Starting phenix.real_space_refine on Thu May 29 03:01:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gs9_51543/05_2025/9gs9_51543_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gs9_51543/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gs9_51543/05_2025/9gs9_51543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gs9_51543/05_2025/9gs9_51543.map" model { file = "/net/cci-nas-00/data/ceres_data/9gs9_51543/05_2025/9gs9_51543_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gs9_51543/05_2025/9gs9_51543_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ASP:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 15, 'ARG:plan': 10} 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: 17.97, per 1000 atoms: 0.57 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: 8.17 Conformation dependent library (CDL) restraints added in 4.2 seconds 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7138 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 40 sheets defined 36.2% alpha, 8.4% beta 29 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 10.95 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: 10.68 Time building geometry restraints manager: 9.21 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: 2.070 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: 0.030 Extract box with map and model: 1.330 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 74.050 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.450 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (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 TRP 0.017 0.002 TRP D 142 HIS 0.012 0.002 HIS I 372 PHE 0.021 0.002 PHE D 303 TYR 0.021 0.002 TYR G 9 ARG 0.086 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.25252 ( 1023) hydrogen bonds : angle 8.22525 ( 2802) SS BOND : bond 0.37192 ( 9) SS BOND : angle 15.90038 ( 18) covalent geometry : bond 0.01507 (32647) covalent geometry : angle 1.82420 (44721) 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 : 3.491 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: 1.3418 time to fit residues: 602.0808 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 : 3.486 ------------------------------------------------------------------------------- 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 319 optimal weight: 10.0000 chunk 286 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 296 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 180 optimal weight: 0.6980 chunk 220 optimal weight: 20.0000 chunk 343 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 115 ASN A 674 ASN B 93 GLN C 67 ASN C 83 HIS C 93 GLN C 225 ASN D 66 HIS D 93 GLN D 315 ASN E 83 HIS E 93 GLN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN F 216 GLN G 321 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS H 79 GLN H 166 GLN I 52 HIS I 168 ASN ** J 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 GLN J 253 ASN J 367 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.126307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067638 restraints weight = 69560.235| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.90 r_work: 0.2789 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 32660 Z= 0.167 Angle : 0.729 21.894 44739 Z= 0.384 Chirality : 0.044 0.363 4966 Planarity : 0.004 0.049 5358 Dihedral : 17.419 179.533 5499 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.72 % Favored : 95.81 % Rotamer: Outliers : 2.23 % Allowed : 9.04 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.67 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3679 helix: 0.22 (0.14), residues: 1259 sheet: 0.05 (0.21), residues: 537 loop : -1.45 (0.13), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 308 HIS 0.034 0.002 HIS I 372 PHE 0.038 0.002 PHE J 29 TYR 0.011 0.001 TYR J 358 ARG 0.008 0.000 ARG J 61 Details of bonding type rmsd hydrogen bonds : bond 0.05098 ( 1023) hydrogen bonds : angle 4.84601 ( 2802) SS BOND : bond 0.01434 ( 9) SS BOND : angle 3.89013 ( 18) covalent geometry : bond 0.00362 (32647) covalent geometry : angle 0.72455 (44721) Misc. bond : bond 0.00802 ( 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 237 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 167 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8598 (tt) REVERT: A 147 TRP cc_start: 0.8678 (p90) cc_final: 0.8313 (p-90) REVERT: A 477 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8856 (tm-30) REVERT: A 567 MET cc_start: 0.9536 (ttp) cc_final: 0.9288 (ttp) REVERT: A 592 LEU cc_start: 0.9291 (mt) cc_final: 0.8922 (mt) REVERT: A 593 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7819 (mtm110) REVERT: A 682 MET cc_start: 0.8280 (ptm) cc_final: 0.8050 (ptm) REVERT: A 692 MET cc_start: 0.9351 (mmm) cc_final: 0.8957 (mmm) REVERT: B 340 MET cc_start: 0.9250 (mtm) cc_final: 0.9046 (mtm) REVERT: D 74 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: D 340 MET cc_start: 0.8610 (mtp) cc_final: 0.8380 (mtp) REVERT: E 74 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7967 (pt0) REVERT: G 236 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8441 (mt0) REVERT: G 297 GLN cc_start: 0.7895 (mm110) cc_final: 0.6984 (pt0) REVERT: H 5 