Starting phenix.real_space_refine on Mon Jul 6 00:38:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gs9_51543/07_2026/9gs9_51543_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gs9_51543/07_2026/9gs9_51543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gs9_51543/07_2026/9gs9_51543_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gs9_51543/07_2026/9gs9_51543_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gs9_51543/07_2026/9gs9_51543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gs9_51543/07_2026/9gs9_51543.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 109 5.49 5 S 131 5.16 5 C 19824 2.51 5 N 5407 2.21 5 O 6239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31710 Number of models: 1 Model: "" Number of chains: 13 Chain: "1" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1291 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 8, 'rna3p_pur': 20, 'rna3p_pyr': 14} Link IDs: {'rna2p': 24, 'rna3p': 35} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "2" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 793 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "3" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 222 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5013 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 658} Chain breaks: 8 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 589 Unresolved non-hydrogen angles: 750 Unresolved non-hydrogen dihedrals: 491 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 5, 'ARG:plan': 10, 'HIS:plan': 3, 'ASN:plan1': 12, 'PHE:plan': 7, 'GLU:plan': 15, 'TRP:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 327 Chain: "B" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2723 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 325} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2777 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "D" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2777 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "E" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2768 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 15, 'TRANS': 329} Chain: "F" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2763 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain: "G" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2477 Classifications: {'peptide': 307} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain breaks: 3 Chain: "H" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1592 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "I" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3261 Classifications: {'peptide': 402} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 386} Chain breaks: 1 Chain: "J" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3253 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 14, 'TRANS': 386} Chain breaks: 1 Time building chain proxies: 6.06, per 1000 atoms: 0.19 Number of scatterers: 31710 At special positions: 0 Unit cell: (189.255, 166.843, 146.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 109 15.00 O 6239 8.00 N 5407 7.00 C 19824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 316 " distance=2.04 Simple disulfide: pdb=" SG CYS I 136 " - pdb=" SG CYS I 139 " distance=2.03 Simple disulfide: pdb=" SG CYS I 169 " - pdb=" SG CYS I 189 " distance=2.03 Simple disulfide: pdb=" SG CYS I 187 " - pdb=" SG CYS I 189 " distance=2.03 Simple disulfide: pdb=" SG CYS J 136 " - pdb=" SG CYS J 139 " distance=2.03 Simple disulfide: pdb=" SG CYS J 136 " - pdb=" SG CYS J 158 " distance=2.94 Simple disulfide: pdb=" SG CYS J 139 " - pdb=" SG CYS J 158 " distance=2.68 Simple disulfide: pdb=" SG CYS J 169 " - pdb=" SG CYS J 189 " distance=2.03 Simple disulfide: pdb=" SG CYS J 187 " - pdb=" SG CYS J 189 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 1320 O4' DG 2 21 .*. O " rejected from bonding due to valence issues. Atom "ATOM 1298 O4' DG 2 20 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7138 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 40 sheets defined 36.2% alpha, 8.4% beta 29 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.691A pdb=" N ASN A 115 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.503A pdb=" N SER A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 removed outlier: 3.994A pdb=" N THR A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 removed outlier: 4.641A pdb=" N SER A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 183 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.518A pdb=" N ASP A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 246 through 252 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 308 through 346 removed outlier: 3.796A pdb=" N GLN A 319 " --> pdb=" O GLN A 315 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TRP A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 372 through 378 Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.835A pdb=" N ASN A 386 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.925A pdb=" N LEU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 480 Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 557 removed outlier: 3.573A pdb=" N HIS A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 593 removed outlier: 3.946A pdb=" N LEU A 588 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 622 removed outlier: 3.522A pdb=" N LEU A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 670 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'B' and resid 104 through 121 Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.919A pdb=" N GLU B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.513A pdb=" N LYS B 169 " --> pdb=" O ASN B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 197 Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.530A pdb=" N SER B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 320 " --> pdb=" O CYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.571A pdb=" N TYR B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 121 Processing helix chain 'C' and resid 122 through 137 removed outlier: 4.111A pdb=" N GLU C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 127 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 177 through 197 Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 298 through 304 Processing helix chain 'C' and resid 305 through 314 removed outlier: 3.553A pdb=" N ALA C 312 " --> pdb=" O TRP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 Processing helix chain 'D' and resid 104 through 122 Processing helix chain 'D' and resid 122 through 137 removed outlier: 4.038A pdb=" N GLU D 126 " --> pdb=" O GLY D 122 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 135 " --> pdb=" O TYR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 Processing helix chain 'D' and resid 177 through 197 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 298 through 304 Processing helix chain 'D' and resid 305 through 314 removed outlier: 3.586A pdb=" N ALA D 312 " --> pdb=" O TRP D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 Processing helix chain 'E' and resid 104 through 121 Processing helix chain 'E' and resid 122 through 138 removed outlier: 3.841A pdb=" N GLU E 126 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 127 " --> pdb=" O GLY E 123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 135 " --> pdb=" O TYR E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 142 Processing helix chain 'E' and resid 177 through 197 removed outlier: 3.520A pdb=" N GLU E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 Processing helix chain 'E' and resid 298 through 304 Processing helix chain 'E' and resid 305 through 320 removed outlier: 3.557A pdb=" N SER E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 312 " --> pdb=" O TRP E 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN E 315 " --> pdb=" O SER E 311 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 338 Processing helix chain 'F' and resid 104 through 122 Processing helix chain 'F' and resid 122 through 138 removed outlier: 3.978A pdb=" N GLU F 126 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE F 135 " --> pdb=" O TYR F 131 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY F 138 " --> pdb=" O ASN F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 142 Processing helix chain 'F' and resid 177 through 197 removed outlier: 3.590A pdb=" N GLU F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 261 Processing helix chain 'F' and resid 298 through 304 Processing helix chain 'F' and resid 305 through 315 removed outlier: 3.642A pdb=" N ASN F 315 " --> pdb=" O SER F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 320 removed outlier: 3.708A pdb=" N ASN F 319 " --> pdb=" O ASN F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 338 Processing helix chain 'G' and resid 104 through 122 Processing helix chain 'G' and resid 123 through 137 removed outlier: 3.566A pdb=" N ILE G 135 " --> pdb=" O TYR G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 170 removed outlier: 3.633A pdb=" N LYS G 169 " --> pdb=" O ASN G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 197 Processing helix chain 'G' and resid 252 through 261 Processing helix chain 'G' and resid 298 through 304 Processing helix chain 'G' and resid 305 through 317 removed outlier: 3.612A pdb=" N SER G 311 " --> pdb=" O GLU G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.554A pdb=" N TYR G 329 " --> pdb=" O ASP G 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 36 Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 72 through 81 removed outlier: 3.515A pdb=" N VAL H 76 " --> pdb=" O GLN H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 110 Processing helix chain 'H' and resid 111 through 130 removed outlier: 3.652A pdb=" N SER H 115 " --> pdb=" O PHE H 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 26 Processing helix chain 'I' and resid 32 through 48 removed outlier: 3.566A pdb=" N LEU I 36 " --> pdb=" O SER I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 63 through 67 Processing helix chain 'I' and resid 70 through 85 Processing helix chain 'I' and resid 136 through 141 Processing helix chain 'I' and resid 147 through 152 removed outlier: 3.685A pdb=" N TRP I 150 " --> pdb=" O LYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 182 Processing helix chain 'I' and resid 205 through 213 Processing helix chain 'I' and resid 229 through 244 removed outlier: 3.552A pdb=" N ALA I 235 " --> pdb=" O THR I 231 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU I 237 " --> pdb=" O ARG I 233 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR I 244 " --> pdb=" O TYR I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 260 removed outlier: 3.742A pdb=" N ASN I 257 " --> pdb=" O ASN I 253 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR I 258 " --> pdb=" O ASP I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 261 through 276 removed outlier: 3.572A pdb=" N VAL I 265 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE I 266 " --> pdb=" O TRP I 262 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU I 272 " --> pdb=" O THR I 268 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU I 273 " --> pdb=" O GLU I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 328 removed outlier: 3.565A pdb=" N TYR I 320 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 338 Processing helix chain 'I' and resid 342 through 351 Processing helix chain 'I' and resid 353 through 363 Processing helix chain 'I' and resid 387 through 397 removed outlier: 3.672A pdb=" N PHE I 397 " --> pdb=" O TYR I 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 26 Processing helix chain 'J' and resid 32 through 48 removed outlier: 3.570A pdb=" N LEU J 36 " --> pdb=" O SER J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 55 Processing helix chain 'J' and resid 63 through 67 Processing helix chain 'J' and resid 70 through 85 Processing helix chain 'J' and resid 120 through 122 No H-bonds generated for 'chain 'J' and resid 120 through 122' Processing helix chain 'J' and resid 136 through 141 Processing helix chain 'J' and resid 147 through 152 removed outlier: 3.643A pdb=" N TRP J 150 " --> pdb=" O LYS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 213 removed outlier: 3.631A pdb=" N HIS J 208 " --> pdb=" O LEU J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 244 removed outlier: 3.608A pdb=" N LEU J 237 " --> pdb=" O ARG J 233 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR J 244 " --> pdb=" O TYR J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 260 removed outlier: 3.603A pdb=" N ASN J 257 " --> pdb=" O ASN J 253 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR J 258 " --> pdb=" O ASP J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 276 removed outlier: 3.552A pdb=" N VAL J 265 " --> pdb=" O LYS J 261 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE J 266 " --> pdb=" O TRP J 262 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU J 272 " --> pdb=" O THR J 268 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU J 273 " --> pdb=" O GLU J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 281 removed outlier: 3.501A pdb=" N LYS J 280 " --> pdb=" O ALA J 277 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU J 281 " --> pdb=" O GLU J 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 277 through 281' Processing helix chain 'J' and resid 311 through 328 removed outlier: 3.707A pdb=" N THR J 323 " --> pdb=" O ASP J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 353 through 363 removed outlier: 3.516A pdb=" N VAL J 357 " --> pdb=" O SER J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 397 removed outlier: 3.535A pdb=" N GLU J 392 " --> pdb=" O ARG J 388 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE J 397 " --> pdb=" O TYR J 393 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 removed outlier: 4.320A pdb=" N ILE A 215 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 141 Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 204 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 207 through 213 current: chain 'A' and resid 526 through 538 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 526 through 538 current: chain 'A' and resid 565 through 568 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 565 through 568 current: chain 'A' and resid 649 through 663 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 649 through 663 current: chain 'A' and resid 689 through 694 Processing sheet with id=AA5, first strand: chain 'A' and resid 234 through 238 removed outlier: 8.237A pdb=" N SER A 456 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU A 259 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 507 through 509 Processing sheet with id=AA7, first strand: chain 'B' and resid 7 through 9 Processing sheet with id=AA8, first strand: chain 'B' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 15 current: chain 'B' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 30 through 31 current: chain 'B' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 161 through 164 current: chain 'B' and resid 247 through 251 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 42 Processing sheet with id=AB1, first strand: chain 'B' and resid 282 through 283 removed outlier: 3.662A pdb=" N VAL B 288 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.780A pdb=" N GLY C 101 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 15 current: chain 'C' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 