 ILE cc_start: 0.9061 (pt) cc_final: 0.8453 (mt) REVERT: J 222 SER cc_start: 0.7373 (m) cc_final: 0.6889 (p) outliers start: 108 outliers final: 80 residues processed: 426 average time/residue: 0.4072 time to fit residues: 279.2147 Evaluate side-chains 416 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 332 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 143 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 262 optimal weight: 0.9980 chunk 164 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 GLN C 83 HIS ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.7325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28468 Z= 0.160 Angle : 0.551 10.312 40228 Z= 0.278 Chirality : 0.036 0.293 4852 Planarity : 0.004 0.069 3725 Dihedral : 20.634 174.657 8400 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.39 % Allowed : 21.43 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2372 helix: 1.02 (0.17), residues: 957 sheet: -0.27 (0.25), residues: 424 loop : -1.61 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 9 HIS 0.007 0.001 HIS B 437 PHE 0.031 0.002 PHE B 740 TYR 0.021 0.001 TYR K 134 ARG 0.007 0.000 ARG K 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 360 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8173 (t0) cc_final: 0.7862 (t0) REVERT: B 389 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8402 (pp) REVERT: B 632 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8317 (ptt90) REVERT: B 650 SER cc_start: 0.7149 (p) cc_final: 0.6822 (p) REVERT: B 655 ASP cc_start: 0.7593 (t70) cc_final: 0.7385 (t0) REVERT: B 727 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7956 (p0) REVERT: B 757 PHE cc_start: 0.7363 (t80) cc_final: 0.7083 (t80) REVERT: C 29 ASN cc_start: 0.7527 (p0) cc_final: 0.7252 (p0) REVERT: C 43 ILE cc_start: 0.5380 (tt) cc_final: 0.5061 (mp) REVERT: D 1 MET cc_start: 0.7712 (ptm) cc_final: 0.7421 (ppp) REVERT: D 126 HIS cc_start: 0.7210 (m-70) cc_final: 0.6991 (m90) REVERT: D 142 MET cc_start: 0.7076 (ttm) cc_final: 0.6864 (ttm) REVERT: D 194 ILE cc_start: 0.8605 (pt) cc_final: 0.8296 (mt) REVERT: D 220 ILE cc_start: 0.9095 (mm) cc_final: 0.8748 (mt) REVERT: D 248 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8551 (pt) REVERT: D 277 ILE cc_start: 0.7743 (mm) cc_final: 0.7442 (mm) REVERT: E 8 TYR cc_start: 0.8203 (m-80) cc_final: 0.7806 (m-80) REVERT: E 58 LEU cc_start: 0.8213 (tt) cc_final: 0.7997 (tt) REVERT: F 65 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7540 (mt0) REVERT: F 82 PHE cc_start: 0.8363 (p90) cc_final: 0.7919 (p90) REVERT: F 132 ARG cc_start: 0.7208 (mtm110) cc_final: 0.6618 (mtp85) REVERT: G 28 GLN cc_start: 0.8969 (tt0) cc_final: 0.8709 (mt0) REVERT: G 41 TYR cc_start: 0.9163 (t80) cc_final: 0.8917 (t80) REVERT: G 68 MET cc_start: 0.8731 (ptm) cc_final: 0.8427 (ptt) REVERT: H 44 ARG cc_start: 0.7591 (tpp-160) cc_final: 0.7031 (mmp-170) REVERT: H 51 GLU cc_start: 0.7748 (tp30) cc_final: 0.7512 (mm-30) REVERT: H 108 LEU cc_start: 0.3999 (OUTLIER) cc_final: 0.3478 (pp) REVERT: I 157 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7510 (tt0) REVERT: J 191 ILE cc_start: 0.9021 (pt) cc_final: 0.8411 (mt) REVERT: J 222 SER cc_start: 0.7224 (m) cc_final: 0.6760 (p) outliers start: 96 outliers final: 72 residues processed: 424 average time/residue: 0.3649 time to fit residues: 246.3176 Evaluate side-chains 415 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 338 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 143 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 206 optimal weight: 0.5980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 GLN B 803 ASN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN D 278 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 HIS G 56 HIS ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.7775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28468 Z= 0.237 Angle : 0.596 11.555 40228 Z= 0.301 Chirality : 0.038 0.191 4852 Planarity : 0.004 0.068 3725 Dihedral : 20.612 174.640 8400 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.57 % Allowed : 21.97 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2372 helix: 1.05 (0.17), residues: 946 sheet: -0.35 (0.25), residues: 428 loop : -1.58 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 9 HIS 0.007 0.001 HIS H 59 PHE 0.033 0.002 PHE B 740 TYR 0.025 0.002 TYR C 138 ARG 0.008 0.001 ARG K 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 