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.7102 (p90) REVERT: I 25 VAL cc_start: 0.0596 (OUTLIER) cc_final: 0.0118 (p) REVERT: I 400 ASP cc_start: 0.8822 (m-30) cc_final: 0.8372 (p0) REVERT: J 46 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: J 162 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7342 (tp-100) REVERT: J 368 THR cc_start: 0.3232 (OUTLIER) cc_final: 0.2904 (p) REVERT: J 378 ILE cc_start: -0.0530 (OUTLIER) cc_final: -0.0836 (tt) outliers start: 70 outliers final: 22 residues processed: 221 average time/residue: 1.2251 time to fit residues: 330.6828 Evaluate side-chains 147 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 3.302 ------------------------------------------------------------------------------- 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 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 236 GLN Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 185 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 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 213 LEU Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 THR Chi-restraints excluded: chain J residue 378 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 145 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 37 optimal weight: 30.0000 chunk 340 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN C 321 ASN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN F 216 GLN G 83 HIS ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS I 66 HIS I 253 ASN I 389 HIS ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.125063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.066813 restraints weight = 69775.116| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.89 r_work: 0.2770 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 32660 Z= 0.163 Angle : 0.651 16.126 44739 Z= 0.341 Chirality : 0.043 0.550 4966 Planarity : 0.004 0.055 5358 Dihedral : 17.144 179.324 5478 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.78 % Favored : 95.79 % Rotamer: Outliers : 2.20 % Allowed : 9.90 % Favored : 87.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.67 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 3679 helix: 0.79 (0.14), residues: 1261 sheet: 0.32 (0.21), residues: 539 loop : -1.22 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 308 HIS 0.016 0.001 HIS I 372 PHE 0.015 0.001 PHE A 163 TYR 0.024 0.001 TYR H 181 ARG 0.005 0.000 ARG A 668 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 1023) hydrogen bonds : angle 4.46662 ( 2802) SS BOND : bond 0.00727 ( 9) SS BOND : angle 2.14874 ( 18) covalent geometry : bond 0.00360 (32647) covalent geometry : angle 0.65013 (44721) Misc. bond : bond 0.01011 ( 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 204 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 135 time to evaluate : 3.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8659 (tt) REVERT: A 147 TRP cc_start: 0.8649 (p90) cc_final: 0.8202 (p-90) REVERT: A 433 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7436 (m-70) REVERT: A 477 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8905 (tm-30) REVERT: A 567 MET cc_start: 0.9548 (ttp) cc_final: 0.9197 (ttp) REVERT: A 592 LEU cc_start: 0.9345 (mt) cc_final: 0.9081 (mt) REVERT: A 603 MET cc_start: 0.9446 (mmt) cc_final: 0.8954 (mmm) REVERT: A 639 MET cc_start: 0.9346 (ptt) cc_final: 0.9006 (pmt) REVERT: A 668 ARG cc_start: 0.9038 (mmm-85) cc_final: 0.8746 (tpp80) REVERT: A 682 MET cc_start: 0.8314 (ptm) cc_final: 0.8021 (ptm) REVERT: A 692 MET cc_start: 0.9322 (mmm) cc_final: 0.8988 (mmm) REVERT: B 113 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8496 (mm-30) REVERT: B 227 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8568 (mmmm) REVERT: B 308 TRP cc_start: 0.8669 (t60) cc_final: 0.8343 (t60) REVERT: B 340 MET cc_start: 0.9298 (mtm) cc_final: 0.8941 (mtm) REVERT: C 153 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: D 58 ASN cc_start: 0.9113 (p0) cc_final: 0.8881 (p0) REVERT: D 74 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: D 340 MET cc_start: 0.8946 (mtp) cc_final: 0.8744 (mtp) REVERT: E 62 GLN cc_start: 0.7785 (pp30) cc_final: 0.7569 (pp30) REVERT: E 74 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8056 (pt0) REVERT: E 226 ASP cc_start: 0.8902 (p0) cc_final: 0.8685 (p0) REVERT: G 236 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8429 (mt0) REVERT: G 297 GLN cc_start: 0.8004 (mm110) cc_final: 0.7092 (pt0) REVERT: G 340 MET cc_start: 0.7453 (ptp) cc_final: 0.7243 (ptp) REVERT: H 5 TYR cc_start: 0.7231 (p90) cc_final: 0.6803 (p90) REVERT: H 186 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.8841 (t0) REVERT: I 25 VAL cc_start: 0.1214 (OUTLIER) cc_final: 0.0733 (p) REVERT: I 228 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6847 (ppp) REVERT: I 400 ASP cc_start: 0.8859 (m-30) cc_final: 0.8453 (OUTLIER) REVERT: J 228 MET cc_start: -0.3309 (mmt) cc_final: -0.3707 (mpp) REVERT: J 307 GLN cc_start: 0.6731 (tm-30) cc_final: 0.6123 (mm-40) outliers start: 69 outliers final: 28 residues processed: 186 average time/residue: 1.2329 time to fit residues: 281.2279 Evaluate side-chains 153 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 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 