Starting phenix.real_space_refine on Tue Feb 20 23:22:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/02_2024/7xg3_33184_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/02_2024/7xg3_33184.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/02_2024/7xg3_33184_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/02_2024/7xg3_33184_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/02_2024/7xg3_33184_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/02_2024/7xg3_33184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/02_2024/7xg3_33184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/02_2024/7xg3_33184_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg3_33184/02_2024/7xg3_33184_updated.pdb" } resolution = 3.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4742 atoms to isotropic. 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 127 5.49 5 S 105 5.16 5 C 14965 2.51 5 N 4317 2.21 5 O 4853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 194": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 320": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H ARG 207": "NH1" <-> "NH2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L GLU 142": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L ARG 557": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24368 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1897 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "B" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1709 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 17, 'TRANS': 201} Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2482 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 18, 'TRANS': 309} Chain breaks: 1 Chain: "D" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2485 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain breaks: 1 Chain: "E" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2445 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain breaks: 1 Chain: "F" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2437 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 18, 'TRANS': 303} Chain breaks: 1 Chain: "G" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1899 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 13, 'TRANS': 235} Chain breaks: 2 Chain: "H" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain: "I" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1317 Classifications: {'RNA': 61} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 13, 'rna3p_pur': 26, 'rna3p_pyr': 11} Link IDs: {'rna2p': 23, 'rna3p': 37} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 616 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "L" Number of atoms: 4542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4542 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 31, 'TRANS': 562} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 248 SG CYS A 33 37.545 91.107 19.864 1.00 60.29 S Time building chain proxies: 13.25, per 1000 atoms: 0.54 Number of scatterers: 24368 At special positions: 0 Unit cell: (107.8, 140.8, 178.2, 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 105 16.00 P 127 15.00 O 4853 8.00 N 4317 7.00 C 14965 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.70 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 33 " 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 29 sheets defined 32.9% alpha, 14.2% beta 27 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 11.12 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.620A pdb=" N ASP A 9 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN A 10 " --> pdb=" O ILE A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 150 through 163 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 209 through 218 removed outlier: 3.796A pdb=" N TYR A 217 " --> pdb=" O TRP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 45 through 48 No H-bonds generated for 'chain 'B' and resid 45 through 48' Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 67 through 81 Processing helix chain 'C' and resid 83 through 90 Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.632A pdb=" N GLU C 157 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ARG C 158 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 160 " --> pdb=" O GLU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 201 through 222 Processing helix chain 'C' and resid 269 through 284 removed outlier: 5.117A pdb=" N THR C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 332 removed outlier: 3.689A pdb=" N GLY C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 96 through 104 Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 154 through 156 No H-bonds generated for 'chain 'D' and resid 154 through 156' Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 201 through 221 Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'E' and resid 67 through 79 Processing helix chain 'E' and resid 83 through 89 Processing helix chain 'E' and resid 96 through 103 Processing helix chain 'E' and resid 118 through 125 Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 155 through 157 No H-bonds generated for 'chain 'E' and resid 155 through 157' Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 269 through 280 Processing helix chain 'E' and resid 320 through 330 Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'F' and resid 84 through 89 Processing helix chain 'F' and resid 96 through 103 Processing helix chain 'F' and resid 118 through 124 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 201 through 215 Processing helix chain 'F' and resid 269 through 280 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'G' and resid 67 through 80 Processing helix chain 'G' and resid 83 through 88 Processing helix chain 'G' and resid 96 through 103 Processing helix chain 'G' and resid 118 through 125 Processing helix chain 'G' and resid 154 through 158 Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 269 through 284 removed outlier: 4.869A pdb=" N THR G 283 " --> pdb=" O LEU G 279 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 331 Processing helix chain 'G' and resid 336 through 342 Processing helix chain 'H' and resid 16 through 26 Processing helix chain 'H' and resid 32 through 38 Processing helix chain 'H' and resid 70 through 94 Proline residue: H 82 - end of helix Processing helix chain 'H' and resid 132 through 139 Processing helix chain 'H' and resid 142 through 163 removed outlier: 4.068A pdb=" N VAL H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE H 147 " --> pdb=" O THR H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 230 No H-bonds generated for 'chain 'H' and resid 227 through 230' Processing helix chain 'L' and resid 11 through 13 No H-bonds generated for 'chain 'L' and resid 11 through 13' Processing helix chain 'L' and resid 19 through 30 Processing helix chain 'L' and resid 41 through 43 No H-bonds generated for 'chain 'L' and resid 41 through 43' Processing helix chain 'L' and resid 45 through 59 removed outlier: 4.045A pdb=" N LYS L 59 " --> pdb=" O ALA L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 77 removed outlier: 4.391A pdb=" N TRP L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN L 74 " --> pdb=" O ALA L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 88 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'L' and resid 102 through 111 Processing helix chain 'L' and resid 115 through 121 Processing helix chain 'L' and resid 130 through 139 Processing helix chain 'L' and resid 147 through 153 removed outlier: 3.752A pdb=" N LEU L 153 " --> pdb=" O ASP L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 186 removed outlier: 4.266A pdb=" N SER L 183 " --> pdb=" O VAL L 179 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN L 184 " --> pdb=" O ALA L 180 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR L 185 " --> pdb=" O MET L 181 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR L 186 " --> pdb=" O ARG L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 238 through 248 removed outlier: 4.692A pdb=" N GLU L 242 " --> pdb=" O HIS L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 263 Processing helix chain 'L' and resid 275 through 286 removed outlier: 4.009A pdb=" N VAL L 286 " --> pdb=" O THR L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 318 Processing helix chain 'L' and resid 329 through 344 Processing helix chain 'L' and resid 371 through 378 Processing helix chain 'L' and resid 399 through 404 Processing helix chain 'L' and resid 421 through 425 removed outlier: 3.687A pdb=" N ALA L 425 " --> pdb=" O TRP L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 442 through 458 Processing helix chain 'L' and resid 470 through 487 removed outlier: 5.603A pdb=" N ALA L 482 " --> pdb=" O GLY L 478 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA L 483 " --> pdb=" O ARG L 479 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASP L 486 " --> pdb=" O ALA L 482 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ARG L 487 " --> pdb=" O ALA L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 509 Processing helix chain 'L' and resid 520 through 522 No H-bonds generated for 'chain 'L' and resid 520 through 522' Processing helix chain 'L' and resid 537 through 539 No H-bonds generated for 'chain 'L' and resid 537 through 539' Processing helix chain 'L' and resid 559 through 568 Processing helix chain 'L' and resid 570 through 587 removed outlier: 4.000A pdb=" N ARG L 587 " --> pdb=" O GLN L 583 " (cutoff:3.500A) Processing helix chain 'L' and resid 614 through 622 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 45 Processing sheet with id= B, first strand: chain 'A' and resid 91 through 93 removed outlier: 6.443A pdb=" N HIS A 138 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 114 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 72 through 75 removed outlier: 6.527A pdb=" N ALA B 128 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B 10 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 55 through 58 removed outlier: 4.580A pdb=" N GLU B 55 " --> pdb=" O LYS B 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 80 through 86 Processing sheet with id= F, first strand: chain 'B' and resid 196 through 200 Processing sheet with id= G, first strand: chain 'C' and resid 144 through 146 removed outlier: 6.478A pdb=" N ARG C 8 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE C 300 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 45 through 50 Processing sheet with id= I, first strand: chain 'C' and resid 174 through 181 Processing sheet with id= J, first strand: chain 'D' and resid 144 through 146 removed outlier: 5.955A pdb=" N ARG D 8 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE D 300 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 45 through 51 Processing sheet with id= L, first strand: chain 'D' and resid 174 through 181 Processing sheet with id= M, first strand: chain 'E' and resid 144 through 146 removed outlier: 6.298A pdb=" N ARG E 8 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE E 300 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 21 through 23 Processing sheet with id= O, first strand: chain 'E' and resid 45 through 51 Processing sheet with id= P, first strand: chain 'E' and resid 174 through 181 Processing sheet with id= Q, first strand: chain 'F' and resid 144 through 146 removed outlier: 6.055A pdb=" N ARG F 8 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE F 300 " --> pdb=" O ARG F 8 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 20 through 23 Processing sheet with id= S, first strand: chain 'F' and resid 45 through 51 Processing sheet with id= T, first strand: chain 'F' and resid 174 through 180 Processing sheet with id= U, first strand: chain 'G' and resid 298 