Starting phenix.real_space_refine on Thu Nov 20 07:05:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gs9_51543/11_2025/9gs9_51543_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gs9_51543/11_2025/9gs9_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_51543/11_2025/9gs9_51543_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gs9_51543/11_2025/9gs9_51543_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gs9_51543/11_2025/9gs9_51543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gs9_51543/11_2025/9gs9_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-2.0-5881/lib/python3.9/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: 7.19, per 1000 atoms: 0.23 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: 2.89 Conformation dependent library (CDL) restraints added in 1.3 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: 3.72 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: 5.77 Time building geometry restraints manager: 3.80 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: 44710 12.76 - 25.53: 5 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: 4898 0.197 - 0.394: 59 0.394 - 0.591: 3 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.870 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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= 1.314 Angle : 1.852 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 covalent geometry : bond 0.01507 (32647) covalent geometry : angle 1.82420 (44721) SS BOND : bond 0.37192 ( 9) SS BOND : angle 15.90038 ( 18) hydrogen bonds : bond 0.25252 ( 1023) hydrogen bonds : angle 8.22525 ( 2802) Misc. bond : bond 0.54119 ( 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 : 1.213 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: 0.9148 (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: 0.6902 (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: 0.7138 time to fit residues: 318.1401 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 : 1.226 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 68 ASN F 93 GLN F 216 GLN G 83 HIS G 319 ASN G 321 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN H 166 GLN I 52 HIS I 168 ASN I 253 ASN I 328 ASN I 379 ASN ** J 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 GLN J 253 ASN J 367 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.126986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.068240 restraints weight = 70154.683| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.90 r_work: 0.2789 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 32660 Z= 0.159 Angle : 0.720 21.742 44739 Z= 0.378 Chirality : 0.043 0.350 4966 Planarity : 0.004 0.047 5358 Dihedral : 17.419 178.964 5499 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.59 % Favored : 95.95 % Rotamer: Outliers : 2.30 % Allowed : 8.91 % Favored : 88.79 % 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: -0.90 (0.13), residues: 3679 helix: 0.26 (0.14), residues: 1259 sheet: 0.14 (0.21), residues: 527 loop : -1.42 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 61 TYR 0.014 0.001 TYR J 320 PHE 0.032 0.001 PHE J 29 TRP 0.019 0.001 TRP C 308 HIS 0.024 0.001 HIS I 372 Details of bonding type rmsd covalent geometry : bond 0.00334 (32647) covalent geometry : angle 0.71686 (44721) SS BOND : bond 0.00588 ( 9) SS BOND : angle 3.50635 ( 18) hydrogen bonds : bond 0.04980 ( 1023) hydrogen bonds : angle 4.79288 ( 2802) Misc. bond : bond 0.01004 ( 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 243 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 171 time to evaluate : 1.309 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: A 44 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8554 (tt) REVERT: A 147 TRP cc_start: 0.8605 (p90) cc_final: 0.8247 (p-90) REVERT: A 477 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8687 (tm-30) REVERT: A 567 MET cc_start: 0.9509 (ttp) cc_final: 0.9260 (ttp) REVERT: A 592 LEU cc_start: 0.9278 (mt) cc_final: 0.8926 (mt) REVERT: A 593 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7713 (mtm110) REVERT: A 682 MET cc_start: 0.8078 (ptm) cc_final: 0.7875 (ptm) REVERT: A 692 MET cc_start: 0.9271 (mmm) cc_final: 0.8888 (mmm) REVERT: B 10 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8697 (m-30) REVERT: D 74 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: D 340 MET cc_start: 0.8375 (mtp) cc_final: 0.8143 (mtp) REVERT: E 74 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7686 (pt0) REVERT: E 226 ASP cc_start: 0.8700 (p0) cc_final: 0.8499 (p0) REVERT: F 340 MET cc_start: 0.8765 (mtp) cc_final: 0.8548 (mtp) REVERT: G 297 GLN cc_start: 0.7868 (mm110) cc_final: 0.6993 (pt0) REVERT: H 5 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.7069 (p90) REVERT: I 25 VAL cc_start: -0.0102 (OUTLIER) cc_final: -0.0595 (p) REVERT: I 374 MET cc_start: 0.7597 (tpp) cc_final: 0.7302 (pp-130) REVERT: I 400 ASP cc_start: 0.8761 (m-30) cc_final: 0.8347 (p0) REVERT: J 42 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8850 (pt0) REVERT: J 162 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7186 (tp-100) REVERT: J 228 MET cc_start: -0.3295 (mmt) cc_final: -0.3786 (mpp) REVERT: J 368 THR cc_start: 0.3206 (OUTLIER) cc_final: 0.2935 (p) REVERT: J 371 ARG cc_start: 0.0337 (OUTLIER) cc_final: -0.0053 (mmt180) REVERT: J 378 ILE cc_start: -0.0742 (OUTLIER) cc_final: -0.1006 (tt) outliers start: 72 outliers final: 24 residues processed: 226 average time/residue: 0.6026 time to fit residues: 165.2477 Evaluate side-chains 151 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 10 ASP 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 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 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 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 372 HIS Chi-restraints excluded: chain I residue 373 LYS 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 162 GLN Chi-restraints excluded: chain J residue 185 THR 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 371 ARG 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: 4.9990 chunk 203 optimal weight: 5.9990 chunk 350 optimal weight: 9.9990 chunk 110 optimal weight: 0.0670 chunk 64 optimal weight: 3.9990 chunk 302 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 336 optimal weight: 8.9990 chunk 254 optimal weight: 0.0010 chunk 104 optimal weight: 0.9980 chunk 307 optimal weight: 50.0000 overall best weight: 0.9926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 ASN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS ** I 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 389 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.125782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067476 restraints weight = 69804.509| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.87 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: 0.8443 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 32660 Z= 0.139 Angle : 0.626 17.639 44739 Z= 0.328 Chirality : 0.042 0.357 4966 Planarity : 0.003 0.047 5358 Dihedral : 17.110 179.491 5481 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.70 % Favored : 95.90 % Rotamer: Outliers : 2.04 % Allowed : 10.41 % Favored : 87.55 % 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: -0.39 (0.13), residues: 3679 helix: 0.85 (0.14), residues: 1262 sheet: 0.34 (0.22), residues: 538 loop : -1.23 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 388 TYR 0.021 0.001 TYR H 181 PHE 0.021 0.001 PHE J 386 TRP 0.018 0.001 TRP G 308 HIS 0.011 0.001 HIS I 372 Details of bonding type rmsd covalent geometry : bond 0.00305 (32647) covalent geometry : angle 0.62495 (44721) SS BOND : bond 0.00623 ( 9) SS BOND : angle 2.07425 ( 18) hydrogen bonds : bond 0.04239 ( 1023) hydrogen bonds : angle 4.41639 ( 2802) Misc. bond : bond 0.00554 ( 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 199 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 135 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8602 (tt) REVERT: A 147 TRP cc_start: 0.8627 (p90) cc_final: 0.8254 (p-90) REVERT: A 477 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8765 (tm-30) REVERT: A 567 MET cc_start: 0.9507 (ttp) cc_final: 0.9154 (ttp) REVERT: A 592 LEU cc_start: 0.9365 (mt) cc_final: 0.9053 (mt) REVERT: A 593 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7944 (ptm-80) REVERT: A 603 MET cc_start: 0.9401 (mmt) cc_final: 0.8917 (mmm) REVERT: A 639 MET cc_start: 0.9227 (ptt) cc_final: 0.8842 (pmt) REVERT: A 668 ARG cc_start: 0.9009 (mmm-85) cc_final: 0.8651 (tpp80) REVERT: A 682 MET cc_start: 0.8018 (ptm) cc_final: 0.7758 (ptm) REVERT: A 692 MET cc_start: 0.9239 (mmm) cc_final: 0.8915 (mmm) REVERT: B 113 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8321 (mm-30) REVERT: B 227 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8592 (mmmm) REVERT: B 308 TRP cc_start: 0.8597 (t60) cc_final: 0.8291 (t60) REVERT: C 153 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: D 58 ASN cc_start: 0.8948 (p0) cc_final: 0.8696 (p0) REVERT: D 74 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: E 35 ASP cc_start: 0.8595 (p0) cc_final: 0.8352 (p0) REVERT: E 74 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7785 (pt0) REVERT: E 226 ASP cc_start: 0.8730 (p0) cc_final: 0.8505 (p0) REVERT: G 297 GLN cc_start: 0.7969 (mm110) cc_final: 0.7054 (pt0) REVERT: G 340 MET cc_start: 0.7230 (ptp) cc_final: 0.6924 (ptp) REVERT: H 5 TYR cc_start: 0.7416 (p90) cc_final: 0.6939 (p90) REVERT: H 186 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8832 (t0) REVERT: I 25 VAL cc_start: 0.1291 (OUTLIER) cc_final: 0.0809 (p) REVERT: I 228 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6291 (ppp) REVERT: I 279 MET cc_start: 0.7689 (tpt) cc_final: 0.7219 (mtm) REVERT: I 374 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7621 (pmt) REVERT: I 400 ASP cc_start: 0.8807 (m-30) cc_final: 0.8380 (OUTLIER) REVERT: J 228 MET cc_start: -0.3194 (mmt) cc_final: -0.3562 (mpp) REVERT: J 307 GLN cc_start: 0.6701 (tm-30) cc_final: 0.6120 (mm-40) outliers start: 64 outliers final: 23 residues processed: 185 average time/residue: 0.6459 time to fit residues: 144.6037 Evaluate side-chains 145 