364 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 389 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8293 (pp) REVERT: B 466 GLN cc_start: 0.5676 (OUTLIER) cc_final: 0.5445 (pp30) REVERT: B 632 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8339 (ptt90) REVERT: B 650 SER cc_start: 0.7415 (p) cc_final: 0.7063 (p) REVERT: B 774 HIS cc_start: 0.8838 (OUTLIER) cc_final: 0.8561 (p-80) REVERT: C 29 ASN cc_start: 0.7702 (p0) cc_final: 0.6885 (p0) REVERT: C 43 ILE cc_start: 0.5750 (tt) cc_final: 0.5172 (mp) REVERT: D 1 MET cc_start: 0.7758 (ptm) cc_final: 0.7469 (ppp) REVERT: D 194 ILE cc_start: 0.8768 (pt) cc_final: 0.8520 (mt) REVERT: D 220 ILE cc_start: 0.9121 (mm) cc_final: 0.8786 (mt) REVERT: D 248 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8578 (pt) REVERT: F 65 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7500 (mt0) REVERT: F 82 PHE cc_start: 0.8415 (p90) cc_final: 0.8000 (p90) REVERT: F 132 ARG cc_start: 0.7613 (mtm110) cc_final: 0.7078 (mtp85) REVERT: G 28 GLN cc_start: 0.9016 (tt0) cc_final: 0.8746 (mt0) REVERT: G 68 MET cc_start: 0.8670 (ptm) cc_final: 0.8351 (ptt) REVERT: H 44 ARG cc_start: 0.7656 (tpp-160) cc_final: 0.7046 (mmp-170) REVERT: H 51 GLU cc_start: 0.7773 (tp30) cc_final: 0.7547 (mm-30) REVERT: I 13 SER cc_start: 0.7450 (OUTLIER) cc_final: 0.6389 (t) REVERT: I 157 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7609 (tt0) REVERT: J 191 ILE cc_start: 0.9076 (pt) cc_final: 0.8487 (mt) REVERT: K 134 TYR cc_start: 0.8121 (t80) cc_final: 0.7749 (t80) outliers start: 100 outliers final: 76 residues processed: 435 average time/residue: 0.3663 time to fit residues: 255.1745 Evaluate side-chains 417 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 335 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 143 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 231 optimal weight: 0.4980 chunk 243 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 665 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN I 240 ASN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.7972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28468 Z= 0.205 Angle : 0.581 12.322 40228 Z= 0.293 Chirality : 0.037 0.185 4852 Planarity : 0.004 0.064 3725 Dihedral : 20.602 174.063 8400 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.39 % Allowed : 22.38 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2372 helix: 1.10 (0.17), residues: 957 sheet: -0.32 (0.25), residues: 422 loop : -1.69 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 9 HIS 0.007 0.001 HIS B 437 PHE 0.032 0.002 PHE B 740 TYR 0.025 0.002 TYR D 108 ARG 0.008 0.001 ARG K 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 352 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 389 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8282 (pp) REVERT: B 632 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8336 (ptt90) REVERT: B 727 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.7972 (p0) REVERT: B 774 HIS cc_start: 0.8882 (OUTLIER) cc_final: 0.8612 (p-80) REVERT: C 43 ILE cc_start: 0.5209 (tt) cc_final: 0.4810 (mp) REVERT: C 147 ASP cc_start: 0.6346 (p0) cc_final: 0.5992 (p0) REVERT: D 1 MET cc_start: 0.7741 (ptm) cc_final: 0.7409 (ppp) REVERT: D 194 ILE cc_start: 0.8806 (pt) cc_final: 0.8595 (mt) REVERT: D 220 ILE cc_start: 0.9120 (mm) cc_final: 0.8804 (mt) REVERT: D 248 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8574 (pt) REVERT: E 8 TYR cc_start: 0.8198 (m-80) cc_final: 0.7834 (m-80) REVERT: F 82 PHE cc_start: 0.8303 (p90) cc_final: 0.7871 (p90) REVERT: F 132 ARG cc_start: 0.7632 (mtm110) cc_final: 0.7092 (mtp85) REVERT: G 28 GLN cc_start: 0.8992 (tt0) cc_final: 0.8773 (mt0) REVERT: G 41 TYR cc_start: 0.9151 (t80) cc_final: 0.8933 (t80) REVERT: G 68 MET cc_start: 0.8678 (ptm) cc_final: 0.8394 (ptt) REVERT: H 44 ARG cc_start: 0.7714 (tpp-160) cc_final: 0.7196 (mmp-170) REVERT: H 51 GLU cc_start: 0.7823 (tp30) cc_final: 0.7519 (mm-30) REVERT: I 157 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7676 (tt0) REVERT: J 191 ILE cc_start: 0.9043 (pt) cc_final: 0.8497 (mt) REVERT: J 240 ASN cc_start: 0.7645 (t0) cc_final: 0.7346 (t0) outliers start: 96 outliers final: 80 residues processed: 417 average time/residue: 0.3654 time to fit residues: 245.3422 Evaluate side-chains 416 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 331 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 