through 301 removed outlier: 3.755A pdb=" N THR G 6 " --> pdb=" O ASP G 301 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 45 through 50 Processing sheet with id= W, first strand: chain 'H' and resid 102 through 109 removed outlier: 3.748A pdb=" N PHE H 60 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA H 65 " --> pdb=" O SER H 58 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 112 through 114 removed outlier: 4.024A pdb=" N GLU H 113 " --> pdb=" O ARG H 207 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.995A pdb=" N GLY H 177 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU H 203 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE H 175 " --> pdb=" O GLU H 203 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 180 through 185 Processing sheet with id= AA, first strand: chain 'L' and resid 412 through 414 removed outlier: 6.289A pdb=" N ILE L 34 " --> pdb=" O ALA L 413 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA L 384 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA L 37 " --> pdb=" O ALA L 384 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU L 386 " --> pdb=" O ALA L 37 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 251 through 254 Processing sheet with id= AC, first strand: chain 'L' and resid 427 through 429 removed outlier: 6.681A pdb=" N LYS L 597 " --> pdb=" O LEU L 428 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2169 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 7.91 Time building geometry restraints manager: 10.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4443 1.33 - 1.45: 6765 1.45 - 1.57: 13472 1.57 - 1.70: 257 1.70 - 1.82: 193 Bond restraints: 25130 Sorted by residual: bond pdb=" O3' 23G I 61 " pdb=" PC 23G I 61 " ideal model delta sigma weight residual 1.334 1.604 -0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C4' 23G I 61 " pdb=" O4' 23G I 61 " ideal model delta sigma weight residual 1.663 1.429 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C4' 23G I 61 " pdb=" C3' 23G I 61 " ideal model delta sigma weight residual 1.302 1.517 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C2' 23G I 61 " pdb=" O2' 23G I 61 " ideal model delta sigma weight residual 1.250 1.427 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" N3 23G I 61 " pdb=" C4 23G I 61 " ideal model delta sigma weight residual 1.502 1.354 0.148 2.00e-02 2.50e+03 5.48e+01 ... (remaining 25125 not shown) Histogram of bond angle deviations from ideal: 94.00 - 102.41: 198 102.41 - 110.82: 9018 110.82 - 119.24: 12681 119.24 - 127.65: 12361 127.65 - 136.06: 413 Bond angle restraints: 34671 Sorted by residual: angle pdb=" C3' G I 26 " pdb=" C2' G I 26 " pdb=" O2' G I 26 " ideal model delta sigma weight residual 114.60 124.72 -10.12 1.50e+00 4.44e-01 4.55e+01 angle pdb=" C4' U I 21 " pdb=" C3' U I 21 " pdb=" O3' U I 21 " ideal model delta sigma weight residual 109.40 119.00 -9.60 1.50e+00 4.44e-01 4.10e+01 angle pdb=" C4' A I 27 " pdb=" C3' A I 27 " pdb=" O3' A I 27 " ideal model delta sigma weight residual 109.40 100.31 9.09 1.50e+00 4.44e-01 3.67e+01 angle pdb=" C4' DC K 23 " pdb=" C3' DC K 23 " pdb=" O3' DC K 23 " ideal model delta sigma weight residual 110.00 118.69 -8.69 1.50e+00 4.44e-01 3.36e+01 angle pdb=" O3' G I 26 " pdb=" C3' G I 26 " pdb=" C2' G I 26 " ideal model delta sigma weight residual 109.50 117.94 -8.44 1.50e+00 4.44e-01 3.17e+01 ... (remaining 34666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 14166 35.95 - 71.91: 730 71.91 - 107.86: 50 107.86 - 143.81: 2 143.81 - 179.77: 9 Dihedral angle restraints: 14957 sinusoidal: 6926 harmonic: 8031 Sorted by residual: dihedral pdb=" C4' C I 31 " pdb=" C3' C I 31 " pdb=" C2' C I 31 " pdb=" C1' C I 31 " ideal model delta sinusoidal sigma weight residual -35.00 33.42 -68.42 1 8.00e+00 1.56e-02 9.48e+01 dihedral pdb=" C5' C I 31 " pdb=" C4' C I 31 " pdb=" C3' C I 31 " pdb=" O3' C I 31 " ideal model delta sinusoidal sigma weight residual 147.00 80.19 66.81 1 8.00e+00 1.56e-02 9.09e+01 dihedral pdb=" O4' C I 6 " pdb=" C1' C I 6 " pdb=" N1 C I 6 " pdb=" C2 C I 6 " ideal model delta sinusoidal sigma weight residual 200.00 49.79 150.21 1 1.50e+01 4.44e-03 7.97e+01 ... (remaining 14954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3668 0.121 - 0.242: 259 0.242 - 0.363: 18 0.363 - 0.484: 3 0.484 - 0.605: 6 Chirality restraints: 3954 Sorted by residual: chirality pdb=" CB VAL E 5 " pdb=" CA VAL E 5 " pdb=" CG1 VAL E 5 " pdb=" CG2 VAL E 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" CB VAL F 194 " pdb=" CA VAL F 194 " pdb=" CG1 VAL F 194 " pdb=" CG2 VAL F 194 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" CB ILE L 619 " pdb=" CA ILE L 619 " pdb=" CG1 ILE L 619 " pdb=" CG2 ILE L 619 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.55 2.00e-01 2.50e+01 7.48e+00 ... (remaining 3951 not shown) Planarity restraints: 4034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 612 " -0.043 2.00e-02 2.50e+03 3.68e-02 3.39e+01 pdb=" CG TRP L 612 " 0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP L 612 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TRP L 612 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP L 612 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP L 612 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP L 612 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 612 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 612 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP L 612 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 242 " 0.026 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C GLY D 242 " -0.092 2.00e-02 2.50e+03 pdb=" O GLY D 242 " 0.036 2.00e-02 2.50e+03 pdb=" N LEU D 243 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 212 " 0.032 2.00e-02 2.50e+03 3.14e-02 2.46e+01 pdb=" CG TRP H 212 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP H 212 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP H 212 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 212 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 212 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 212 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 212 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 212 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 212 " 0.003 2.00e-02 2.50e+03 ... (remaining 4031 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 62 2.29 - 2.94: 10570 2.94 - 3.60: 37497 3.60 - 4.25: 61748 4.25 - 4.90: 99029 Nonbonded interactions: 208906 Sorted by model distance: nonbonded pdb=" N4 C I 48 " pdb=" O6 G I 60 " model vdw 1.641 2.520 nonbonded pdb=" NH2 ARG L 557 " pdb=" OE2 GLU L 562 " model vdw 1.707 2.520 nonbonded pdb=" OG SER H 190 " pdb=" CD2 LEU H 192 " model vdw 1.731 3.460 nonbonded pdb=" O ILE F 185 " pdb=" CD2 LEU F 188 " model vdw 1.778 3.460 nonbonded pdb=" CB LYS D 244 " pdb=" O6 DG K 32 " model vdw 1.810 3.440 ... (remaining 208901 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 216 or resid 240 through 343)) selection = (chain 'D' and (resid 1 through 216 or resid 240 through 343)) selection = (chain 'E' and (resid 1 through 216 or resid 240 through 343)) selection = (chain 'F' and resid 1 through 343) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 10.510 Check model and map are aligned: 0.360 Set scattering table: 0.240 Process input model: 76.430 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:15.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 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 : 0.007 0.270 25130 Z= 0.461 Angle : 1.123 13.990 34671 Z= 0.652 Chirality : 0.068 0.605 3954 Planarity : 0.009 0.115 4034 Dihedral : 20.213 179.768 9809 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 1.26 % Allowed : 20.26 % Favored : 78.48 % 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: -2.38 (0.14), residues: 2803 helix: -1.66 (0.14), residues: 975 sheet: -1.08 (0.22), residues: 474 loop : -1.61 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.004 TRP L 612 HIS 0.017 0.002 HIS L 141 PHE 0.071 0.003 PHE F 341 TYR 0.058 0.003 TYR A 217 ARG 0.019 0.001 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 402 time to evaluate : 2.783 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: A 24 GLU cc_start: 0.6368 (pm20) cc_final: 0.6032 (pm20) REVERT: A 116 HIS cc_start: 0.7420 (t-90) cc_final: 0.7090 (t-90) REVERT: C 168 MET cc_start: 0.7084 (tpp) cc_final: 0.6586 (tpt) REVERT: D 1 MET cc_start: 0.6569 (tpt) cc_final: 0.6328 (tpt) REVERT: D 139 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.5610 (mpt) REVERT: E 188 LEU cc_start: 0.4913 (OUTLIER) cc_final: 0.4430 (pt) REVERT: E 210 ASP cc_start: 0.5723 (m-30) cc_final: 0.5404 (m-30) REVERT: F 193 ASP cc_start: 0.5719 (OUTLIER) cc_final: 0.4846 (p0) REVERT: H 59 ASN cc_start: 0.6869 (p0) cc_final: 0.6603 (p0) REVERT: H 165 MET cc_start: 0.1708 (ppp) cc_final: 0.1243 (ppp) REVERT: L 362 MET cc_start: 0.3644 (tpt) cc_final: 0.3437 (tpt) outliers start: 29 outliers final: 5 residues processed: 421 average time/residue: 1.2116 time to fit residues: 595.7165 Evaluate side-chains 344 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 336 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 139 MET Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 45 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 0.0970 chunk 169 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 280 ASN ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN E 284 ASN F 2 GLN ** F 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 GLN L 283 GLN L 556 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25130 Z= 0.224 Angle : 0.716 12.617 34671 Z= 0.366 Chirality : 0.045 0.288 3954 Planarity : 0.006 0.072 4034 Dihedral : 20.221 179.096 4741 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 4.00 % Allowed : 21.96 % Favored : 74.04 % 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: -1.50 (0.15), residues: 2803 helix: -0.50 (0.15), residues: 995 sheet: -0.98 (0.22), residues: 477 loop : -1.29 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 311 HIS 0.008 0.001 HIS L 141 PHE 0.017 0.001 PHE E 133 TYR 0.017 0.001 TYR C 47 ARG 0.016 0.001 ARG D 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 370 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7456 (m-30) cc_final: 0.6944 (p0) REVERT: A 116 HIS cc_start: 0.7436 (t-90) cc_final: 0.7031 (t-90) REVERT: C 1 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6745 (ppp) REVERT: C 47 TYR cc_start: 0.6150 (m-10) cc_final: 0.5911 (m-10) REVERT: D 1 MET cc_start: 0.6841 (tpt) cc_final: 0.6571 (tpt) REVERT: D 169 MET cc_start: 0.6573 (ttm) cc_final: 0.6250 (mtp) REVERT: E 37 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.5798 (pmt-80) REVERT: F 160 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6004 (tt) REVERT: F 193 ASP cc_start: 0.5506 (OUTLIER) cc_final: 0.4675 (p0) REVERT: G 63 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6385 (mm-40) REVERT: H 54 LEU cc_start: 0.5666 (pt) cc_final: 0.5456 (pt) REVERT: H 59 ASN cc_start: 0.6890 (p0) cc_final: 0.6526 (p0) REVERT: H 62 GLN cc_start: 0.7210 (mp10) cc_final: 0.6721 (mp10) REVERT: H 159 GLN cc_start: 0.5335 (tt0) cc_final: 0.4483 (tt0) REVERT: L 45 LYS cc_start: 0.5320 (ttpt) cc_final: 0.4880 (ttmt) REVERT: L 131 ARG cc_start: 0.1757 (OUTLIER) cc_final: 0.1153 (pmm150) REVERT: L 231 ASP cc_start: 0.5193 (OUTLIER) cc_final: 0.4779 (p0) REVERT: L 512 ILE cc_start: 0.4014 (OUTLIER) cc_final: 0.3744 (tp) outliers start: 92 outliers final: 31 residues processed: 429 average time/residue: 1.1466 time to fit residues: 580.7355 Evaluate side-chains 352 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 314 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain G residue 14 PHE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain L residue 131 ARG