30 through 31 current: chain 'C' and resid 161 through 164 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 42 Processing sheet with id=AB5, first strand: chain 'C' and resid 239 through 241 Processing sheet with id=AB6, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AB7, first strand: chain 'D' and resid 101 through 102 removed outlier: 3.575A pdb=" N GLY D 101 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 13 through 15 current: chain 'D' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 30 through 31 current: chain 'D' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 161 through 164 current: chain 'D' and resid 247 through 251 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 35 through 42 Processing sheet with id=AC1, first strand: chain 'D' and resid 262 through 264 Processing sheet with id=AC2, first strand: chain 'D' and resid 282 through 283 Processing sheet with id=AC3, first strand: chain 'E' and resid 101 through 102 removed outlier: 3.710A pdb=" N GLY E 101 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 13 through 15 current: chain 'E' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 30 through 31 current: chain 'E' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 161 through 164 current: chain 'E' and resid 247 through 251 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 35 through 42 Processing sheet with id=AC6, first strand: chain 'E' and resid 262 through 264 Processing sheet with id=AC7, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AC8, first strand: chain 'F' and resid 101 through 102 removed outlier: 3.792A pdb=" N GLY F 101 " --> pdb=" O LYS F 8 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 13 through 15 current: chain 'F' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 30 through 31 current: chain 'F' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 161 through 164 current: chain 'F' and resid 247 through 251 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 35 through 42 Processing sheet with id=AD2, first strand: chain 'F' and resid 222 through 223 removed outlier: 4.248A pdb=" N GLN F 236 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 282 through 283 Processing sheet with id=AD4, first strand: chain 'G' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 13 through 15 current: chain 'G' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 30 through 31 current: chain 'G' and resid 161 through 163 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 161 through 163 current: chain 'G' and resid 247 through 251 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 70 through 74 removed outlier: 3.548A pdb=" N ARG H 142 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 262 through 264 Processing sheet with id=AD7, first strand: chain 'G' and resid 282 through 283 removed outlier: 3.601A pdb=" N ASP G 283 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL G 288 " --> pdb=" O ASP G 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'H' and resid 4 through 10 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 4 through 10 current: chain 'H' and resid 55 through 60 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'H' and resid 148 through 154 Processing sheet with id=AE1, first strand: chain 'I' and resid 98 through 103 removed outlier: 4.105A pdb=" N SER I 100 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA I 109 " --> pdb=" O SER I 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 340 through 341 Processing sheet with id=AE3, first strand: chain 'J' and resid 98 through 103 removed outlier: 4.024A pdb=" N SER J 100 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA J 109 " --> pdb=" O SER J 100 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 340 through 341 949 hydrogen bonds defined for protein. 2658 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 5.40 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.55 - 0.83: 1 0.83 - 1.12: 0 1.12 - 1.40: 13373 1.40 - 1.68: 19103 1.68 - 1.97: 170 Bond restraints: 32647 Sorted by residual: bond pdb=" O3' C 1 40 " pdb=" P G 1 41 " ideal model delta sigma weight residual 1.607 0.551 1.056 1.50e-02 4.44e+03 4.95e+03 bond pdb=" C ASN J 28 " pdb=" N PHE J 29 " ideal model delta sigma weight residual 1.332 1.966 -0.633 1.40e-02 5.10e+03 2.05e+03 bond pdb=" N VAL D 30 " pdb=" CA VAL D 30 " ideal model delta sigma weight residual 1.458 1.495 -0.037 7.70e-03 1.69e+04 2.34e+01 bond pdb=" C LYS G 38 " pdb=" O LYS G 38 " ideal model delta sigma weight residual 1.235 1.173 0.062 1.30e-02 5.92e+03 2.29e+01 bond pdb=" N VAL E 30 " pdb=" CA VAL E 30 " ideal model delta sigma weight residual 1.458 1.494 -0.036 7.70e-03 1.69e+04 2.17e+01 ... (remaining 32642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.76: 44709 12.76 - 25.53: 6 25.53 - 38.29: 3 38.29 - 51.06: 0 51.06 - 63.82: 3 Bond angle restraints: 44721 Sorted by residual: angle pdb=" O ASN J 28 " pdb=" C ASN J 28 " pdb=" N PHE J 29 " ideal model delta sigma weight residual 122.38 60.14 62.24 1.08e+00 8.57e-01 3.32e+03 angle pdb=" CA ASN J 28 " pdb=" C ASN J 28 " pdb=" N PHE J 29 " ideal model delta sigma weight residual 116.84 175.46 -58.62 1.12e+00 7.97e-01 2.74e+03 angle pdb=" O3' C 1 40 " pdb=" P G 1 41 " pdb=" OP1 G 1 41 " ideal model delta sigma weight residual 108.00 44.18 63.82 3.00e+00 1.11e-01 4.53e+02 angle pdb=" C3' C 1 40 " pdb=" O3' C 1 40 " pdb=" P G 1 41 " ideal model delta sigma weight residual 120.20 149.75 -29.55 1.50e+00 4.44e-01 3.88e+02 angle pdb=" O3' C 1 40 " pdb=" P G 1 41 " pdb=" O5' G 1 41 " ideal model delta sigma weight residual 104.00 131.16 -27.16 1.50e+00 4.44e-01 3.28e+02 ... (remaining 44716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 18785 35.39 - 70.79: 733 70.79 - 106.18: 40 106.18 - 141.58: 3 141.58 - 176.97: 7 Dihedral angle restraints: 19568 sinusoidal: 8586 harmonic: 10982 Sorted by residual: dihedral pdb=" CA ASN A 418 " pdb=" C ASN A 418 " pdb=" N LEU A 419 " pdb=" CA LEU A 419 " ideal model delta harmonic sigma weight residual -180.00 -129.11 -50.89 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" N MET I 374 " pdb=" C MET I 374 " pdb=" CA MET I 374 " pdb=" CB MET I 374 " ideal model delta harmonic sigma weight residual 122.80 147.69 -24.89 0 2.50e+00 1.60e-01 9.91e+01 dihedral pdb=" CA ASN J 28 " pdb=" C ASN J 28 " pdb=" N PHE J 29 " pdb=" CA PHE J 29 " ideal model delta harmonic sigma weight residual 180.00 130.76 49.24 0 5.00e+00 4.00e-02 9.70e+01 ... (remaining 19565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 4899 0.197 - 0.394: 57 0.394 - 0.591: 4 0.591 - 0.788: 2 0.788 - 0.984: 4 Chirality restraints: 4966 Sorted by residual: chirality pdb=" CA MET I 374 " pdb=" N MET I 374 " pdb=" C MET I 374 " pdb=" CB MET I 374 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" C3' U 1 13 " pdb=" C4' U 1 13 " pdb=" O3' U 1 13 " pdb=" C2' U 1 13 " both_signs ideal model delta sigma weight residual False -2.74 -1.92 -0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" CA LYS I 373 " pdb=" N LYS I 373 " pdb=" C LYS I 373 " pdb=" CB LYS I 373 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.60e+01 ... (remaining 4963 not shown) Planarity restraints: 5358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 367 " -0.032 2.00e-02 2.50e+03 6.76e-02 4.58e+01 pdb=" C GLN I 367 " 0.117 2.00e-02 2.50e+03 pdb=" O GLN I 367 " -0.044 2.00e-02 2.50e+03 pdb=" N THR I 368 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 21 " -0.011 9.50e-02 1.11e+02 4.48e-02 2.48e+01 pdb=" NE ARG A 21 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 21 " -0.086 2.00e-02 2.50e+03 pdb=" NH1 ARG A 21 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 21 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 20 " 0.100 9.50e-02 1.11e+02 