249 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 121 CYS Chi-restraints excluded: chain G residue 236 GLN 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 265 VAL Chi-restraints excluded: chain I residue 279 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 160 LYS Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 357 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 279 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 281 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 313 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 345 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 438 HIS D 298 ASN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN G 342 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 ASN I 246 GLN ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.122168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064105 restraints weight = 70431.491| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.84 r_work: 0.2689 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 32660 Z= 0.337 Angle : 0.702 13.826 44739 Z= 0.368 Chirality : 0.047 0.455 4966 Planarity : 0.004 0.043 5358 Dihedral : 17.082 175.549 5471 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.94 % Favored : 95.71 % Rotamer: Outliers : 2.01 % Allowed : 11.14 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 3679 helix: 0.93 (0.14), residues: 1263 sheet: 0.24 (0.22), residues: 512 loop : -1.18 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 308 HIS 0.031 0.002 HIS F 66 PHE 0.019 0.002 PHE B 332 TYR 0.015 0.002 TYR H 60 ARG 0.007 0.001 ARG D 87 Details of bonding type rmsd hydrogen bonds : bond 0.05032 ( 1023) hydrogen bonds : angle 4.50444 ( 2802) SS BOND : bond 0.00502 ( 9) SS BOND : angle 3.45516 ( 18) covalent geometry : bond 0.00769 (32647) covalent geometry : angle 0.69859 (44721) Misc. bond : bond 0.01284 ( 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 177 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 114 time to evaluate : 4.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8593 (tt) REVERT: A 433 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7508 (m-70) REVERT: A 477 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8926 (tm-30) REVERT: A 567 MET cc_start: 0.9542 (ttp) cc_final: 0.9196 (ttp) REVERT: A 592 LEU cc_start: 0.9361 (mt) cc_final: 0.9142 (mt) REVERT: A 603 MET cc_start: 0.9459 (mmt) cc_final: 0.9011 (mmm) REVERT: A 668 ARG cc_start: 0.9096 (mmm-85) cc_final: 0.8812 (tpp80) REVERT: A 682 MET cc_start: 0.8406 (ptm) cc_final: 0.8163 (ptm) REVERT: A 692 MET cc_start: 0.9432 (mmm) cc_final: 0.9029 (mmm) REVERT: B 113 GLU cc_start: 0.8783 (mp0) cc_final: 0.8528 (mm-30) REVERT: B 227 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8633 (mmmm) REVERT: B 308 TRP cc_start: 0.8810 (t60) cc_final: 0.8609 (t60) REVERT: B 340 MET cc_start: 0.9371 (mtm) cc_final: 0.8971 (mtm) REVERT: C 153 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: D 74 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8659 (mp0) REVERT: E 35 ASP cc_start: 0.8855 (p0) cc_final: 0.8569 (p0) REVERT: E 74 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8054 (pt0) REVERT: E 226 ASP cc_start: 0.8899 (p0) cc_final: 0.8647 (p0) REVERT: H 60 TYR cc_start: 0.6935 (t80) cc_final: 0.6713 (t80) REVERT: I 25 VAL cc_start: 0.1095 (OUTLIER) cc_final: 0.0605 (p) REVERT: I 400 ASP cc_start: 0.8898 (m-30) cc_final: 0.8496 (p0) REVERT: J 47 LEU cc_start: 0.8425 (mt) cc_final: 0.8127 (mp) REVERT: J 142 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7402 (pm20) REVERT: J 228 MET cc_start: -0.3195 (mmt) cc_final: -0.3627 (mpp) REVERT: J 307 GLN cc_start: 0.6573 (tm-30) cc_final: 0.6025 (mm-40) outliers start: 63 outliers final: 26 residues processed: 164 average time/residue: 1.2775 time to fit residues: 257.0397 Evaluate side-chains 138 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain 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 341 PHE 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 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 142 GLU Chi-restraints excluded: chain J residue 160 LYS 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 70 optimal weight: 0.8980 chunk 303 optimal weight: 0.2980 chunk 368 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 170 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 334 optimal weight: 9.9990 chunk 221 optimal weight: 0.0970 chunk 86 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 ** I 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 379 ASN J 52 HIS ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.124971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.067646 restraints weight = 69546.372| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.82 r_work: 0.2779 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 32660 Z= 0.116 Angle : 0.591 13.032 44739 Z= 0.309 Chirality : 0.041 0.376 4966 Planarity : 0.003 0.043 5358 Dihedral : 17.046 175.735 5468 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.64 % Favored : 96.00 % Rotamer: Outliers : 1.56 % Allowed : 11.88 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.13), residues: 