Chi-restraints excluded: chain L residue 231 ASP Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 512 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 264 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 262 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN D 343 GLN ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 106 ASN E 155 ASN ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN F 2 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 GLN L 141 HIS L 450 GLN L 472 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 25130 Z= 0.391 Angle : 0.774 12.107 34671 Z= 0.396 Chirality : 0.048 0.296 3954 Planarity : 0.006 0.066 4034 Dihedral : 20.194 179.847 4727 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 6.04 % Allowed : 21.52 % Favored : 72.43 % 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: -1.48 (0.15), residues: 2803 helix: -0.34 (0.16), residues: 1006 sheet: -1.26 (0.22), residues: 472 loop : -1.30 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 177 HIS 0.008 0.002 HIS C 81 PHE 0.027 0.002 PHE E 133 TYR 0.028 0.002 TYR G 99 ARG 0.009 0.001 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 346 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7274 (p0) REVERT: B 138 GLN cc_start: 0.7281 (tt0) cc_final: 0.6996 (tt0) REVERT: C 1 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6535 (ppp) REVERT: D 141 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6023 (mp0) REVERT: D 181 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.4931 (tpp80) REVERT: E 1 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7018 (ttm) REVERT: E 266 ARG cc_start: 0.5015 (OUTLIER) cc_final: 0.4671 (mpp-170) REVERT: E 295 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7633 (m-10) REVERT: F 8 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6850 (tpp80) REVERT: F 160 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.5956 (tt) REVERT: F 176 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8138 (p) REVERT: G 63 GLN cc_start: 0.7274 (mm-40) cc_final: 0.6890 (mm-40) REVERT: G 79 LEU cc_start: 0.7538 (tp) cc_final: 0.6529 (mt) REVERT: G 320 GLU cc_start: 0.7462 (tp30) cc_final: 0.7178 (tp30) REVERT: L 65 VAL cc_start: 0.5070 (t) cc_final: 0.4368 (p) REVERT: L 131 ARG cc_start: 0.1744 (OUTLIER) cc_final: 0.1084 (pmm150) REVERT: L 207 MET cc_start: 0.2715 (ppp) cc_final: 0.2050 (ptm) REVERT: L 512 ILE cc_start: 0.3690 (OUTLIER) cc_final: 0.3454 (tp) REVERT: L 573 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6661 (pt) outliers start: 139 outliers final: 54 residues processed: 448 average time/residue: 1.1095 time to fit residues: 586.9763 Evaluate side-chains 380 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 313 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 266 ARG Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 295 TYR Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain G residue 14 PHE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 131 ARG Chi-restraints excluded: chain L residue 231 ASP Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 490 VAL Chi-restraints excluded: chain L residue 512 ILE Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 573 ILE Chi-restraints excluded: chain L residue 595 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 0.4980 chunk 199 optimal weight: 5.9990 chunk 137 optimal weight: 0.0870 chunk 29 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 chunk 138 optimal weight: 0.4980 chunk 251 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 ASN ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25130 Z= 0.217 Angle : 0.665 10.257 34671 Z= 0.337 Chirality : 0.044 0.243 3954 Planarity : 0.005 0.057 4034 Dihedral : 19.988 179.763 4727 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.52 % Allowed : 24.61 % Favored : 70.87 % 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: -1.14 (0.15), residues: 2803 helix: 0.05 (0.16), residues: 999 sheet: -1.16 (0.22), residues: 459 loop : -1.15 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 177 HIS 0.008 0.001 HIS L 141 PHE 0.016 0.001 PHE C 129 TYR 0.012 0.001 TYR E 164 ARG 0.005 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 350 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7108 (p0) REVERT: C 1 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.6254 (ppp) REVERT: C 340 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: F 10 ILE cc_start: 0.6722 (OUTLIER) cc_final: 0.6187 (mt) REVERT: F 160 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.5946 (tt) REVERT: G 79 LEU cc_start: 0.7410 (tp) cc_final: 0.6674 (mt) REVERT: H 145 LYS cc_start: 0.5789 (mmtp) cc_final: 0.5524 (mptt) REVERT: H 212 TRP cc_start: 0.4770 (m100) cc_final: 0.4444 (m100) REVERT: L 65 VAL cc_start: 0.5040 (t) cc_final: 0.4357 (p) REVERT: L 131 ARG cc_start: 0.1857 (OUTLIER) cc_final: 0.1016 (pmm150) REVERT: L 512 ILE cc_start: 0.3814 (OUTLIER) cc_final: 0.3586 (tp) REVERT: L 573 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6640 (pt) outliers start: 104 outliers final: 39 residues processed: 420 average time/residue: 1.1331 time to fit residues: 563.7682 Evaluate side-chains 361 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 314 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 14 PHE Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 131 ARG Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 512 ILE Chi-restraints excluded: chain L residue 573 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 240 optimal weight: 0.0470 chunk 194 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN B 150 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 343 GLN ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 ASN ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN F 2 GLN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25130 Z= 0.259 Angle : 0.690 15.483 34671 Z= 0.345 Chirality : 0.044 0.325 3954 