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 593 ARG Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 226 ASP 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 249 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 249 VAL 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 201 VAL Chi-restraints excluded: chain I residue 228 MET 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 46 GLU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 259 optimal weight: 4.9990 chunk 337 optimal weight: 10.0000 chunk 48 optimal weight: 50.0000 chunk 133 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 158 ASN A 438 HIS D 298 ASN F 216 GLN G 342 GLN H 2 GLN I 181 ASN ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.123299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.065355 restraints weight = 69827.422| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.81 r_work: 0.2718 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 32660 Z= 0.260 Angle : 0.663 19.214 44739 Z= 0.344 Chirality : 0.044 0.418 4966 Planarity : 0.004 0.042 5358 Dihedral : 17.052 176.131 5471 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.64 % Favored : 96.00 % Rotamer: Outliers : 1.76 % Allowed : 11.11 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.19 (0.13), residues: 3679 helix: 1.07 (0.14), residues: 1260 sheet: 0.40 (0.22), residues: 520 loop : -1.13 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 87 TYR 0.016 0.001 TYR H 161 PHE 0.017 0.002 PHE A 163 TRP 0.020 0.001 TRP C 308 HIS 0.032 0.001 HIS F 66 Details of bonding type rmsd covalent geometry : bond 0.00593 (32647) covalent geometry : angle 0.66025 (44721) SS BOND : bond 0.00660 ( 9) SS BOND : angle 3.23008 ( 18) hydrogen bonds : bond 0.04561 ( 1023) hydrogen bonds : angle 4.39089 ( 2802) Misc. bond : bond 0.00957 ( 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 176 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 121 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8543 (tt) REVERT: A 433 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7432 (m-70) REVERT: A 477 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8958 (tm-30) REVERT: A 567 MET cc_start: 0.9534 (ttp) cc_final: 0.9164 (ttp) REVERT: A 592 LEU cc_start: 0.9369 (mt) cc_final: 0.9089 (mt) REVERT: A 593 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8339 (ptm-80) REVERT: A 603 MET cc_start: 0.9451 (mmt) cc_final: 0.9010 (mmm) REVERT: A 682 MET cc_start: 0.8337 (ptm) cc_final: 0.8074 (ptm) REVERT: A 692 MET cc_start: 0.9407 (mmm) cc_final: 0.9080 (mmm) REVERT: B 113 GLU cc_start: 0.8802 (mp0) cc_final: 0.8550 (mm-30) REVERT: B 227 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8608 (mmmm) REVERT: B 308 TRP cc_start: 0.8780 (t60) cc_final: 0.8542 (t60) REVERT: C 153 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: D 58 ASN cc_start: 0.9120 (p0) cc_final: 0.8901 (p0) REVERT: D 74 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8710 (mp0) REVERT: E 35 ASP cc_start: 0.8903 (p0) cc_final: 0.8699 (p0) REVERT: E 74 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8126 (pt0) REVERT: E 226 ASP cc_start: 0.8851 (p0) cc_final: 0.8640 (p0) REVERT: H 5 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6814 (p90) REVERT: H 28 MET cc_start: 0.7223 (tmm) cc_final: 0.6966 (tmm) REVERT: H 60 TYR cc_start: 0.6869 (t80) cc_final: 0.6660 (t80) REVERT: I 25 VAL cc_start: 0.1108 (OUTLIER) cc_final: 0.0613 (p) REVERT: I 400 ASP cc_start: 0.8892 (m-30) cc_final: 0.8488 (p0) REVERT: J 140 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7841 (mp) REVERT: J 142 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: J 228 MET cc_start: -0.3379 (mmt) cc_final: -0.3624 (mpp) REVERT: J 307 GLN cc_start: 0.6482 (tm-30) cc_final: 0.6044 (mm-40) REVERT: J 374 MET cc_start: -0.0058 (tpt) cc_final: -0.0278 (tpt) outliers start: 55 outliers final: 27 residues processed: 165 average time/residue: 0.6269 time to fit residues: 125.8450 Evaluate side-chains 144 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 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 E residue 249 VAL Chi-restraints excluded: chain F residue 26 ASP 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 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 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 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: 0.9990 chunk 348 optimal weight: 20.0000 chunk 48 optimal weight: 50.0000 chunk 252 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 231 optimal weight: 0.9980 chunk 351 optimal weight: 5.9990 chunk 339 optimal weight: 8.9990 chunk 208 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 320 optimal weight: 20.