5.95e-02 2.05e+01 pdb=" NE ARG A 20 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 20 " 0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG A 20 " -0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 20 " -0.021 2.00e-02 2.50e+03 ... (remaining 5355 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.44: 17 1.44 - 2.30: 88 2.30 - 3.17: 23203 3.17 - 4.03: 84155 4.03 - 4.90: 149555 Warning: very small nonbonded interaction distances. Nonbonded interactions: 257018 Sorted by model distance: nonbonded pdb=" CD GLN F 62 " pdb=" ND1 HIS I 372 " model vdw 0.571 2.680 nonbonded pdb=" SG CYS J 158 " pdb=" CD LYS J 160 " model vdw 0.596 3.800 nonbonded pdb=" CA ASP F 63 " pdb=" SD MET I 374 " model vdw 0.675 3.830 nonbonded pdb=" CB ASP F 63 " pdb=" CG MET I 374 " model vdw 0.856 3.840 nonbonded pdb=" OD1 ASP F 63 " pdb=" CA MET I 374 " model vdw 0.888 3.470 ... (remaining 257013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 40 or resid 67 through 225 or resid 234 through \ 319 or resid 321 through 342)) selection = (chain 'C' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 40 or resid 67 through 225 or resid 234 through 3 \ 19 or resid 321 through 342)) selection = (chain 'D' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 40 or resid 67 through 225 or resid 234 through 3 \ 19 or resid 321 through 342)) selection = (chain 'E' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 40 or resid 67 through 225 or resid 234 through 3 \ 19 or resid 321 through 342)) selection = (chain 'F' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 40 or resid 67 through 225 or resid 234 through 3 \ 19 or resid 321 through 342)) selection = (chain 'G' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 342)) } ncs_group { reference = (chain 'I' and resid 5 through 405) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.040 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.017 1.056 32660 Z= 1.315 Angle : 1.849 63.824 44739 Z= 1.340 Chirality : 0.092 0.984 4966 Planarity : 0.003 0.068 5358 Dihedral : 17.443 176.970 12403 Min Nonbonded Distance : 0.571 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 1.41 % Allowed : 4.62 % Favored : 93.97 % Rotamer: Outliers : 3.32 % Allowed : 3.93 % Favored : 92.75 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.67 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.12), residues: 3679 helix: -1.50 (0.12), residues: 1222 sheet: -0.43 (0.21), residues: 513 loop : -1.82 (0.12), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.001 ARG A 21 TYR 0.021 0.002 TYR G 9 PHE 0.021 0.002 PHE D 303 TRP 0.017 0.002 TRP D 142 HIS 0.012 0.002 HIS I 372 Details of bonding type rmsd/Z covalent geometry : bond 0.01506 / 1.13 (32647) covalent geometry : angle 1.82118 / 1.33 (44721) SS BOND : bond 0.37192 / 31.10 ( 9) SS BOND : angle 15.90038 / 21.49 ( 18) hydrogen bonds : bond 0.25252 / 25.05 ( 1023) hydrogen bonds : angle 8.22525 / 10.25 ( 2802) Misc. bond : bond 0.54119 / 43.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 297 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.7732 (OUTLIER) cc_final: 0.7466 (m) REVERT: A 44 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8608 (tt) REVERT: A 147 TRP cc_start: 0.8929 (p90) cc_final: 0.8475 (p-90) REVERT: A 477 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8226 (tm-30) REVERT: A 592 LEU cc_start: 0.9301 (mt) cc_final: 0.8999 (mt) REVERT: A 603 MET cc_start: 0.9195 (mmm) cc_final: 0.8969 (mmm) REVERT: A 682 MET cc_start: 0.7759 (ptm) cc_final: 0.7433 (ptm) REVERT: A 692 MET cc_start: 0.9149 (mmm) cc_final: 0.8734 (mmm) REVERT: B 308 TRP cc_start: 0.8495 (t60) cc_final: 0.8165 (t60) REVERT: C 116 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7867 (mt-10) REVERT: H 21 THR cc_start: 0.8094 (m) cc_final: 0.7851 (p) REVERT: H 28 MET cc_start: 0.6492 (ttp) cc_final: 0.6145 (ttp) REVERT: I 25 VAL cc_start: -0.1660 (OUTLIER) cc_final: -0.2416 (p) REVERT: I 354 VAL cc_start: 0.4306 (OUTLIER) cc_final: 0.4020 (t) REVERT: I 400 ASP cc_start: 0.7335 (m-30) cc_final: 0.6903 (p0) REVERT: J 133 ILE cc_start: 0.7690 (mp) cc_final: 0.7404 (tp) REVERT: J 247 THR cc_start: 0.7102 (OUTLIER) cc_final: 0.6746 (p) REVERT: J 343 VAL cc_start: 0.2521 (OUTLIER) cc_final: 0.2300 (p) REVERT: J 373 LYS cc_start: 0.0867 (OUTLIER) cc_final: -0.0515 (mptt) REVERT: J 378 ILE cc_start: -0.1579 (OUTLIER) cc_final: -0.1868 (tt) outliers start: 104 outliers final: 14 residues processed: 377 average time/residue: 0.6273 time to fit residues: 280.6182 Evaluate side-chains 154 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 354 VAL Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain I residue 373 LYS Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 343 VAL Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain J residue 377 ARG Chi-restraints excluded: chain J residue 378 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0470 chunk 298 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 674 ASN B 93 GLN C 67 ASN C 83 HIS C 93 GLN C 225 ASN D 66 HIS D 93 GLN D 315 ASN E 83 HIS E 93 GLN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN F 216 GLN G 321 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN H 166 GLN I 52 HIS ** J 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 GLN J 367 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.126532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067741 restraints weight = 69724.578| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.87 r_work: 0.2784 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 32660 Z= 0.178 Angle : 0.740 16.316 44739 Z= 0.404 Chirality : 0.044 0.377 4966 Planarity : 0.004 0.056 5358 Dihedral : 17.428 179.992 5499 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.81 % Favored : 95.73 % Rotamer: Outliers : 2.39 % Allowed : 9.32 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.67 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.13), residues: 3679 helix: 0.12 (0.14), residues: 1256 sheet: 0.06 (0.21), residues: 521 loop : -1.50 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 74 TYR 0.013 0.001 TYR J 178 PHE 0.027 0.002 PHE J 29 TRP 0.018 0.001 TRP C 308 HIS 0.033 0.002 HIS I 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (32647) covalent geometry : angle 0.73288 / 0.40 (44721) SS BOND : bond 0.01200 / 0.85 ( 9) SS BOND : angle 5.12249 / 6.93 ( 18) hydrogen bonds : bond 0.06363 / 6.39 ( 1023) hydrogen bonds : angle 5.01960 / 6.32 ( 2802) Misc. bond : bond 0.01211 / 1.18 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 165 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.9254 (pttm) cc_final: 0.8945 (pmmt) REVERT: A 44 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8505 (tt) REVERT: A 147 TRP cc_start: 0.8632 (p90) cc_final: 0.8174 (p-90) REVERT: A 477 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8739 (tm-30) REVERT: A 592 LEU cc_start: 0.9278 (mt) cc_final: 0.8935 (mt) REVERT: A 593 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7922 (ptm-80) REVERT: A 682 MET cc_start: 0.8172 (ptm) cc_final: 0.7895 (ptm) REVERT: A 692 MET cc_start: 0.9276 (mmm) cc_final: 0.8846 (mmm) REVERT: D 74 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: E 74 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7670 (pt0) REVERT: E 226 ASP cc_start: 0.8666 (p0) cc_final: 0.8462 (p0) REVERT: G 236 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: H 5 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6938 (p90) REVERT: I 25 VAL cc_start: 0.0121 (OUTLIER) cc_final: -0.0436 (p) REVERT: I 374 MET cc_start: 0.7773 (tpp) cc_final: 0.7506 (pmt) REVERT: I 400 ASP cc_start: 0.8686 (m-30) cc_final: 0.8223 (p0) REVERT: J 42 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8814 (pt0) REVERT: J 368 THR cc_start: 0.3228 (OUTLIER) cc_final: 0.2824 (p) REVERT: J 378 ILE cc_start: -0.0619 (OUTLIER) cc_final: -0.0912 (tt) outliers start: 75 outliers final: 24 residues processed: 226 average time/residue: 0.5795 time to fit residues: 159.6855 Evaluate side-chains 145 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 THR Chi-restraints excluded: chain J residue 378 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 189 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 350 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 302 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 336 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 307 optimal weight: 50.