Planarity : 0.005 0.055 4034 Dihedral : 19.929 179.667 4727 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.00 % Allowed : 24.83 % Favored : 70.17 % 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: -1.08 (0.15), residues: 2803 helix: 0.14 (0.16), residues: 1006 sheet: -1.25 (0.22), residues: 460 loop : -1.11 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 177 HIS 0.006 0.001 HIS L 508 PHE 0.027 0.002 PHE F 341 TYR 0.015 0.002 TYR A 79 ARG 0.007 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 320 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7138 (p0) REVERT: A 99 ASN cc_start: 0.5766 (m-40) cc_final: 0.4800 (m110) REVERT: A 198 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: A 202 GLU cc_start: 0.6113 (mm-30) cc_final: 0.5860 (mm-30) REVERT: B 79 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7856 (p0) REVERT: C 1 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.6275 (ppp) REVERT: C 340 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: D 1 MET cc_start: 0.6917 (tpt) cc_final: 0.6703 (tpt) REVERT: D 145 MET cc_start: 0.6586 (mtm) cc_final: 0.6217 (mtm) REVERT: D 180 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6228 (ptt90) REVERT: E 266 ARG cc_start: 0.4961 (OUTLIER) cc_final: 0.4604 (mpp-170) REVERT: F 10 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6203 (mt) REVERT: F 145 MET cc_start: 0.7896 (mtp) cc_final: 0.7539 (mtm) REVERT: F 160 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.5904 (tt) REVERT: G 79 LEU cc_start: 0.7448 (tp) cc_final: 0.6657 (mp) REVERT: H 39 MET cc_start: 0.4740 (mmm) cc_final: 0.4321 (mmm) REVERT: H 62 GLN cc_start: 0.6924 (mp10) cc_final: 0.6563 (mp10) REVERT: L 65 VAL cc_start: 0.4991 (t) cc_final: 0.4335 (p) REVERT: L 131 ARG cc_start: 0.1941 (OUTLIER) cc_final: 0.1063 (pmm150) REVERT: L 298 VAL cc_start: 0.6685 (t) cc_final: 0.6413 (p) REVERT: L 512 ILE cc_start: 0.3901 (OUTLIER) cc_final: 0.3664 (tp) REVERT: L 573 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6681 (pt) outliers start: 115 outliers final: 49 residues processed: 399 average time/residue: 1.1414 time to fit residues: 538.6097 Evaluate side-chains 370 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 309 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 266 ARG Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 14 PHE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain L residue 131 ARG Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 512 ILE Chi-restraints excluded: chain L residue 573 ILE Chi-restraints excluded: chain L residue 595 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 0.2980 chunk 253 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 165 optimal weight: 0.0010 chunk 69 optimal weight: 0.6980 chunk 281 optimal weight: 10.0000 chunk 233 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 147 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN E 68 ASN E 247 ASN E 284 ASN F 2 GLN F 284 ASN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25130 Z= 0.203 Angle : 0.663 15.094 34671 Z= 0.331 Chirality : 0.043 0.330 3954 Planarity : 0.005 0.056 4034 Dihedral : 19.784 178.890 4727 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.17 % Allowed : 26.22 % Favored : 69.61 % 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: -0.91 (0.15), residues: 2803 helix: 0.35 (0.17), residues: 999 sheet: -1.17 (0.22), residues: 462 loop : -1.05 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 177 HIS 0.007 0.001 HIS L 141 PHE 0.026 0.001 PHE F 341 TYR 0.015 0.001 TYR C 47 ARG 0.007 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 333 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7079 (p0) REVERT: A 99 ASN cc_start: 0.5686 (m-40) cc_final: 0.4840 (m110) REVERT: A 151 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 198 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: A 202 GLU cc_start: 0.6030 (mm-30) cc_final: 0.5750 (mm-30) REVERT: C 1 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.6211 (ppp) REVERT: D 145 MET cc_start: 0.6610 (mtm) cc_final: 0.6314 (mtm) REVERT: E 266 ARG cc_start: 0.4952 (OUTLIER) cc_final: 0.4607 (mpp-170) REVERT: F 145 MET cc_start: 0.7828 (mtp) cc_final: 0.7492 (mtm) REVERT: F 160 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.5873 (tt) REVERT: G 79 LEU cc_start: 0.7428 (tp) cc_final: 0.6662 (mp) REVERT: H 39 MET cc_start: 0.4892 (mmm) cc_final: 0.4547 (mmm) REVERT: H 212 TRP cc_start: 0.4752 (m100) cc_final: 0.4515 (m100) REVERT: L 65 VAL cc_start: 0.5031 (t) cc_final: 0.4324 (p) REVERT: L 131 ARG cc_start: 0.2135 (OUTLIER) cc_final: 0.1208 (pmm150) REVERT: L 207 MET cc_start: 0.2610 (ppp) cc_final: 0.1970 (ptm) REVERT: L 298 VAL cc_start: 0.6667 (t) cc_final: 0.6408 (p) REVERT: L 512 ILE cc_start: 0.3922 (OUTLIER) cc_final: 0.3706 (tp) REVERT: L 573 ILE cc_start: 0.6905 (OUTLIER) cc_final: 0.6638 (pt) outliers start: 96 outliers final: 53 residues processed: 400 average time/residue: 1.1006 time to fit residues: 527.2357 Evaluate side-chains 372 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 311 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 266 ARG Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 14 PHE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 131 ARG Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 512 ILE Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 573 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 160 optimal weight: 0.0470 chunk 205 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 237 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 129 optimal weight: 0.0020 overall best weight: 0.5488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN E 247 ASN E 284 ASN F 2 GLN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25130 Z= 0.215 Angle : 0.668 16.413 34671 Z= 0.332 Chirality : 0.043 0.324 3954 Planarity : 0.005 0.056 4034 Dihedral : 19.690 179.373 4727 