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS F 216 GLN I 246 GLN ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.123373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065908 restraints weight = 69935.063| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.78 r_work: 0.2745 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 32660 Z= 0.211 Angle : 0.648 37.748 44739 Z= 0.331 Chirality : 0.043 0.473 4966 Planarity : 0.004 0.052 5358 Dihedral : 16.997 175.009 5468 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.97 % Favored : 95.73 % Rotamer: Outliers : 1.85 % Allowed : 11.46 % Favored : 86.69 % 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: -0.04 (0.13), residues: 3679 helix: 1.21 (0.14), residues: 1263 sheet: 0.39 (0.22), residues: 516 loop : -1.02 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 668 TYR 0.013 0.001 TYR H 74 PHE 0.016 0.001 PHE A 163 TRP 0.022 0.001 TRP G 308 HIS 0.013 0.001 HIS I 372 Details of bonding type rmsd covalent geometry : bond 0.00481 (32647) covalent geometry : angle 0.64505 (44721) SS BOND : bond 0.00448 ( 9) SS BOND : angle 3.38035 ( 18) hydrogen bonds : bond 0.04137 ( 1023) hydrogen bonds : angle 4.25699 ( 2802) Misc. bond : bond 0.01038 ( 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 172 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 114 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8594 (tt) REVERT: A 433 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7506 (m-70) REVERT: A 477 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8906 (tm-30) REVERT: A 567 MET cc_start: 0.9528 (ttp) cc_final: 0.9142 (ttp) REVERT: A 592 LEU cc_start: 0.9356 (mt) cc_final: 0.9071 (mt) REVERT: A 593 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8123 (mtm110) REVERT: A 603 MET cc_start: 0.9514 (mmt) cc_final: 0.9015 (mmm) REVERT: A 682 MET cc_start: 0.8324 (ptm) cc_final: 0.8061 (ptm) REVERT: A 692 MET cc_start: 0.9403 (mmm) cc_final: 0.9069 (mmm) REVERT: B 113 GLU cc_start: 0.8718 (mp0) cc_final: 0.8438 (mm-30) REVERT: B 227 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8643 (mmmm) REVERT: B 308 TRP cc_start: 0.8793 (t60) cc_final: 0.8469 (t60) REVERT: B 340 MET cc_start: 0.8801 (mtt) cc_final: 0.8545 (mtt) REVERT: C 153 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: D 58 ASN cc_start: 0.9170 (p0) cc_final: 0.8946 (p0) REVERT: D 74 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8657 (mp0) REVERT: D 303 PHE cc_start: 0.9676 (OUTLIER) cc_final: 0.8778 (t80) REVERT: E 74 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8110 (pt0) REVERT: E 226 ASP cc_start: 0.8889 (p0) cc_final: 0.8652 (p0) REVERT: G 297 GLN cc_start: 0.8345 (mm110) cc_final: 0.7620 (pt0) REVERT: H 5 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6816 (p90) REVERT: H 60 TYR cc_start: 0.7024 (t80) cc_final: 0.6763 (t80) REVERT: I 25 VAL cc_start: 0.0120 (OUTLIER) cc_final: -0.0314 (p) REVERT: I 400 ASP cc_start: 0.8878 (m-30) cc_final: 0.8464 (p0) REVERT: J 23 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7725 (ttt-90) REVERT: J 228 MET cc_start: -0.3488 (mmt) cc_final: -0.3886 (mpp) REVERT: J 307 GLN cc_start: 0.6318 (tm-30) cc_final: 0.5916 (mm-40) outliers start: 58 outliers final: 28 residues processed: 161 average time/residue: 0.5885 time to fit residues: 117.0187 Evaluate side-chains 143 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 26 ASP 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 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 343 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 378 ILE 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 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: 50.0000 chunk 10 optimal weight: 0.6980 chunk 203 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 293 optimal weight: 0.0470 chunk 328 optimal weight: 6.9990 chunk 356 optimal weight: 0.0030 chunk 245 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 overall best weight: 0.9492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS J 389 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.124431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.067411 restraints weight = 69393.684| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.80 r_work: 0.2775 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3357 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= 0.132 Angle : 0.577 13.119 44739 Z= 0.301 Chirality : 0.041 0.354 4966 Planarity : 0.003 0.043 5358 Dihedral : 16.984 175.329 5468 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.78 % Favored : 95.95 % Rotamer: Outliers : 1.69 % Allowed : 12.26 % Favored : 86.05 % 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: 0.18 (0.13), residues: 3679 helix: 1.37 (0.14), residues: 1265 sheet: 0.65 (0.23), residues: 501 loop : -0.90 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 668 TYR 0.013 0.001 TYR H 74 PHE 0.014 0.001 PHE D 332 TRP 0.024 0.001 TRP C 308 HIS 0.009 0.001 HIS I 372 Details of bonding type rmsd covalent geometry : bond 0.00290 (32647) covalent geometry : angle 0.57378 (44721) SS BOND : bond 0.00385 ( 9) SS BOND : angle 3.00648 ( 18) hydrogen bonds : bond 0.03626 ( 1023) hydrogen bonds : angle 4.08918 ( 2802) Misc. bond : bond 0.01014 ( 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 169 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6043 (tpp) REVERT: A 44 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8484 (tt) REVERT: A 433 