3679 helix: 1.21 (0.14), residues: 1263 sheet: 0.49 (0.22), residues: 513 loop : -0.97 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 308 HIS 0.029 0.001 HIS F 66 PHE 0.015 0.001 PHE D 332 TYR 0.015 0.001 TYR H 74 ARG 0.003 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 1023) hydrogen bonds : angle 4.18100 ( 2802) SS BOND : bond 0.00485 ( 9) SS BOND : angle 3.46708 ( 18) covalent geometry : bond 0.00246 (32647) covalent geometry : angle 0.58698 (44721) Misc. bond : bond 0.00893 ( 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 170 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8605 (tt) REVERT: A 433 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7525 (m-70) REVERT: A 477 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8903 (tm-30) REVERT: A 567 MET cc_start: 0.9528 (ttp) cc_final: 0.9147 (ttp) REVERT: A 592 LEU cc_start: 0.9357 (mt) cc_final: 0.9129 (mt) REVERT: A 603 MET cc_start: 0.9494 (mmt) cc_final: 0.9052 (mmm) REVERT: A 639 MET cc_start: 0.9358 (ptt) cc_final: 0.9048 (pmt) REVERT: A 668 ARG cc_start: 0.9091 (mmm-85) cc_final: 0.8826 (tpp80) REVERT: A 682 MET cc_start: 0.8276 (ptm) cc_final: 0.8016 (ptm) REVERT: A 692 MET cc_start: 0.9396 (mmm) cc_final: 0.9044 (mmm) REVERT: B 113 GLU cc_start: 0.8809 (mp0) cc_final: 0.8514 (mm-30) REVERT: B 308 TRP cc_start: 0.8712 (t60) cc_final: 0.8380 (t60) REVERT: B 340 MET cc_start: 0.9325 (mtm) cc_final: 0.8963 (mtm) REVERT: C 153 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: D 74 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8474 (mp0) REVERT: D 303 PHE cc_start: 0.9661 (OUTLIER) cc_final: 0.8759 (t80) REVERT: E 74 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8012 (pt0) REVERT: E 226 ASP cc_start: 0.8906 (p0) cc_final: 0.8659 (p0) REVERT: G 297 GLN cc_start: 0.8282 (mm110) cc_final: 0.7354 (pt0) REVERT: H 5 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.6846 (p90) REVERT: H 60 TYR cc_start: 0.7003 (t80) cc_final: 0.6773 (t80) REVERT: I 25 VAL cc_start: 0.0324 (OUTLIER) cc_final: -0.0100 (p) REVERT: I 228 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7231 (pp-130) REVERT: I 400 ASP cc_start: 0.8866 (m-30) cc_final: 0.8460 (p0) REVERT: J 23 ARG cc_start: 0.7900 (ttp-110) cc_final: 0.7383 (ptm160) REVERT: J 43 GLU cc_start: 0.9184 (tp30) cc_final: 0.8952 (tp30) REVERT: J 47 LEU cc_start: 0.8349 (mt) cc_final: 0.8128 (mp) REVERT: J 228 MET cc_start: -0.3555 (mmt) cc_final: -0.3971 (mpp) REVERT: J 307 GLN cc_start: 0.6429 (tm-30) cc_final: 0.5928 (mm-40) outliers start: 49 outliers final: 23 residues processed: 160 average time/residue: 1.2055 time to fit residues: 238.8455 Evaluate side-chains 147 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 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 62 LEU Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 37 optimal weight: 0.0020 chunk 312 optimal weight: 20.0000 chunk 159 optimal weight: 2.9990 chunk 228 optimal weight: 0.0980 chunk 332 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 374 optimal weight: 0.0870 chunk 354 optimal weight: 20.0000 chunk 48 optimal weight: 50.0000 chunk 91 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 overall best weight: 1.2370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 GLN G 319 ASN ** G 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 379 ASN ** 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 = 0.4052 r_free = 0.4052 target = 0.124381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066938 restraints weight = 70257.854| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.82 r_work: 0.2755 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 32660 Z= 0.147 Angle : 0.580 12.287 44739 Z= 0.303 Chirality : 0.041 0.366 4966 Planarity : 0.003 0.044 5358 Dihedral : 16.997 174.845 5468 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.02 % Favored : 95.73 % Rotamer: Outliers : 1.82 % Allowed : 11.94 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 3679 helix: 1.36 (0.14), residues: 1265 sheet: 0.53 (0.23), residues: 516 loop : -0.91 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 308 HIS 0.035 0.001 HIS F 66 PHE 0.014 0.001 PHE B 332 TYR 0.014 0.001 TYR H 74 ARG 0.005 0.000 ARG I 371 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 1023) hydrogen bonds : angle 4.08123 ( 2802) SS BOND : bond 0.00454 ( 9) SS BOND : angle 2.88721 ( 18) covalent geometry : bond 0.00329 (32647) covalent geometry : angle 0.57694 (44721) Misc. bond : bond 0.01132 ( 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 179 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 4.