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.52 % Allowed : 26.39 % Favored : 69.09 % 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: -0.78 (0.16), residues: 2803 helix: 0.48 (0.17), residues: 1005 sheet: -1.08 (0.22), residues: 472 loop : -1.02 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 177 HIS 0.007 0.001 HIS L 141 PHE 0.022 0.001 PHE F 341 TYR 0.019 0.001 TYR C 47 ARG 0.007 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 330 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7055 (p0) REVERT: A 99 ASN cc_start: 0.5811 (m-40) cc_final: 0.4771 (m110) REVERT: A 151 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7535 (mm-30) REVERT: A 198 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: A 202 GLU cc_start: 0.6086 (mm-30) cc_final: 0.5777 (mm-30) REVERT: B 79 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7523 (p0) REVERT: C 1 MET cc_start: 0.6541 (OUTLIER) cc_final: 0.6109 (ptm) REVERT: D 182 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.5864 (pmt) REVERT: E 124 MET cc_start: 0.6857 (mtt) cc_final: 0.6641 (mtm) REVERT: F 160 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5889 (tt) REVERT: F 341 PHE cc_start: 0.6909 (t80) cc_final: 0.6605 (t80) REVERT: G 14 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5699 (t80) REVERT: G 79 LEU cc_start: 0.7245 (tp) cc_final: 0.6446 (mp) REVERT: L 65 VAL cc_start: 0.5028 (t) cc_final: 0.4318 (p) REVERT: L 131 ARG cc_start: 0.2146 (OUTLIER) cc_final: 0.1264 (pmm150) REVERT: L 298 VAL cc_start: 0.6610 (t) cc_final: 0.6376 (p) REVERT: L 573 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6648 (pt) outliers start: 104 outliers final: 56 residues processed: 403 average time/residue: 1.0958 time to fit residues: 523.6466 Evaluate side-chains 378 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 313 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 14 PHE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 131 ARG Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 573 ILE Chi-restraints excluded: chain L residue 595 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN E 247 ASN E 284 ASN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25130 Z= 0.263 Angle : 0.696 17.054 34671 Z= 0.346 Chirality : 0.044 0.334 3954 Planarity : 0.005 0.055 4034 Dihedral : 19.707 179.969 4727 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.35 % Allowed : 26.48 % Favored : 69.17 % 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: -0.85 (0.16), residues: 2803 helix: 0.43 (0.17), residues: 999 sheet: -1.14 (0.22), residues: 465 loop : -1.05 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 177 HIS 0.007 0.001 HIS F 81 PHE 0.024 0.002 PHE C 129 TYR 0.017 0.002 TYR C 47 ARG 0.010 0.001 ARG H 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 320 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7046 (p0) REVERT: A 99 ASN cc_start: 0.6027 (OUTLIER) cc_final: 0.4977 (m110) REVERT: A 198 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: A 202 GLU cc_start: 0.6076 (mm-30) cc_final: 0.5744 (mm-30) REVERT: B 79 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7526 (p0) REVERT: C 1 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.6044 (ptm) REVERT: D 1 MET cc_start: 0.6944 (tpt) cc_final: 0.6701 (tpt) REVERT: D 40 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7577 (tp) REVERT: D 180 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6499 (ptt90) REVERT: E 124 MET cc_start: 0.6932 (mtt) cc_final: 0.6719 (mtt) REVERT: F 10 ILE cc_start: 0.6722 (OUTLIER) cc_final: 0.6200 (mt) REVERT: F 145 MET cc_start: 0.7902 (mtp) cc_final: 0.7596 (mtm) REVERT: F 160 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.5908 (tt) REVERT: F 341 PHE cc_start: 0.6947 (t80) cc_final: 0.6656 (t80) REVERT: G 14 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5754 (t80) REVERT: G 79 LEU cc_start: 0.7274 (tp) cc_final: 0.6508 (mp) REVERT: H 39 MET cc_start: 0.4776 (mmm) cc_final: 0.4473 (mmm) REVERT: H 90 LYS cc_start: 0.7010 (mmtm) cc_final: 0.6766 (mmtm) REVERT: L 65 VAL cc_start: 0.4957 (t) cc_final: 0.4210 (p) REVERT: L 131 ARG cc_start: 0.1854 (OUTLIER) cc_final: 0.1012 (pmm150) REVERT: L 207 MET cc_start: 0.2989 (ppp) cc_final: 0.2429 (ptm) REVERT: L 298 VAL cc_start: 0.6714 (t) cc_final: 0.6482 (p) REVERT: L 573 ILE cc_start: 0.6912 (OUTLIER) cc_final: 0.6652 (pt) REVERT: L 585 LEU cc_start: 0.3980 (OUTLIER) cc_final: 0.2854 (pp) outliers start: 100 outliers final: 60 residues processed: 389 average time/residue: 1.1446 time to fit residues: 529.2144 Evaluate side-chains 388 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 315 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 14 PHE Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 131 ARG Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 573 ILE Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 595 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 0.6980 chunk 268 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 113 optimal weight: 0.0980 chunk 205 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 chunk 236 optimal weight: 3.9990 chunk 247 optimal weight: 0.4980 chunk 260 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN E 284 ASN F 2 GLN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25130 Z= 0.209 Angle : 0.680 17.701 34671 Z= 0.335 Chirality : 0.043 0.308 3954 Planarity : 0.005 0.055 4034 Dihedral : 19.645 178.946 4727 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.09 % Allowed : 26.96 % Favored : 68.96 % 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: -0.73 (0.16), residues: 2803 helix: 0.56 (0.17), residues: 1001 sheet: -1.07 (0.22), residues: 467 loop : -1.01 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 212 HIS 0.006 0.001 HIS L 141 PHE 0.032 0.001 PHE C 129 TYR 0.017 0.001 TYR E 164 ARG 0.008 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 340 