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7519 (m90) REVERT: A 477 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8870 (tm-30) REVERT: A 567 MET cc_start: 0.9547 (ttp) cc_final: 0.9134 (ttp) REVERT: A 592 LEU cc_start: 0.9368 (mt) cc_final: 0.9069 (mt) REVERT: A 593 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8125 (mtm110) REVERT: A 603 MET cc_start: 0.9508 (mmt) cc_final: 0.9022 (mmm) REVERT: A 639 MET cc_start: 0.9357 (ptt) cc_final: 0.9050 (pmt) REVERT: A 692 MET cc_start: 0.9327 (mmm) cc_final: 0.9013 (mmm) REVERT: B 113 GLU cc_start: 0.8749 (mp0) cc_final: 0.8422 (mm-30) REVERT: B 227 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8676 (mmmm) REVERT: B 308 TRP cc_start: 0.8780 (t60) cc_final: 0.8494 (t60) REVERT: C 153 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: C 285 GLU cc_start: 0.8665 (mp0) cc_final: 0.8278 (mp0) REVERT: D 58 ASN cc_start: 0.9164 (p0) cc_final: 0.8932 (p0) REVERT: D 74 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: D 303 PHE cc_start: 0.9662 (OUTLIER) cc_final: 0.8773 (t80) REVERT: E 62 GLN cc_start: 0.7819 (pp30) cc_final: 0.7307 (pp30) REVERT: E 74 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8029 (pt0) REVERT: E 226 ASP cc_start: 0.8901 (p0) cc_final: 0.8673 (p0) REVERT: G 297 GLN cc_start: 0.8363 (mm110) cc_final: 0.7672 (pt0) REVERT: H 5 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6756 (p90) REVERT: H 60 TYR cc_start: 0.7121 (t80) cc_final: 0.6851 (t80) REVERT: H 186 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8846 (t0) REVERT: I 228 MET cc_start: 0.7619 (pp-130) cc_final: 0.7409 (pp-130) REVERT: I 400 ASP cc_start: 0.8871 (m-30) cc_final: 0.8503 (p0) REVERT: J 142 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: J 228 MET cc_start: -0.3950 (mmt) cc_final: -0.4218 (mpp) REVERT: J 307 GLN cc_start: 0.6514 (tm-30) cc_final: 0.6106 (mm-40) REVERT: J 374 MET cc_start: 0.0456 (tpt) cc_final: 0.0175 (tpt) outliers start: 53 outliers final: 25 residues processed: 158 average time/residue: 0.6105 time to fit residues: 117.7205 Evaluate side-chains 146 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 A residue 593 ARG 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 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 5 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 186 ASN 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 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 62 LEU Chi-restraints excluded: chain J residue 142 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 7.9990 chunk 183 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 344 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 336 optimal weight: 8.9990 chunk 51 optimal weight: 40.0000 chunk 304 optimal weight: 50.0000 chunk 52 optimal weight: 50.0000 chunk 81 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN E 236 GLN 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 ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.121760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064056 restraints weight = 70656.929| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.85 r_work: 0.2686 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 32660 Z= 0.318 Angle : 0.667 14.971 44739 Z= 0.345 Chirality : 0.045 0.449 4966 Planarity : 0.004 0.045 5358 Dihedral : 16.970 173.711 5463 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.08 % Favored : 95.65 % Rotamer: Outliers : 1.92 % Allowed : 12.26 % Favored : 85.82 % 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: 0.00 (0.13), residues: 3679 helix: 1.28 (0.14), residues: 1262 sheet: 0.22 (0.22), residues: 527 loop : -0.95 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 668 TYR 0.015 0.002 TYR C 309 PHE 0.019 0.002 PHE B 332 TRP 0.026 0.002 TRP G 308 HIS 0.009 0.001 HIS I 372 Details of bonding type rmsd covalent geometry : bond 0.00732 (32647) covalent geometry : angle 0.66543 (44721) SS BOND : bond 0.00393 ( 9) SS BOND : angle 2.62994 ( 18) hydrogen bonds : bond 0.04724 ( 1023) hydrogen bonds : angle 4.28957 ( 2802) Misc. bond : bond 0.01453 ( 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 170 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 110 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6005 (tpp) REVERT: A 44 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8502 (tt) REVERT: A 433 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7629 (m-70) REVERT: A 477 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8918 (tm-30) REVERT: A 567 MET cc_start: 0.9544 (ttp) cc_final: 0.9204 (ttp) REVERT: A 593 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8288 (mtm110) REVERT: A 603 MET cc_start: 0.9549 (mmt) cc_final: 0.9113 (mmm) REVERT: A 692 MET cc_start: 0.9433 (mmm) cc_final: 0.9134 (mmm) REVERT: B 113 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8459 (mm-30) REVERT: B 227 LYS cc_start: 0.8935 (mmmt) cc_final: 0.8674 (mmmm) REVERT: B 308 TRP cc_start: 0.8850 (t60) cc_final: 0.8629 (t60) REVERT: C 153 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8587 (tt0) REVERT: C 285 GLU cc_start: 0.8771 (mp0) cc_final: 0.8317 (mp0) REVERT: D 74 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8675 (mp0) REVERT: D 303 PHE cc_start: 0.9720 (OUTLIER) cc_final: 0.8842 (t80) REVERT: E 62 GLN cc_start: 0.7709 (pp30) cc_final: 0.7361 (pp30) REVERT: E 74 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8104 (pt0) REVERT: F 323 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8970 (mppt) REVERT: G 340 MET cc_start: 0.7946 (pmm) cc_final: 0.7464 (ptp) REVERT: H 60 TYR cc_start: 0.6984 (t80) cc_final: 0.6724 (t80) REVERT: I 228 MET cc_start: 0.7659 (pp-130) cc_final: 0.7397 (pp-130) REVERT: I 400 ASP cc_start: 0.8882 (m-30) cc_final: 0.8438 (p0) REVERT: J 23 ARG cc_start: 0.7955 (ttt-90) cc_final: 0.7747 (ptt-90) REVERT: J 142 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: J 228 MET cc_start: -0.3820 (mmt) cc_final: -0.4110 (mpp) REVERT: J 307 GLN cc_start: 0.6516 (tm-30) cc_final: 0.6247 (mm-40) outliers start: 60 outliers final: 28 residues processed: 157 average time/residue: 0.6113 time to fit residues: 117.1591 Evaluate side-chains 144 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 A residue 593 ARG Chi-restraints excluded: chain B residue 113 GLU 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 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 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 323 LYS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 341 PHE 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 265 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 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 I residue 404 MET Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 142 GLU 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: 1.9990 chunk 170 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 313 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN I 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.123611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.065554 restraints weight = 69932.959| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.93 r_work: 0.2759 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32660 Z= 0.142 Angle : 0.585 15.470 44739 Z= 0.303 Chirality : 0.041 0.421 4966 Planarity : 0.003 0.049 5358 Dihedral : 16.995 175.298 5463 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.56 % Favored : 96.19 % Rotamer: Outliers : 1.31 % Allowed : 12.90 % Favored : 85.79 % 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: 0.23 (0.14), residues: 3679 helix: 1.44 (0.15), residues: 1267 sheet: 0.44 (0.23), residues: 516 loop : -0.83 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 668 TYR 0.013 0.001 TYR H 74 PHE 0.017 0.001 PHE F 108 TRP 0.027 0.001 TRP C 308 HIS 0.007 0.001 HIS I 372 Details of bonding type rmsd covalent geometry : bond 0.00317 (32647) covalent geometry : angle 0.58309 (44721) SS BOND : bond 0.00354 ( 9) SS BOND : angle 2.49575 ( 18) hydrogen bonds : bond 0.03679 ( 1023) hydrogen bonds : angle 4.06003 ( 2802) Misc. bond : bond 0.01472 ( 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 154 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6047 (tpp) REVERT: A 44 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8429 (tt) REVERT: A 433 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7433 (m90) REVERT: A 477 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8684 (tm-30) REVERT: A 567 MET cc_start: 0.9462 (ttp) cc_final: 0.9058 (ttp) REVERT: A 592 LEU cc_start: 0.9337 (mt) cc_final: 0.9020 (mt) REVERT: A 593 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8134 (mtm110) REVERT: A 603 MET cc_start: 0.9503 (mmt) cc_final: 0.9001 (mmm) REVERT: A 639 MET cc_start: 0.9271 (ptt) cc_final: 0.8975 (pmt) REVERT: A 692 MET cc_start: 0.9351 (mmm) cc_final: 0.8959 (mmm) REVERT: B 113 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8263 (mm-30) REVERT: B 227 LYS cc_start: 0.8941 (mmmt) cc_final: 0.8673 (mmmm) REVERT: B 308 TRP cc_start: 0.8725 (t60) cc_final: 0.8399 (t60) REVERT: C 153 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: C 285 GLU cc_start: 0.8448 (mp0) cc_final: 0.7984 (mp0) REVERT: D 74 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: D 303 PHE cc_start: 0.9640 (OUTLIER) cc_final: 0.8760 (t80) REVERT: E 62 GLN cc_start: 0.7735 (pp30) cc_final: 0.7297 (pp30) REVERT: E 74 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7694 (pt0) REVERT: G 297 GLN cc_start: 0.8287 (mm110) cc_final: 0.7466 (pt0) REVERT: G 340 MET cc_start: 0.7670 (pmm) cc_final: 0.7325 (OUTLIER) REVERT: I 228 MET cc_start: 0.7745 (pp-130) cc_final: 0.7108 (pp-130) REVERT: I 400 ASP cc_start: 0.8877 (m-30) cc_final: 0.8572 (p0) REVERT: J 173 TYR cc_start: 0.9086 (m-80) cc_final: 0.8824 (m-80) REVERT: J 228 MET cc_start: -0.3999 (mmt) cc_final: -0.4289 (mpp) REVERT: J 374 MET cc_start: 0.0399 (tpt) cc_final: 0.0156 (tpt) outliers start: 41 outliers final: 29 residues processed: 145 average time/residue: 0.6266 time to fit residues: 111.3111 Evaluate side-chains 142 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 A residue 593 ARG Chi-restraints excluded: chain B