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8540 (tt) REVERT: A 433 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7521 (m-70) REVERT: A 477 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8929 (tm-30) REVERT: A 567 MET cc_start: 0.9546 (ttp) cc_final: 0.9131 (ttp) REVERT: A 592 LEU cc_start: 0.9338 (mt) cc_final: 0.9127 (mt) REVERT: A 603 MET cc_start: 0.9496 (mmt) cc_final: 0.9012 (mmm) REVERT: A 639 MET cc_start: 0.9357 (ptt) cc_final: 0.9032 (pmt) REVERT: A 668 ARG cc_start: 0.9108 (mmm-85) cc_final: 0.8822 (tpp80) REVERT: A 692 MET cc_start: 0.9352 (mmm) cc_final: 0.9041 (mmm) REVERT: B 113 GLU cc_start: 0.8764 (mp0) cc_final: 0.8456 (mm-30) REVERT: B 308 TRP cc_start: 0.8767 (t60) cc_final: 0.8450 (t60) REVERT: B 340 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.8960 (mtm) REVERT: C 153 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: D 74 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8626 (mp0) REVERT: D 303 PHE cc_start: 0.9656 (OUTLIER) cc_final: 0.8800 (t80) REVERT: E 74 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8044 (pt0) REVERT: E 226 ASP cc_start: 0.8926 (p0) cc_final: 0.8703 (p0) REVERT: F 323 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8801 (mppt) REVERT: G 297 GLN cc_start: 0.8314 (mm110) cc_final: 0.7470 (pt0) REVERT: H 5 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6818 (p90) REVERT: H 60 TYR cc_start: 0.7058 (t80) cc_final: 0.6748 (t80) REVERT: H 186 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8641 (t0) REVERT: I 228 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7436 (pp-130) REVERT: I 279 MET cc_start: 0.7260 (tpt) cc_final: 0.6865 (mtm) REVERT: I 400 ASP cc_start: 0.8817 (m-30) cc_final: 0.8473 (p0) REVERT: J 43 GLU cc_start: 0.9215 (tp30) cc_final: 0.8955 (tp30) REVERT: J 47 LEU cc_start: 0.8409 (mt) cc_final: 0.8142 (mp) REVERT: J 228 MET cc_start: -0.3793 (mmt) cc_final: -0.4213 (mpp) REVERT: J 307 GLN cc_start: 0.6302 (tm-30) cc_final: 0.5914 (mm-40) outliers start: 57 outliers final: 28 residues processed: 166 average time/residue: 1.2029 time to fit residues: 247.0208 Evaluate side-chains 152 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 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 228 MET Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 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 406 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 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 74 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 295 optimal weight: 20.0000 chunk 266 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 170 optimal weight: 0.0030 overall best weight: 1.7996 ------------------------------------------------------------------------------- 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** F 216 GLN ** G 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 379 ASN ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 389 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.123572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.066233 restraints weight = 70173.400| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.79 r_work: 0.2739 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32660 Z= 0.181 Angle : 0.589 17.092 44739 Z= 0.307 Chirality : 0.042 0.379 4966 Planarity : 0.003 0.043 5358 Dihedral : 16.974 174.695 5463 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.00 % Favored : 95.76 % Rotamer: Outliers : 1.69 % Allowed : 12.32 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3679 helix: 1.43 (0.14), residues: 1265 sheet: 0.55 (0.23), residues: 507 loop : -0.86 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 308 HIS 0.043 0.001 HIS F 66 PHE 0.015 0.001 PHE A 163 TYR 0.013 0.001 TYR H 74 ARG 0.003 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 1023) hydrogen bonds : angle 4.06831 ( 2802) SS BOND : bond 0.00341 ( 9) SS BOND : angle 2.44196 ( 18) covalent geometry : bond 0.00410 (32647) covalent geometry : angle 0.58745 (44721) Misc. bond : bond 0.00858 ( 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 174 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 4.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.5972 (tpp) REVERT: A 44 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8487 (tt) REVERT: A 238 GLU cc_start: 0.8958 (tt0) cc_final: 0.8370 (tm-30) REVERT: A 433 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7537 (m-70) REVERT: A 477 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8942 (tm-30) REVERT: A 567 MET cc_start: 0.9550 (ttp) cc_final: 0.9172 (ttp) REVERT: A 603 MET cc_start: 0.9506 (mmt) cc_final: 0.9000 (mmm) REVERT: A 668 ARG cc_start: 0.9109 (mmm-85) cc_final: 0.8826 (tpp80) REVERT: A 692 MET cc_start: 0.9402 (mmm) cc_final: 0.9073 (mmm) REVERT: B 113 GLU cc_start: 0.8779 (mp0) cc_final: 0.8476 (mm-30) REVERT: B 308 TRP cc_start: 0.8807 (t60) cc_final: 0.8495 (t60) REVERT: B 340 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8989 (mtm) REVERT: C 153 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: D 74 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8642 (mp0) REVERT: D 303 PHE cc_start: 0.9657 (OUTLIER) cc_final: 0.8819 (t80) REVERT: E 62 GLN cc_start: 0.7854 (pp30) cc_final: 0.7534 (pp30) REVERT: E 74 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8062 (pt0) REVERT: F 323 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8804 (mppt) REVERT: H 5 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6819 (p90) REVERT: H 60 TYR cc_start: 0.7144 (t80) cc_final: 0.6878 (t80) REVERT: H 186 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8656 (t0) REVERT: I 228 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7203 (pp-130) REVERT: I 279 MET cc_start: 0.7309 (tpt) cc_final: 0.6895 (mtm) REVERT: I 400 ASP cc_start: 0.8833 (m-30) cc_final: 0.8493 (p0) REVERT: J 23 ARG cc_start: 0.7878 (ttt-90) cc_final: 0.7597 (ptt-90) REVERT: J 43 GLU cc_start: 0.9217 (tp30) cc_final: 0.8922 (tp30) REVERT: J 47 LEU cc_start: 0.8345 (mt) cc_final: 0.7988 (mp) REVERT: J 173 TYR cc_start: 0.9085 (m-80) cc_final: 0.8803 (m-80) REVERT: J 228 MET cc_start: -0.4023 (mmt) cc_final: -0.4370 (mpp) REVERT: J 307 GLN cc_start: 0.6502 (tm-30) cc_final: 0.6096 (mm-40) outliers start: 53 outliers final: 29 residues processed: 162 average time/residue: 1.4025 time to fit residues: 279.2412 Evaluate side-chains 152 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 340 MET 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 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 228 MET Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 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 406 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 79 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 364 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 chunk 377 optimal weight: 9.9990 chunk 251 optimal weight: 0.0470 chunk 23 optimal weight: 0.0070 chunk 201 optimal weight: 0.8980 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 236 GLN F 216 GLN G 342 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 372 HIS ** 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 = 0.4054 r_free = 0.4054 target = 0.124556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.067548 restraints weight = 69991.414| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.84 r_work: 0.2784 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 32660 Z= 0.130 Angle : 0.575 17.893 44739 Z= 0.298 Chirality : 0.041 0.350 4966 Planarity : 0.003 0.045 5358 Dihedral : 16.978 176.317 5463 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.75 % Favored : 96.03 % Rotamer: Outliers : 1.56 % Allowed : 12.80 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3679 helix: 1.50 (0.14), residues: 1265 sheet: 0.71 (0.23), residues: 505 loop : -0.81 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 308 HIS 0.059 0.001 HIS F 66 PHE 0.018 0.001 PHE F 108 TYR 0.013 0.001 TYR H 74 ARG 0.003 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 1023) hydrogen bonds : angle 3.95304 ( 2802) SS BOND : bond 0.00294 ( 9) SS BOND : angle 2.11395 ( 18) covalent geometry : bond 0.00285 (32647) covalent geometry : angle 0.57342 (44721) Misc. bond : bond 0.01379 ( 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 169 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 120 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7361 (mtp) cc_final: 0.6170 (tpp) REVERT: A 44 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8479 (tt) REVERT: A 238 GLU cc_start: 0.8809 (tt0) cc_final: 0.8413 (tm-30) REVERT: A 433 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7527 (m-70) REVERT: A 477 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8871 (tm-30) REVERT: A 567 MET cc_start: 0.9556 (ttp) cc_final: 0.9155 (ttp) REVERT: A 587 GLN cc_start: 0.9232 (tt0) cc_final: 0.8690 (tp40) REVERT: A 603 MET cc_start: 0.9497 (mmt) cc_final: 0.9005 (mmm) REVERT: A 639 MET cc_start: 0.9360 (ptt) cc_final: 0.9051 (pmt) REVERT: A 668 ARG cc_start: 0.9090 (mmm-85) cc_final: 0.8768 (tpp80) REVERT: A 692 MET cc_start: 0.9371 (mmm) cc_final: 0.9044 (mmm) REVERT: B 113 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8399 (mm-30) REVERT: B 227 LYS cc_start: 0.8609 (mtmp) cc_final: 0.8097 (ptpp) REVERT: B 308 TRP cc_start: 0.8796 (t60) cc_final: 0.8479 (t60) REVERT: B 321 ASN cc_start: 0.8725 (p0) cc_final: 0.8482 (p0) REVERT: B 340 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.9044 (mtm) REVERT: C 153 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: D 74 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8536 (mp0) REVERT: D 232 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: D 303 PHE cc_start: 0.9654 (OUTLIER) cc_final: 0.8831 (t80) REVERT: E 62 GLN cc_start: 0.7727 (pp30) cc_final: 0.7419 (pp30) REVERT: E 74 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8032 (pt0) REVERT: E 226 ASP cc_start: 0.9050 (p0) cc_final: 0.8429 (p0) REVERT: F 323 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8832 (mppt) REVERT: G 297 GLN cc_start: 0.8239 (mm110) cc_final: 0.7427 (pt0) REVERT: H 5 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6783 (p90) REVERT: H 60 TYR cc_start: 0.7130 (t80) cc_final: 0.6891 (t80) REVERT: I 228 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7641 (pp-130) REVERT: I 279 MET cc_start: 0.7335 (tpt) cc_final: 0.6911 (mtm) REVERT: I 400 ASP cc_start: 0.8894 (m-30) cc_final: 0.8592 (p0) REVERT: J 43 GLU cc_start: 0.9220 (tp30) cc_final: 0.8908 (tp30) REVERT: J 47 LEU cc_start: 0.8389 (mt) cc_final: 0.7990 (mp) REVERT: J 173 TYR cc_start: 0.9094 (m-80) cc_final: 0.8808 (m-80) REVERT: J 228 MET cc_start: -0.4170 (mmt) cc_final: -0.4513 (mpp) REVERT: J 307 GLN cc_start: 0.6494 (tm-30) cc_final: 0.6090 (mm-40) outliers start: 49 outliers final: 29 residues processed: 159 average time/residue: 1.2654 time to fit residues: 247.5140 Evaluate side-chains 148 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 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 