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS A 158 ASN A 438 HIS D 298 ASN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN F 216 GLN G 83 HIS ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS I 389 HIS J 253 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.122971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.068186 restraints weight = 70401.727| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.21 r_work: 0.2713 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 32660 Z= 0.308 Angle : 0.741 23.125 44739 Z= 0.392 Chirality : 0.047 0.468 4966 Planarity : 0.005 0.062 5358 Dihedral : 17.177 179.559 5481 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.86 % Favored : 95.73 % Rotamer: Outliers : 2.30 % Allowed : 10.19 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.67 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 3679 helix: 0.66 (0.14), residues: 1260 sheet: 0.13 (0.22), residues: 518 loop : -1.33 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 668 TYR 0.021 0.002 TYR H 181 PHE 0.021 0.002 PHE B 332 TRP 0.020 0.002 TRP A 681 HIS 0.028 0.002 HIS F 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.31 (32647) covalent geometry : angle 0.73382 / 0.39 (44721) SS BOND : bond 0.00839 / 0.60 ( 9) SS BOND : angle 5.25241 / 6.90 ( 18) hydrogen bonds : bond 0.05426 / 5.41 ( 1023) hydrogen bonds : angle 4.73878 / 5.97 ( 2802) Misc. bond : bond 0.01371 / 1.18 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 122 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8549 (tt) REVERT: A 147 TRP cc_start: 0.8680 (p90) cc_final: 0.8418 (p90) REVERT: A 433 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7300 (m-70) REVERT: A 477 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8762 (tm-30) REVERT: A 592 LEU cc_start: 0.9386 (mt) cc_final: 0.9098 (mt) REVERT: A 593 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.8063 (ptm-80) REVERT: A 603 MET cc_start: 0.9412 (mmt) cc_final: 0.8908 (mmm) REVERT: A 682 MET cc_start: 0.8238 (ptm) cc_final: 0.7993 (ptm) REVERT: A 692 MET cc_start: 0.9352 (mmm) cc_final: 0.8938 (mmm) REVERT: B 227 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8566 (mmmm) REVERT: B 340 MET cc_start: 0.9009 (mtm) cc_final: 0.8733 (mtm) REVERT: C 153 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: D 58 ASN cc_start: 0.9040 (p0) cc_final: 0.8798 (p0) REVERT: D 74 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: E 74 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7798 (pt0) REVERT: E 226 ASP cc_start: 0.8757 (p0) cc_final: 0.8520 (p0) REVERT: G 236 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8443 (mt0) REVERT: H 5 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6689 (p90) REVERT: H 186 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8832 (t0) REVERT: I 25 VAL cc_start: 0.0227 (OUTLIER) cc_final: -0.0303 (p) REVERT: I 228 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6677 (pp-130) REVERT: I 279 MET cc_start: 0.7051 (tpt) cc_final: 0.6819 (mtm) REVERT: I 374 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7378 (ppp) REVERT: I 400 ASP cc_start: 0.8848 (m-30) cc_final: 0.8394 (OUTLIER) REVERT: J 228 MET cc_start: -0.1989 (mpt) cc_final: -0.3190 (mpp) REVERT: J 307 GLN cc_start: 0.6466 (tm-30) cc_final: 0.6028 (mm-40) outliers start: 72 outliers final: 28 residues processed: 177 average time/residue: 0.5610 time to fit residues: 121.8740 Evaluate side-chains 143 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 121 CYS Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 343 VAL Chi-restraints excluded: chain J residue 357 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 259 optimal weight: 0.6980 chunk 337 optimal weight: 10.0000 chunk 48 optimal weight: 50.0000 chunk 133 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 214 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 30.0000 chunk 198 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN H 2 GLN ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.124953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.067360 restraints weight = 69816.625| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.82 r_work: 0.2762 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 32660 Z= 0.135 Angle : 0.616 16.662 44739 Z= 0.330 Chirality : 0.042 0.370 4966 Planarity : 0.003 0.045 5358 Dihedral : 17.129 178.203 5471 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.72 % Favored : 95.95 % Rotamer: Outliers : 1.92 % Allowed : 10.73 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 3679 helix: 0.97 (0.14), residues: 1261 sheet: 0.38 (0.22), residues: 516 loop : -1.14 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 23 TYR 0.021 0.001 TYR H 74 PHE 0.016 0.001 PHE A 163 TRP 0.021 0.001 TRP G 308 HIS 0.008 0.001 HIS I 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (32647) covalent geometry : angle 0.61121 / 0.33 (44721) SS BOND : bond 0.00430 / 0.35 ( 9) SS BOND : angle 3.80329 / 5.00 ( 18) hydrogen bonds : bond 0.04263 / 4.46 ( 1023) hydrogen bonds : angle 4.43009 / 5.58 ( 2802) Misc. bond : bond 0.00698 / 0.67 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 126 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7466 (mtp) cc_final: 0.6548 (ttm) REVERT: A 44 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8617 (tt) REVERT: A 433 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.7296 (m-70) REVERT: A 477 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8770 (tm-30) REVERT: A 592 LEU cc_start: 0.9360 (mt) cc_final: 0.9060 (mt) REVERT: A 603 MET cc_start: 0.9425 (mmt) cc_final: 0.8914 (mmm) REVERT: A 682 MET cc_start: 0.8150 (ptm) cc_final: 0.7837 (ptm) REVERT: A 692 MET cc_start: 0.9349 (mmm) cc_final: 0.9001 (mmm) REVERT: B 227 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8597 (mmmm) REVERT: B 308 TRP cc_start: 0.8640 (t60) cc_final: 0.8342 (t60) REVERT: B 340 MET cc_start: 0.9027 (mtm) cc_final: 0.8757 (mtm) REVERT: C 153 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: D 58 ASN cc_start: 0.9033 (p0) cc_final: 0.8795 (p0) REVERT: D 74 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: D 303 PHE cc_start: 0.9671 (OUTLIER) cc_final: 0.8688 (t80) REVERT: E 74 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7775 (pt0) REVERT: E 226 ASP cc_start: 0.8730 (p0) cc_final: 0.8476 (p0) REVERT: H 5 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6825 (p90) REVERT: I 25 VAL cc_start: 0.1572 (OUTLIER) cc_final: 0.1062 (p) REVERT: I 228 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7123 (pp-130) REVERT: I 374 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7580 (pmt) REVERT: I 400 ASP cc_start: 0.8881 (m-30) cc_final: 0.8464 (OUTLIER) REVERT: J 142 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: J 228 MET cc_start: -0.2330 (mpt) cc_final: -0.3599 (mpp) REVERT: J 307 GLN cc_start: 0.6662 (tm-30) cc_final: 0.6065 (mm-40) outliers start: 60 outliers final: 26 residues processed: 170 average time/residue: 0.6018 time to fit residues: 125.2718 Evaluate side-chains 147 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain G residue 121 CYS Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 357 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 245 optimal weight: 3.9990 chunk 348 optimal weight: 7.9990 chunk 48 optimal weight: 50.0000 chunk 252 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 231 optimal weight: 3.9990 chunk 351 optimal weight: 2.9990 chunk 339 optimal weight: 20.0000 chunk 208 optimal weight: 0.0470 chunk 166 optimal weight: 0.9990 chunk 320 optimal weight: 30.0000 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 321 ASN E 62 GLN F 216 GLN G 342 GLN ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 389 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.123399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065438 restraints weight = 70194.645| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.80 r_work: 0.2726 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32660 Z= 0.225 Angle : 0.637 18.707 44739 Z= 0.338 Chirality : 0.043 0.414 4966 Planarity : 0.004 0.046 5358 Dihedral : 17.061 177.242 5468 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.05 % Favored : 95.65 % Rotamer: Outliers : 1.79 % Allowed : 11.69 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 3679 helix: 1.11 (0.14), residues: 1261 sheet: 0.34 (0.22), residues: 521 loop : -1.10 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 593 TYR 0.016 0.001 TYR H 74 PHE 0.017 0.001 PHE B 332 TRP 0.012 0.001 TRP A 681 HIS 0.035 0.001 HIS F 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (32647) covalent geometry : angle 0.63328 / 0.34 (44721) SS BOND : bond 0.00449 / 0.39 ( 9) SS BOND : angle 3.33138 / 4.37 ( 18) hydrogen bonds : bond 0.04423 / 4.52 ( 1023) hydrogen bonds : angle 4.36386 / 5.49 ( 2802) Misc. bond : bond 0.00701 / 0.65 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 115 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7459 (mtp) cc_final: 0.6010 (ttp) REVERT: A 44 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8594 (tt) REVERT: A 433 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7542 (m-70) REVERT: A 477 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8913 (tm-30) REVERT: A 592 LEU cc_start: 0.9323 (mt) cc_final: 0.9035 (mt) REVERT: A 603 MET cc_start: 0.9459 (mmt) cc_final: 0.9008 (mmm) REVERT: A 682 MET cc_start: 0.8348 (ptm) cc_final: 0.8081 (ptm) REVERT: A 692 MET cc_start: 0.9377 (mmm) cc_final: 0.9063 (mmm) REVERT: B 227 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8630 (mmmm) REVERT: B 308 TRP cc_start: 0.8809 (t60) cc_final: 0.8500 (t60) REVERT: B 340 MET cc_start: 0.9250 (mtm) cc_final: 0.8889 (mtm) REVERT: C 153 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8498 (tt0) REVERT: D 58 ASN cc_start: 0.9183 (p0) cc_final: 0.8940 (p0) REVERT: D 74 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8706 (mp0) REVERT: D 303 PHE cc_start: 0.9676 (OUTLIER) cc_final: 0.8741 (t80) REVERT: E 74 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8061 (pt0) REVERT: E 226 ASP cc_start: 0.8892 (p0) cc_final: 0.8671 (p0) REVERT: H 5 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6793 (p90) REVERT: I 25 VAL cc_start: 0.1092 (OUTLIER) cc_final: 0.0578 (p) REVERT: I 400 ASP cc_start: 0.8846 (m-30) cc_final: 0.8404 (p0) REVERT: J 23 ARG cc_start: 0.7912 (ttt-90) cc_final: 0.7687 (ttp-110) REVERT: J 228 MET cc_start: -0.2223 (mpt) cc_final: -0.3568 (mpp) REVERT: J 307 GLN cc_start: 0.6597 (tm-30) cc_final: 0.6039 (mm-40) outliers start: 56 outliers final: 30 residues processed: 158 average time/residue: 0.6102 time to fit residues: 117.3869 Evaluate side-chains 141 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 121 CYS Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 357 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 366 optimal weight: 40.0000 chunk 10 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 293 optimal weight: 10.0000 chunk 328 optimal weight: 5.9990 chunk 356 optimal weight: 0.2980 chunk 245 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN G 319 ASN ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 376 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.124733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.067244 restraints weight = 69654.479| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.87 r_work: 0.2769 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 32660 Z= 0.128 Angle : 0.636 37.429 44739 Z= 0.329 Chirality : 0.043 0.786 4966 Planarity : 0.003 0.044 5358 Dihedral : 17.076 176.581 5468 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.00 % Favored : 95.73 % Rotamer: Outliers : 1.82 % Allowed : 11.88 % Favored : 86.30 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.13), residues: 3679 helix: 1.23 (0.14), residues: 1261 sheet: 0.50 (0.23), residues: 513 loop : -0.97 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 593 TYR 0.016 0.001 TYR H 74 PHE 0.015 0.001 PHE A 163 TRP 0.023 0.001 TRP G 308 HIS 0.018 0.001 HIS F 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (32647) covalent geometry : angle 0.63356 / 0.33 (44721) SS BOND : bond 0.00368 / 0.30 ( 9) SS BOND : angle 2.95242 / 3.95 ( 18) hydrogen bonds : bond 0.03927 / 4.12 ( 1023) hydrogen bonds : angle 4.21310 / 5.30 ( 2802) Misc. bond : bond 0.01512 / 1.40 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 109 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.5929 (ttp) REVERT: A 44 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8595 (tt) REVERT: A 433 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7520 (m-70) REVERT: A 477 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8921 (tm-30) REVERT: A 592 LEU cc_start: 0.9350 (mt) cc_final: 0.9076 (mt) REVERT: A 603 MET cc_start: 0.9501 (mmt) cc_final: 0.9007 (mmm) REVERT: A 682 MET cc_start: 0.8325 (ptm) cc_final: 0.8046 (ptm) REVERT: A 692 MET cc_start: 0.9370 (mmm) cc_final: 0.8945 (mmm) REVERT: B 308 TRP cc_start: 0.8782 (t60) cc_final: 0.8483 (t60) REVERT: B 340 MET cc_start: 0.9298 (mtm) cc_final: 0.8886 (mtm) REVERT: C 153 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: D 58 ASN cc_start: 0.9203 (p0) cc_final: 0.8954 (p0) REVERT: D 74 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: D 303 PHE cc_start: 0.9680 (OUTLIER) cc_final: 0.8705 (t80) REVERT: E 74 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8007 (pt0) REVERT: E 226 ASP cc_start: 0.8878 (p0) cc_final: 0.8663 (p0) REVERT: G 297 GLN cc_start: 0.8256 (mm110) cc_final: 0.7302 (pt0) REVERT: H 5 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6755 (p90) REVERT: I 25 VAL cc_start: 0.1077 (OUTLIER) cc_final: 0.0584 (p) REVERT: I 228 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6977 (pp-130) REVERT: I 400 ASP cc_start: 0.8837 (m-30) cc_final: 0.8434 (OUTLIER) REVERT: J 23 ARG cc_start: 0.8001 (ttt-90) cc_final: 0.7760 (ttp-110) REVERT: J 142 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7462 (pm20) REVERT: J 228 MET cc_start: -0.2440 (mpt) cc_final: -0.3824 (mpp) REVERT: J 307 GLN cc_start: 0.6517 (tm-30) cc_final: 0.5965 (mm-40) outliers start: 57 outliers final: 31 residues processed: 156 average time/residue: 0.5841 time to fit residues: 112.3244 Evaluate side-chains 146 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain I residue 404 MET Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 357 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 344 optimal weight: 9.9990 chunk 153 optimal weight: 0.0170 chunk 336 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 304 optimal weight: 40.0000 chunk 52 optimal weight: 30.0000 chunk 81 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 216 GLN I 246 GLN ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.123775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.066242 restraints weight = 