residue 113 GLU 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 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 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 341 PHE 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 265 VAL Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 368 THR 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 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: 0.6980 chunk 328 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 218 optimal weight: 0.7980 chunk 295 optimal weight: 5.9990 chunk 184 optimal weight: 0.0470 chunk 104 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 HIS ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN J 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.124241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.066113 restraints weight = 69721.499| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.91 r_work: 0.2784 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32660 Z= 0.120 Angle : 0.571 15.553 44739 Z= 0.295 Chirality : 0.041 0.408 4966 Planarity : 0.003 0.053 5358 Dihedral : 16.936 177.370 5463 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.00 % Favored : 95.76 % Rotamer: Outliers : 1.50 % Allowed : 12.84 % Favored : 85.66 % 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: 0.35 (0.14), residues: 3679 helix: 1.54 (0.15), residues: 1267 sheet: 0.55 (0.23), residues: 518 loop : -0.77 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 668 TYR 0.021 0.001 TYR H 60 PHE 0.014 0.001 PHE D 332 TRP 0.037 0.001 TRP G 308 HIS 0.006 0.001 HIS I 372 Details of bonding type rmsd covalent geometry : bond 0.00262 (32647) covalent geometry : angle 0.56953 (44721) SS BOND : bond 0.00350 ( 9) SS BOND : angle 2.30585 ( 18) hydrogen bonds : bond 0.03424 ( 1023) hydrogen bonds : angle 3.94369 ( 2802) Misc. bond : bond 0.01196 ( 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 160 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6121 (tpp) REVERT: A 44 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8338 (mp) REVERT: A 477 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8851 (tm-30) REVERT: A 567 MET cc_start: 0.9526 (ttp) cc_final: 0.9148 (ttp) REVERT: A 592 LEU cc_start: 0.9355 (mt) cc_final: 0.9049 (mt) REVERT: A 593 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8192 (mtm110) REVERT: A 603 MET cc_start: 0.9520 (mmt) cc_final: 0.9036 (mmm) REVERT: A 639 MET cc_start: 0.9356 (ptt) cc_final: 0.9117 (pmt) REVERT: A 692 MET cc_start: 0.9345 (mmm) cc_final: 0.9069 (mmm) REVERT: B 113 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8459 (mm-30) REVERT: B 227 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8662 (mmmm) REVERT: B 308 TRP cc_start: 0.8840 (t60) cc_final: 0.8531 (t60) REVERT: C 153 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: C 285 GLU cc_start: 0.8733 (mp0) cc_final: 0.8288 (mp0) REVERT: D 74 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8538 (mp0) REVERT: D 232 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: D 303 PHE cc_start: 0.9710 (OUTLIER) cc_final: 0.8937 (t80) REVERT: E 62 GLN cc_start: 0.7836 (pp30) cc_final: 0.7392 (pp30) REVERT: E 74 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7935 (pt0) REVERT: E 226 ASP cc_start: 0.9036 (p0) cc_final: 0.8730 (p0) REVERT: G 241 LYS cc_start: 0.9402 (tttt) cc_final: 0.8950 (ttmm) REVERT: G 297 GLN cc_start: 0.8301 (mm110) cc_final: 0.7546 (pt0) REVERT: H 5 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.6707 (p90) REVERT: H 152 MET cc_start: 0.6375 (ppp) cc_final: 0.5858 (ppp) REVERT: I 400 ASP cc_start: 0.8847 (m-30) cc_final: 0.8480 (OUTLIER) REVERT: J 23 ARG cc_start: 0.7753 (ttt-90) cc_final: 0.7551 (ptt-90) REVERT: J 173 TYR cc_start: 0.9099 (m-80) cc_final: 0.8821 (m-80) REVERT: J 228 MET cc_start: -0.4062 (mmt) cc_final: -0.4336 (mpp) outliers start: 47 outliers final: 35 residues processed: 151 average time/residue: 0.6057 time to fit residues: 112.7430 Evaluate side-chains 152 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 593 ARG Chi-restraints excluded: chain B residue 113 GLU 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 153 GLU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 35 ASP 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 340 MET 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 130 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 185 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 368 THR 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 62 LEU Chi-restraints excluded: chain J residue 115 VAL 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: 2.9990 chunk 148 optimal weight: 2.9990 chunk 317 optimal weight: 0.0060 chunk 271 optimal weight: 0.9990 chunk 48 optimal weight: 50.0000 chunk 178 optimal weight: 0.8980 chunk 54 optimal weight: 0.0980 chunk 50 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.124631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.066694 restraints weight = 70112.367| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.95 r_work: 0.2798 