260 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 342 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 332 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 285 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.123262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064834 restraints weight = 69831.479| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.87 r_work: 0.2744 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32660 Z= 0.196 Angle : 0.601 14.611 44739 Z= 0.313 Chirality : 0.042 0.394 4966 Planarity : 0.004 0.048 5358 Dihedral : 16.942 174.674 5463 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.08 % Favored : 95.73 % Rotamer: Outliers : 1.56 % Allowed : 12.96 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3679 helix: 1.53 (0.14), residues: 1267 sheet: 0.57 (0.23), residues: 507 loop : -0.77 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP G 308 HIS 0.066 0.001 HIS F 66 PHE 0.015 0.001 PHE B 332 TYR 0.013 0.001 TYR G 219 ARG 0.003 0.000 ARG D 87 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 1023) hydrogen bonds : angle 3.99329 ( 2802) SS BOND : bond 0.00319 ( 9) SS BOND : angle 2.07984 ( 18) covalent geometry : bond 0.00446 (32647) covalent geometry : angle 0.60013 (44721) Misc. bond : bond 0.01164 ( 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 162 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6102 (tpp) REVERT: A 44 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8462 (tt) REVERT: A 238 GLU cc_start: 0.8850 (tt0) cc_final: 0.8314 (tm-30) REVERT: A 433 HIS cc_start: 0.8143 (OUTLIER) cc_final: 0.7573 (m-70) REVERT: A 477 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8815 (tm-30) REVERT: A 567 MET cc_start: 0.9545 (ttp) cc_final: 0.9182 (ttp) REVERT: A 587 GLN cc_start: 0.9273 (tt0) cc_final: 0.8702 (tp40) REVERT: A 603 MET cc_start: 0.9520 (mmt) cc_final: 0.9041 (mmm) REVERT: A 692 MET cc_start: 0.9395 (mmm) cc_final: 0.9084 (mmm) REVERT: B 113 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8477 (mm-30) REVERT: B 227 LYS cc_start: 0.8765 (mtmp) cc_final: 0.8439 (mtmp) REVERT: B 308 TRP cc_start: 0.8842 (t60) cc_final: 0.8491 (t60) REVERT: B 340 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.9007 (mtm) REVERT: C 153 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: D 74 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8653 (mp0) REVERT: D 232 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: D 303 PHE cc_start: 0.9712 (OUTLIER) cc_final: 0.8896 (t80) REVERT: E 62 GLN cc_start: 0.7655 (pp30) cc_final: 0.7301 (pp30) REVERT: E 74 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8036 (pt0) REVERT: F 323 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8958 (mppt) REVERT: H 5 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6848 (p90) REVERT: H 60 TYR cc_start: 0.7032 (t80) cc_final: 0.6820 (t80) REVERT: H 186 ASN cc_start: 0.8936 (t0) cc_final: 0.8735 (t0) REVERT: I 228 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7640 (pp-130) REVERT: I 279 MET cc_start: 0.7319 (tpt) cc_final: 0.6934 (mtm) REVERT: I 400 ASP cc_start: 0.8824 (m-30) cc_final: 0.8495 (p0) REVERT: J 23 ARG cc_start: 0.7772 (ttt-90) cc_final: 0.7565 (ptt-90) REVERT: J 43 GLU cc_start: 0.9272 (tp30) cc_final: 0.8943 (tp30) REVERT: J 47 LEU cc_start: 0.8397 (mt) cc_final: 0.8023 (mp) REVERT: J 173 TYR cc_start: 0.9091 (m-80) cc_final: 0.8822 (m-80) REVERT: J 228 MET cc_start: -0.4161 (mmt) cc_final: -0.4499 (mpp) REVERT: J 307 GLN cc_start: 0.6375 (tm-30) cc_final: 0.5983 (mm-40) outliers start: 49 outliers final: 33 residues processed: 152 average time/residue: 1.1539 time to fit residues: 217.4230 Evaluate side-chains 155 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 3.341 ------------------------------------------------------------------------------- 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 566 VAL 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 B residue 340 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 153 GLU 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 249 VAL Chi-restraints excluded: chain E residue 317 ILE 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 323 LYS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 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 404 MET 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 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 201 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 356 optimal weight: 8.9990 chunk 332 optimal weight: 30.0000 chunk 135 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 368 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 284 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.122923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.064463 restraints weight = 70424.087| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.91 r_work: 0.2735 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 32660 Z= 0.223 Angle : 0.605 13.079 44739 Z= 0.314 Chirality : 0.042 0.403 4966 Planarity : 0.004 0.042 5358 Dihedral : 16.936 174.500 5463 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.71 % Rotamer: Outliers : 1.44 % Allowed : 13.28 