143 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 0.9990 chunk 258 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 179 optimal weight: 7.9990 chunk 270 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 22 optimal weight: 30.0000 chunk 166 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN E 69 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 HIS ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.8046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28468 Z= 0.164 Angle : 0.571 12.999 40228 Z= 0.287 Chirality : 0.037 0.178 4852 Planarity : 0.004 0.064 3725 Dihedral : 20.562 173.814 8400 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.93 % Allowed : 23.07 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.18), residues: 2372 helix: 1.17 (0.17), residues: 959 sheet: -0.28 (0.26), residues: 422 loop : -1.69 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 9 HIS 0.013 0.001 HIS B 437 PHE 0.032 0.002 PHE B 740 TYR 0.025 0.002 TYR D 108 ARG 0.008 0.001 ARG K 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 346 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 389 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8308 (pp) REVERT: B 632 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8295 (ptt90) REVERT: B 650 SER cc_start: 0.7500 (p) cc_final: 0.7254 (p) REVERT: B 727 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7968 (p0) REVERT: B 768 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8595 (t) REVERT: B 774 HIS cc_start: 0.8916 (OUTLIER) cc_final: 0.8671 (p-80) REVERT: C 147 ASP cc_start: 0.6103 (p0) cc_final: 0.5771 (p0) REVERT: D 1 MET cc_start: 0.7692 (ptm) cc_final: 0.7365 (ppp) REVERT: D 194 ILE cc_start: 0.8815 (pt) cc_final: 0.8609 (mt) REVERT: D 220 ILE cc_start: 0.9128 (mm) cc_final: 0.8833 (mt) REVERT: D 222 CYS cc_start: 0.8057 (m) cc_final: 0.7779 (m) REVERT: D 248 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8576 (pt) REVERT: E 8 TYR cc_start: 0.8204 (m-80) cc_final: 0.7851 (m-80) REVERT: E 46 LYS cc_start: 0.8998 (pptt) cc_final: 0.8680 (pttp) REVERT: F 82 PHE cc_start: 0.8251 (p90) cc_final: 0.7758 (p90) REVERT: F 132 ARG cc_start: 0.7477 (mtm110) cc_final: 0.6914 (mtp85) REVERT: G 28 GLN cc_start: 0.8978 (tt0) cc_final: 0.8769 (mt0) REVERT: G 41 TYR cc_start: 0.9141 (t80) cc_final: 0.8887 (t80) REVERT: G 68 MET cc_start: 0.8682 (ptm) cc_final: 0.8386 (ptt) REVERT: H 44 ARG cc_start: 0.7739 (tpp-160) cc_final: 0.7246 (mmp-170) REVERT: H 51 GLU cc_start: 0.7841 (tp30) cc_final: 0.7552 (mm-30) REVERT: I 157 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7668 (tt0) REVERT: J 191 ILE cc_start: 0.9020 (pt) cc_final: 0.8466 (mt) REVERT: J 240 ASN cc_start: 0.7370 (t0) cc_final: 0.7154 (t0) REVERT: K 99 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8564 (p) REVERT: K 134 TYR cc_start: 0.7910 (t80) cc_final: 0.7693 (t80) outliers start: 86 outliers final: 72 residues processed: 406 average time/residue: 0.3673 time to fit residues: 238.7722 Evaluate side-chains 413 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 334 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 143 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 9.9990 chunk 229 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 198 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 216 optimal weight: 0.0170 chunk 90 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN E 69 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.140533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.106159 restraints weight = 50018.150| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.18 r_work: 0.3225 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.8126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28468 Z= 0.169 Angle : 0.573 12.805 40228 Z= 0.288 Chirality : 0.036 0.202 4852 Planarity : 0.004 0.062 3725 Dihedral : 20.530 173.911 8400 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.84 % Allowed : 23.39 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2372 helix: 1.17 (0.17), residues: 966 sheet: -0.30 (0.26), residues: 422 loop : -1.68 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 9 HIS 0.013 0.001 HIS J 143 PHE 0.033 0.002 PHE B 740 TYR 0.023 0.002 TYR D 108 ARG 0.009 0.001 ARG I 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6293.56 seconds wall clock time: 114 minutes 28.44 seconds (6868.44 seconds total)