70498.435| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.82 r_work: 0.2745 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 32660 Z= 0.183 Angle : 0.612 20.686 44739 Z= 0.323 Chirality : 0.043 0.406 4966 Planarity : 0.003 0.044 5358 Dihedral : 17.025 175.442 5468 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.10 % Favored : 95.57 % Rotamer: Outliers : 1.60 % Allowed : 12.39 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.13), residues: 3679 helix: 1.33 (0.14), residues: 1263 sheet: 0.48 (0.23), residues: 511 loop : -0.92 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 87 TYR 0.016 0.001 TYR H 74 PHE 0.016 0.001 PHE A 163 TRP 0.010 0.001 TRP A 681 HIS 0.024 0.001 HIS F 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (32647) covalent geometry : angle 0.61003 / 0.32 (44721) SS BOND : bond 0.00383 / 0.31 ( 9) SS BOND : angle 2.78920 / 3.66 ( 18) hydrogen bonds : bond 0.04074 / 4.20 ( 1023) hydrogen bonds : angle 4.19045 / 5.25 ( 2802) Misc. bond : bond 0.01363 / 1.25 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8597 (tt) REVERT: A 433 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7541 (m-70) REVERT: A 477 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8922 (tm-30) REVERT: A 592 LEU cc_start: 0.9325 (mt) cc_final: 0.9059 (mt) REVERT: A 603 MET cc_start: 0.9514 (mmt) cc_final: 0.9053 (mmm) REVERT: A 682 MET cc_start: 0.8318 (ptm) cc_final: 0.8073 (ptm) REVERT: A 692 MET cc_start: 0.9365 (mmm) cc_final: 0.9043 (mmm) REVERT: B 227 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8704 (mtmp) REVERT: B 308 TRP cc_start: 0.8802 (t60) cc_final: 0.8498 (t60) REVERT: B 340 MET cc_start: 0.9309 (mtm) cc_final: 0.8884 (mtm) REVERT: C 153 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: D 58 ASN cc_start: 0.9204 (p0) cc_final: 0.8964 (p0) REVERT: D 74 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8646 (mp0) REVERT: D 303 PHE cc_start: 0.9680 (OUTLIER) cc_final: 0.8801 (t80) REVERT: E 74 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8073 (pt0) REVERT: E 226 ASP cc_start: 0.8909 (p0) cc_final: 0.8677 (p0) REVERT: G 297 GLN cc_start: 0.8377 (mm110) cc_final: 0.7568 (pt0) REVERT: H 186 ASN cc_start: 0.9069 (OUTLIER) cc_final: 0.8802 (t0) REVERT: I 25 VAL cc_start: 0.0236 (OUTLIER) cc_final: -0.0216 (p) REVERT: I 228 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6948 (pp-130) REVERT: I 279 MET cc_start: 0.7302 (tpt) cc_final: 0.7003 (mtm) REVERT: I 400 ASP cc_start: 0.8827 (m-30) cc_final: 0.8416 (p0) REVERT: J 142 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: J 228 MET cc_start: -0.2346 (mpt) cc_final: -0.3690 (mpp) REVERT: J 307 GLN cc_start: 0.6335 (tm-30) cc_final: 0.5956 (mm-40) outliers start: 50 outliers final: 32 residues processed: 150 average time/residue: 0.5630 time to fit residues: 104.0854 Evaluate side-chains 145 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain I residue 404 MET Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 357 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 203 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 294 optimal weight: 20.0000 chunk 115 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 313 optimal weight: 1.9990 chunk 263 optimal weight: 8.9990 chunk 192 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 216 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.124428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.067281 restraints weight = 70081.730| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.82 r_work: 0.2771 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32660 Z= 0.137 Angle : 0.584 19.547 44739 Z= 0.309 Chirality : 0.042 0.383 4966 Planarity : 0.003 0.044 5358 Dihedral : 17.018 174.982 5468 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.94 % Favored : 95.79 % Rotamer: Outliers : 1.60 % Allowed : 12.64 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3679 helix: 1.38 (0.14), residues: 1265 sheet: 0.53 (0.23), residues: 513 loop : -0.83 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 371 TYR 0.012 0.001 TYR I 361 PHE 0.015 0.001 PHE D 332 TRP 0.031 0.001 TRP G 308 HIS 0.030 0.001 HIS F 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (32647) covalent geometry : angle 0.58257 / 0.31 (44721) SS BOND : bond 0.00356 / 0.29 ( 9) SS BOND : angle 2.42368 / 3.22 ( 18) hydrogen bonds : bond 0.03741 / 3.93 ( 1023) hydrogen bonds : angle 4.10151 / 5.12 ( 2802) Misc. bond : bond 0.01031 / 0.89 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 111 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8498 (tt) REVERT: A 433 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7438 (m-70) REVERT: A 477 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8904 (tm-30) REVERT: A 592 LEU cc_start: 0.9366 (mt) cc_final: 0.9112 (mt) REVERT: A 603 MET cc_start: 0.9506 (mmt) cc_final: 0.8999 (mmm) REVERT: A 639 MET cc_start: 0.9384 (ptt) cc_final: 0.9046 (pmt) REVERT: A 682 MET cc_start: 0.8341 (ptm) cc_final: 0.8098 (ptm) REVERT: A 692 MET cc_start: 0.9359 (mmm) cc_final: 0.9041 (mmm) REVERT: B 308 TRP cc_start: 0.8749 (t60) cc_final: 0.8440 (t60) REVERT: B 340 MET cc_start: 0.9337 (mtm) cc_final: 0.8962 (mtm) REVERT: C 153 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8531 (tt0) REVERT: D 58 ASN cc_start: 0.9146 (p0) cc_final: 0.8893 (p0) REVERT: D 74 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8564 (mp0) REVERT: D 232 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: D 303 PHE cc_start: 0.9675 (OUTLIER) cc_final: 0.8839 (t80) REVERT: E 74 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8040 (pt0) REVERT: E 226 ASP cc_start: 0.8885 (p0) cc_final: 0.8676 (p0) REVERT: G 297 GLN cc_start: 0.8376 (mm110) cc_final: 0.7604 (pt0) REVERT: H 5 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6730 (p90) REVERT: I 228 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6976 (pp-130) REVERT: I 279 MET cc_start: 0.7388 (tpt) cc_final: 0.7065 (mtm) REVERT: I 400 ASP cc_start: 0.8873 (m-30) cc_final: 0.8489 (OUTLIER) REVERT: J 142 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: J 228 MET cc_start: -0.2686 (mpt) cc_final: -0.4074 (mpp) REVERT: J 307 GLN cc_start: 0.6495 (tm-30) cc_final: 0.6071 (mm-40) outliers start: 50 outliers final: 29 residues processed: 152 average time/residue: 0.5476 time to fit residues: 102.1555 Evaluate side-chains 141 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain I residue 404 MET Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 173 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 328 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 chunk 218 optimal weight: 2.9990 chunk 295 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.124701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.067683 restraints weight = 69722.762| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.88 r_work: 0.2783 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32660 Z= 0.122 Angle : 0.584 17.721 44739 Z= 0.306 Chirality : 0.042 0.419 4966 Planarity : 0.003 0.044 5358 Dihedral : 16.988 175.389 5467 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.94 % Favored : 95.81 % Rotamer: Outliers : 1.44 % Allowed : 12.99 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3679 helix: 1.44 (0.14), residues: 1264 sheet: 0.62 (0.23), residues: 515 loop : -0.81 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 233 TYR 0.021 0.001 TYR H 181 PHE 0.014 0.001 PHE D 332 TRP 0.015 0.001 TRP G 308 HIS 0.022 0.001 HIS F 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (32647) covalent geometry : angle 0.58202 / 0.31 (44721) SS BOND : bond 0.00355 / 0.29 ( 9) SS BOND : angle 2.31439 / 3.07 ( 18) hydrogen bonds : bond 0.03609 / 3.81 ( 1023) hydrogen bonds : angle 4.06771 / 5.07 ( 2802) Misc. bond : bond 0.00959 / 