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.6960 (p0) REVERT: A 99 ASN cc_start: 0.5880 (m-40) cc_final: 0.4996 (m110) REVERT: A 198 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: A 202 GLU cc_start: 0.6019 (mm-30) cc_final: 0.5688 (mm-30) REVERT: B 79 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7516 (p0) REVERT: C 1 MET cc_start: 0.6483 (OUTLIER) cc_final: 0.6166 (ppp) REVERT: D 1 MET cc_start: 0.6892 (tpt) cc_final: 0.6587 (tpt) REVERT: D 180 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6457 (ptt90) REVERT: D 283 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7827 (p) REVERT: F 145 MET cc_start: 0.7823 (mtp) cc_final: 0.7541 (mtm) REVERT: F 160 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5885 (tt) REVERT: F 341 PHE cc_start: 0.7034 (t80) cc_final: 0.6676 (t80) REVERT: G 14 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.5728 (t80) REVERT: G 79 LEU cc_start: 0.7226 (tp) cc_final: 0.6438 (mp) REVERT: H 39 MET cc_start: 0.4668 (mmm) cc_final: 0.4438 (mmm) REVERT: L 65 VAL cc_start: 0.4899 (t) cc_final: 0.4163 (p) REVERT: L 131 ARG cc_start: 0.2083 (OUTLIER) cc_final: 0.1181 (pmm150) REVERT: L 207 MET cc_start: 0.2918 (ppp) cc_final: 0.2336 (ptm) REVERT: L 298 VAL cc_start: 0.6667 (t) cc_final: 0.6424 (p) REVERT: L 573 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6621 (pt) REVERT: L 585 LEU cc_start: 0.3947 (OUTLIER) cc_final: 0.3717 (mt) outliers start: 94 outliers final: 56 residues processed: 409 average time/residue: 1.1071 time to fit residues: 535.1177 Evaluate side-chains 397 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 330 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 14 PHE Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 131 ARG Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 573 ILE Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain L residue 595 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 0.9990 chunk 276 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 chunk 266 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 178 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN E 247 ASN E 284 ASN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25130 Z= 0.244 Angle : 0.706 17.859 34671 Z= 0.350 Chirality : 0.043 0.320 3954 Planarity : 0.005 0.054 4034 Dihedral : 19.665 179.791 4727 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.35 % Allowed : 27.78 % Favored : 68.87 % 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: -0.77 (0.16), residues: 2803 helix: 0.54 (0.17), residues: 992 sheet: -1.10 (0.22), residues: 467 loop : -1.03 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 212 HIS 0.008 0.001 HIS L 141 PHE 0.032 0.002 PHE C 129 TYR 0.018 0.002 TYR E 164 ARG 0.008 0.000 ARG B 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 337 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.6986 (p0) REVERT: A 99 ASN cc_start: 0.6033 (m-40) cc_final: 0.5005 (m110) REVERT: A 194 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6395 (mt-10) REVERT: A 198 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: B 79 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7498 (p0) REVERT: C 1 MET cc_start: 0.6532 (OUTLIER) cc_final: 0.6064 (ptm) REVERT: D 180 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6504 (ptt90) REVERT: F 145 MET cc_start: 0.7884 (mtp) cc_final: 0.7562 (mtm) REVERT: F 160 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.5841 (tt) REVERT: F 341 PHE cc_start: 0.7101 (t80) cc_final: 0.6781 (t80) REVERT: G 14 PHE cc_start: 0.6191 (OUTLIER) cc_final: 0.5753 (t80) REVERT: G 79 LEU cc_start: 0.7234 (tp) cc_final: 0.6430 (mp) REVERT: H 39 MET cc_start: 0.4692 (mmm) cc_final: 0.4406 (mmm) REVERT: L 65 VAL cc_start: 0.4922 (t) cc_final: 0.4180 (p) REVERT: L 207 MET cc_start: 0.2909 (ppp) cc_final: 0.2331 (ptm) REVERT: L 298 VAL cc_start: 0.6685 (t) cc_final: 0.6448 (p) REVERT: L 516 TRP cc_start: 0.1619 (t60) cc_final: 0.1196 (t60) REVERT: L 573 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6621 (pt) REVERT: L 580 HIS cc_start: 0.5357 (OUTLIER) cc_final: 0.5090 (t-90) outliers start: 77 outliers final: 59 residues processed: 390 average time/residue: 1.1623 time to fit residues: 547.3422 Evaluate side-chains 392 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 324 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 14 PHE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 573 ILE Chi-restraints excluded: chain L residue 580 HIS Chi-restraints excluded: chain L residue 595 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 212 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 0.0870 chunk 231 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 29 optimal weight: 0.0470 chunk 42 optimal weight: 0.0170 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 340 GLN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN E 284 ASN F 2 GLN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS L 251 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.175615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.138887 restraints weight = 43727.515| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.55 r_work: 0.3810 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25130 Z= 0.202 Angle : 0.693 18.169 34671 Z= 0.341 Chirality : 0.043 0.302 3954 Planarity : 0.005 0.054 4034 Dihedral : 19.595 178.892 4727 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.43 % Allowed : 28.13 % Favored : 68.43 % 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 (0.16), residues: 2803 helix: 0.65 (0.17), residues: 996 sheet: -1.01 (0.22), residues: 469 loop : -0.98 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP H 212 HIS 0.011 0.001 HIS L 141 PHE 0.034 0.001 PHE C 129 TYR 0.017 0.001 TYR E 164 ARG 0.011 0.000 ARG L 550 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8714.91 seconds wall clock time: 156 minutes 50.01 seconds (9410.01 seconds total)