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 32660 Z= 0.109 Angle : 0.572 14.911 44739 Z= 0.293 Chirality : 0.041 0.389 4966 Planarity : 0.003 0.054 5358 Dihedral : 16.899 178.116 5463 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 1.25 % Allowed : 13.06 % Favored : 85.70 % 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: 0.43 (0.14), residues: 3679 helix: 1.58 (0.15), residues: 1268 sheet: 0.69 (0.24), residues: 512 loop : -0.73 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 668 TYR 0.013 0.001 TYR H 181 PHE 0.014 0.001 PHE F 108 TRP 0.031 0.001 TRP G 308 HIS 0.007 0.001 HIS F 66 Details of bonding type rmsd covalent geometry : bond 0.00236 (32647) covalent geometry : angle 0.56996 (44721) SS BOND : bond 0.00348 ( 9) SS BOND : angle 2.24266 ( 18) hydrogen bonds : bond 0.03320 ( 1023) hydrogen bonds : angle 3.89940 ( 2802) Misc. bond : bond 0.01113 ( 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 147 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6094 (tpp) REVERT: A 44 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8296 (mp) REVERT: A 184 LEU cc_start: 0.9188 (mt) cc_final: 0.8752 (pt) REVERT: A 477 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8829 (tm-30) REVERT: A 567 MET cc_start: 0.9534 (ttp) cc_final: 0.9155 (ttp) REVERT: A 587 GLN cc_start: 0.9201 (tt0) cc_final: 0.8657 (tp40) REVERT: A 592 LEU cc_start: 0.9372 (mt) cc_final: 0.9093 (mt) REVERT: A 593 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8191 (mtm110) REVERT: A 603 MET cc_start: 0.9508 (mmt) cc_final: 0.9033 (mmm) REVERT: A 639 MET cc_start: 0.9416 (ptt) cc_final: 0.9184 (pmt) REVERT: A 692 MET cc_start: 0.9317 (mmm) cc_final: 0.9054 (mmm) REVERT: B 113 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8486 (mm-30) REVERT: B 227 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8644 (mmmm) REVERT: B 308 TRP cc_start: 0.8833 (t60) cc_final: 0.8485 (t60) REVERT: C 153 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8565 (tt0) REVERT: C 285 GLU cc_start: 0.8740 (mp0) cc_final: 0.8306 (mp0) REVERT: D 74 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: D 232 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: D 303 PHE cc_start: 0.9698 (OUTLIER) cc_final: 0.8889 (t80) REVERT: E 62 GLN cc_start: 0.7864 (pp30) cc_final: 0.7414 (pp30) REVERT: E 74 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7958 (pt0) REVERT: G 241 LYS cc_start: 0.9400 (tttt) cc_final: 0.8948 (ttmm) REVERT: G 297 GLN cc_start: 0.8265 (mm110) cc_final: 0.7536 (pt0) REVERT: G 340 MET cc_start: 0.7837 (pmm) cc_final: 0.7415 (ptp) REVERT: H 5 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6717 (p90) REVERT: H 152 MET cc_start: 0.6017 (ppp) cc_final: 0.5708 (ppp) REVERT: I 228 MET cc_start: 0.7680 (pp-130) cc_final: 0.7230 (pp-130) REVERT: I 400 ASP cc_start: 0.8856 (m-30) cc_final: 0.8496 (OUTLIER) REVERT: J 23 ARG cc_start: 0.7653 (ttt-90) cc_final: 0.7450 (ptt-90) REVERT: J 173 TYR cc_start: 0.9094 (m-80) cc_final: 0.8819 (m-80) REVERT: J 228 MET cc_start: -0.4111 (mmt) cc_final: -0.4384 (mpp) outliers start: 39 outliers final: 28 residues processed: 141 average time/residue: 0.5861 time to fit residues: 101.9554 Evaluate side-chains 143 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 593 ARG Chi-restraints excluded: chain B residue 113 GLU 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 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 98 VAL 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 24 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 368 THR 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 62 LEU 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: 4.9990 chunk 56 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 284 optimal weight: 30.0000 chunk 164 optimal weight: 1.9990 chunk 360 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.124015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.067463 restraints weight = 70689.999| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.21 r_work: 0.2736 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32660 Z= 0.176 Angle : 0.585 14.257 44739 Z= 0.301 Chirality : 0.042 0.379 4966 Planarity : 0.003 0.049 5358 Dihedral : 16.865 176.306 5463 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.94 % Favored : 95.90 % Rotamer: Outliers : 1.34 % Allowed : 13.03 % Favored : 85.63 % 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: 0.42 (0.14), residues: 3679 helix: 1.60 (0.15), residues: 1268 sheet: 0.58 (0.24), residues: 514 loop : -0.72 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 668 TYR 0.015 0.001 TYR I 381 PHE 0.013 0.001 PHE B 332 TRP 0.029 0.001 TRP G 308 HIS 0.006 0.001 HIS F 66 Details of bonding type rmsd covalent geometry : bond 0.00402 (32647) covalent geometry : angle 0.58352 (44721) SS BOND : bond 0.00345 ( 9) SS BOND : angle 2.21663 ( 18) hydrogen bonds : bond 0.03714 ( 1023) hydrogen bonds : angle 3.94512 ( 2802) Misc. bond : bond 0.01083 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19694.97 seconds wall clock time: 333 minutes 47.14 seconds (20027.14 seconds total)