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3679 helix: 1.50 (0.14), residues: 1267 sheet: 0.53 (0.23), residues: 507 loop : -0.78 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 308 HIS 0.045 0.001 HIS F 66 PHE 0.016 0.001 PHE B 332 TYR 0.018 0.001 TYR I 381 ARG 0.004 0.000 ARG D 87 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 1023) hydrogen bonds : angle 4.01869 ( 2802) SS BOND : bond 0.00324 ( 9) SS BOND : angle 2.02968 ( 18) covalent geometry : bond 0.00511 (32647) covalent geometry : angle 0.60414 (44721) Misc. bond : bond 0.00978 ( 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 152 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6019 (tpp) REVERT: A 44 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8330 (mp) REVERT: A 238 GLU cc_start: 0.8824 (tt0) cc_final: 0.8399 (tm-30) REVERT: A 433 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7604 (m-70) REVERT: A 477 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8847 (tm-30) REVERT: A 567 MET cc_start: 0.9520 (ttp) cc_final: 0.9150 (ttp) REVERT: A 587 GLN cc_start: 0.9303 (tt0) cc_final: 0.8734 (tp40) REVERT: A 603 MET cc_start: 0.9539 (mmt) cc_final: 0.9058 (mmm) REVERT: A 692 MET cc_start: 0.9407 (mmm) cc_final: 0.9092 (mmm) REVERT: B 113 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8489 (mm-30) REVERT: B 227 LYS cc_start: 0.8753 (mtmp) cc_final: 0.8551 (mtmp) REVERT: B 308 TRP cc_start: 0.8847 (t60) cc_final: 0.8501 (t60) REVERT: B 340 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.8981 (mtm) REVERT: C 153 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: C 285 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8464 (mp0) REVERT: D 74 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8626 (mp0) REVERT: D 232 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: D 303 PHE cc_start: 0.9709 (OUTLIER) cc_final: 0.8893 (t80) REVERT: E 62 GLN cc_start: 0.7689 (pp30) cc_final: 0.7322 (pp30) REVERT: E 74 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8024 (pt0) REVERT: E 226 ASP cc_start: 0.9186 (p0) cc_final: 0.8901 (p0) REVERT: F 323 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8972 (mppt) REVERT: H 5 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.6937 (p90) REVERT: H 60 TYR cc_start: 0.6942 (t80) cc_final: 0.6703 (t80) REVERT: H 152 MET cc_start: 0.5592 (ppp) cc_final: 0.5335 (ppp) REVERT: I 228 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7693 (pp-130) REVERT: I 279 MET cc_start: 0.7352 (tpt) cc_final: 0.6924 (mtm) REVERT: I 400 ASP cc_start: 0.8849 (m-30) cc_final: 0.8532 (p0) REVERT: J 23 ARG cc_start: 0.7684 (ttt-90) cc_final: 0.7465 (ptt-90) REVERT: J 43 GLU cc_start: 0.9249 (tp30) cc_final: 0.8937 (tp30) REVERT: J 47 LEU cc_start: 0.8463 (mt) cc_final: 0.8069 (mp) REVERT: J 173 TYR cc_start: 0.9124 (m-80) cc_final: 0.8867 (m-80) REVERT: J 228 MET cc_start: -0.4116 (mmt) cc_final: -0.4461 (mpp) REVERT: J 307 GLN cc_start: 0.6396 (tm-30) cc_final: 0.5948 (mm-40) outliers start: 45 outliers final: 32 residues processed: 143 average time/residue: 1.2203 time to fit residues: 214.9802 Evaluate side-chains 150 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 3.413 ------------------------------------------------------------------------------- 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 566 VAL 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 340 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 317 ILE 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 323 LYS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 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 404 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 106 optimal weight: 4.9990 chunk 349 optimal weight: 5.9990 chunk 371 optimal weight: 7.9990 chunk 240 optimal weight: 0.8980 chunk 300 optimal weight: 50.0000 chunk 186 optimal weight: 0.9980 chunk 311 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 315 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN H 29 HIS ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.123860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.065703 restraints weight = 69941.811| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.93 r_work: 0.2766 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32660 Z= 0.148 Angle : 0.569 12.247 44739 Z= 0.295 Chirality : 0.041 0.365 4966 Planarity : 0.003 0.042 5358 Dihedral : 16.920 175.750 5463 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.81 % Favored : 96.00 % Rotamer: Outliers : 1.53 % Allowed : 13.28 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3679 helix: 1.58 (0.14), residues: 1268 sheet: 0.59 (0.24), residues: 511 loop : -0.74 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 308 HIS 0.030 0.001 HIS F 66 PHE 0.014 0.001 PHE F 108 TYR 0.013 0.001 TYR H 74 ARG 0.003 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 1023) hydrogen bonds : angle 3.93017 ( 2802) SS BOND : bond 0.00314 ( 9) SS BOND : angle 1.92410 ( 18) covalent geometry : bond 0.00335 (32647) covalent geometry : angle 0.56781 (44721) Misc. bond : bond 0.00924 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40542.60 seconds wall clock time: 694 minutes 42.07 seconds (41682.07 seconds total)