0.82 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.7300 (mtp) cc_final: 0.5968 (tpp) REVERT: A 44 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 238 GLU cc_start: 0.8726 (tt0) cc_final: 0.8216 (tm-30) REVERT: A 433 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7366 (m-70) REVERT: A 477 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8695 (tm-30) REVERT: A 587 GLN cc_start: 0.9085 (tt0) cc_final: 0.8615 (tp40) REVERT: A 592 LEU cc_start: 0.9338 (mt) cc_final: 0.9093 (mt) REVERT: A 603 MET cc_start: 0.9469 (mmt) cc_final: 0.8961 (mmm) REVERT: A 639 MET cc_start: 0.9262 (ptt) cc_final: 0.8941 (pmt) REVERT: A 692 MET cc_start: 0.9288 (mmm) cc_final: 0.8971 (mmm) REVERT: B 308 TRP cc_start: 0.8642 (t60) cc_final: 0.8323 (t60) REVERT: B 321 ASN cc_start: 0.8573 (p0) cc_final: 0.8365 (p0) REVERT: B 340 MET cc_start: 0.9154 (mtm) cc_final: 0.8829 (mtm) REVERT: C 153 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: D 58 ASN cc_start: 0.9018 (p0) cc_final: 0.8754 (p0) REVERT: D 74 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: D 232 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: D 303 PHE cc_start: 0.9643 (OUTLIER) cc_final: 0.8841 (t80) REVERT: E 74 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7748 (pt0) REVERT: E 226 ASP cc_start: 0.8787 (p0) cc_final: 0.8578 (p0) REVERT: F 62 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6310 (mp10) REVERT: G 297 GLN cc_start: 0.8343 (mm110) cc_final: 0.7595 (pt0) REVERT: H 5 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6776 (p90) REVERT: H 152 MET cc_start: 0.5895 (ppp) cc_final: 0.5525 (ppp) REVERT: I 228 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6947 (pp-130) REVERT: I 279 MET cc_start: 0.7359 (tpt) cc_final: 0.7020 (mtm) REVERT: I 400 ASP cc_start: 0.8825 (m-30) cc_final: 0.8496 (OUTLIER) REVERT: J 142 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7446 (pm20) REVERT: J 173 TYR cc_start: 0.9072 (m-80) cc_final: 0.8816 (m-80) REVERT: J 228 MET cc_start: -0.2818 (mpt) cc_final: -0.4116 (mpp) REVERT: J 307 GLN cc_start: 0.6513 (tm-30) cc_final: 0.6105 (mm-40) outliers start: 45 outliers final: 32 residues processed: 150 average time/residue: 0.5390 time to fit residues: 99.2734 Evaluate side-chains 147 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain I residue 404 MET Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 136 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 317 optimal weight: 30.0000 chunk 271 optimal weight: 5.9990 chunk 48 optimal weight: 40.0000 chunk 178 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 50 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 134 optimal weight: 0.0270 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 216 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.124627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.067726 restraints weight = 70088.601| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.85 r_work: 0.2776 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32660 Z= 0.130 Angle : 0.588 17.754 44739 Z= 0.308 Chirality : 0.041 0.365 4966 Planarity : 0.003 0.043 5358 Dihedral : 16.943 175.778 5467 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.97 % Favored : 95.84 % Rotamer: Outliers : 1.47 % Allowed : 13.15 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3679 helix: 1.48 (0.14), residues: 1265 sheet: 0.66 (0.23), residues: 513 loop : -0.78 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 233 TYR 0.018 0.001 TYR I 381 PHE 0.014 0.001 PHE F 303 TRP 0.035 0.001 TRP G 308 HIS 0.022 0.001 HIS F 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (32647) covalent geometry : angle 0.58609 / 0.31 (44721) SS BOND : bond 0.00345 / 0.29 ( 9) SS BOND : angle 2.22867 / 2.95 ( 18) hydrogen bonds : bond 0.03582 / 3.77 ( 1023) hydrogen bonds : angle 4.02561 / 5.01 ( 2802) Misc. bond : bond 0.00960 / 0.82 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8481 (tt) REVERT: A 238 GLU cc_start: 0.8864 (tt0) cc_final: 0.8320 (tm-30) REVERT: A 433 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7517 (m-70) REVERT: A 477 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8880 (tm-30) REVERT: A 587 GLN cc_start: 0.9148 (tt0) cc_final: 0.8660 (tp40) REVERT: A 592 LEU cc_start: 0.9358 (mt) cc_final: 0.9111 (mt) REVERT: A 603 MET cc_start: 0.9506 (mmt) cc_final: 0.9018 (mmm) REVERT: A 639 MET cc_start: 0.9371 (ptt) cc_final: 0.9030 (pmt) REVERT: A 692 MET cc_start: 0.9378 (mmm) cc_final: 0.9063 (mmm) REVERT: B 308 TRP cc_start: 0.8777 (t60) cc_final: 0.8503 (t60) REVERT: B 340 MET cc_start: 0.9298 (mtm) cc_final: 0.9024 (mtm) REVERT: C 153 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: D 58 ASN cc_start: 0.9214 (p0) cc_final: 0.8982 (p0) REVERT: D 74 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8619 (mp0) REVERT: D 232 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: D 303 PHE cc_start: 0.9666 (OUTLIER) cc_final: 0.8915 (t80) REVERT: E 74 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8025 (pt0) REVERT: E 226 ASP cc_start: 0.8934 (p0) cc_final: 0.8728 (p0) REVERT: F 62 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6128 (mp10) REVERT: F 323 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8776 (mppt) REVERT: G 297 GLN cc_start: 0.8379 (mm110) cc_final: 0.7664 (pt0) REVERT: G 308 TRP cc_start: 0.9006 (t-100) cc_final: 0.8794 (t60) REVERT: H 5 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6769 (p90) REVERT: H 152 MET cc_start: 0.5828 (ppp) cc_final: 0.5464 (ppp) REVERT: I 228 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7451 (pp-130) REVERT: I 400 ASP cc_start: 0.8831 (m-30) cc_final: 0.8502 (OUTLIER) REVERT: J 142 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7446 (pm20) REVERT: J 173 TYR cc_start: 0.9029 (m-80) cc_final: 0.8767 (m-80) REVERT: J 228 MET cc_start: -0.2617 (mpt) cc_final: -0.3867 (mpp) REVERT: J 307 GLN cc_start: 0.6502 (tm-30) cc_final: 0.6265 (mm-40) outliers start: 46 outliers final: 33 residues processed: 147 average time/residue: 0.5556 time to fit residues: 99.1865 Evaluate side-chains 148 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain I residue 404 MET Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 1 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 198 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 284 optimal weight: 20.0000 chunk 164 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 216 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN I 307 GLN I 379 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.124105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.067109 restraints weight = 70147.616| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.83 r_work: 0.2768 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32660 Z= 0.155 Angle : 0.593 17.104 44739 Z= 0.310 Chirality : 0.042 0.382 4966 Planarity : 0.003 0.043 5358 Dihedral : 16.903 175.247 5467 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.00 % Favored : 95.81 % Rotamer: Outliers : 1.47 % Allowed : 13.25 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3679 helix: 1.50 (0.14), residues: 1266 sheet: 0.55 (0.23), residues: 523 loop : -0.76 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 23 TYR 0.014 0.001 TYR I 361 PHE 0.016 0.001 PHE B 332 TRP 0.031 0.001 TRP G 308 HIS 0.020 0.001 HIS F 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (32647) covalent geometry : angle 0.59153 / 0.31 (44721) SS BOND : bond 0.00352 / 0.30 ( 9) SS BOND : angle 2.16618 / 2.88 ( 18) hydrogen bonds : bond 0.03691 / 3.85 ( 1023) hydrogen bonds : angle 4.02255 / 5.01 ( 2802) Misc. bond : bond 0.00957 / 0.82 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16574.30 seconds wall clock time: 281 minutes 38.08 seconds (16898.08 seconds total)