Starting phenix.real_space_refine on Fri Jun 27 07:37:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gs9_51543/06_2025/9gs9_51543_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gs9_51543/06_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_51543/06_2025/9gs9_51543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gs9_51543/06_2025/9gs9_51543.map" model { file = "/net/cci-nas-00/data/ceres_data/9gs9_51543/06_2025/9gs9_51543_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gs9_51543/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 18.97, per 1000 atoms: 0.60 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: 8.29 Conformation dependent library (CDL) restraints added in 4.0 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: 10.96 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: 11.40 Time building geometry restraints manager: 9.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.55 - 0.83: 1 0.83 - 1.12: 0 1.12 - 1.40: 13373 1.40 - 1.68: 19103 1.68 - 1.97: 170 Bond restraints: 32647 Sorted by residual: bond pdb=" O3' C 1 40 " pdb=" P G 1 41 " ideal model delta sigma weight residual 1.607 0.551 1.056 1.50e-02 4.44e+03 4.95e+03 bond pdb=" C ASN J 28 " pdb=" N PHE J 29 " ideal model delta sigma weight residual 1.332 1.966 -0.633 1.40e-02 5.10e+03 2.05e+03 bond pdb=" N VAL D 30 " pdb=" CA VAL D 30 " ideal model delta sigma weight residual 1.458 1.495 -0.037 7.70e-03 1.69e+04 2.34e+01 bond pdb=" C LYS G 38 " pdb=" O LYS G 38 " ideal model delta sigma weight residual 1.235 1.173 0.062 1.30e-02 5.92e+03 2.29e+01 bond pdb=" N VAL E 30 " pdb=" CA VAL E 30 " ideal model delta sigma weight residual 1.458 1.494 -0.036 7.70e-03 1.69e+04 2.17e+01 ... (remaining 32642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.76: 44710 12.76 - 25.53: 5 25.53 - 38.29: 3 38.29 - 51.06: 0 51.06 - 63.82: 3 Bond angle restraints: 44721 Sorted by residual: angle pdb=" O ASN J 28 " pdb=" C ASN J 28 " pdb=" N PHE J 29 " ideal model delta sigma weight residual 122.38 60.14 62.24 1.08e+00 8.57e-01 3.32e+03 angle pdb=" CA ASN J 28 " pdb=" C ASN J 28 " pdb=" N PHE J 29 " ideal model delta sigma weight residual 116.84 175.46 -58.62 1.12e+00 7.97e-01 2.74e+03 angle pdb=" O3' C 1 40 " pdb=" P G 1 41 " pdb=" OP1 G 1 41 " ideal model delta sigma weight residual 108.00 44.18 63.82 3.00e+00 1.11e-01 4.53e+02 angle pdb=" C3' C 1 40 " pdb=" O3' C 1 40 " pdb=" P G 1 41 " ideal model delta sigma weight residual 120.20 149.75 -29.55 1.50e+00 4.44e-01 3.88e+02 angle pdb=" O3' C 1 40 " pdb=" P G 1 41 " pdb=" O5' G 1 41 " ideal model delta sigma weight residual 104.00 131.16 -27.16 1.50e+00 4.44e-01 3.28e+02 ... (remaining 44716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 18785 35.39 - 70.79: 733 70.79 - 106.18: 40 106.18 - 141.58: 3 141.58 - 176.97: 7 Dihedral angle restraints: 19568 sinusoidal: 8586 harmonic: 10982 Sorted by residual: dihedral pdb=" CA ASN A 418 " pdb=" C ASN A 418 " pdb=" N LEU A 419 " pdb=" CA LEU A 419 " ideal model delta harmonic sigma weight residual -180.00 -129.11 -50.89 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" N MET I 374 " pdb=" C MET I 374 " pdb=" CA MET I 374 " pdb=" CB MET I 374 " ideal model delta harmonic sigma weight residual 122.80 147.69 -24.89 0 2.50e+00 1.60e-01 9.91e+01 dihedral pdb=" CA ASN J 28 " pdb=" C ASN J 28 " pdb=" N PHE J 29 " pdb=" CA PHE J 29 " ideal model delta harmonic sigma weight residual 180.00 130.76 49.24 0 5.00e+00 4.00e-02 9.70e+01 ... (remaining 19565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 4898 0.197 - 0.394: 59 0.394 - 0.591: 3 0.591 - 0.788: 2 0.788 - 0.984: 4 Chirality restraints: 4966 Sorted by residual: chirality pdb=" CA MET I 374 " pdb=" N MET I 374 " pdb=" C MET I 374 " pdb=" CB MET I 374 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" C3' U 1 13 " pdb=" C4' U 1 13 " pdb=" O3' U 1 13 " pdb=" C2' U 1 13 " both_signs ideal model delta sigma weight residual False -2.74 -1.92 -0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" CA LYS I 373 " pdb=" N LYS I 373 " pdb=" C LYS I 373 " pdb=" CB LYS I 373 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.60e+01 ... (remaining 4963 not shown) Planarity restraints: 5358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 367 " -0.032 2.00e-02 2.50e+03 6.76e-02 4.58e+01 pdb=" C GLN I 367 " 0.117 2.00e-02 2.50e+03 pdb=" O GLN I 367 " -0.044 2.00e-02 2.50e+03 pdb=" N THR I 368 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 21 " -0.011 9.50e-02 1.11e+02 4.48e-02 2.48e+01 pdb=" NE ARG A 21 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 21 " -0.086 2.00e-02 2.50e+03 pdb=" NH1 ARG A 21 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 21 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 20 " 0.100 9.50e-02 1.11e+02 5.95e-02 2.05e+01 pdb=" NE ARG A 20 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 20 " 0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG A 20 " -0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 20 " -0.021 2.00e-02 2.50e+03 ... (remaining 5355 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.44: 17 1.44 - 2.30: 88 2.30 - 3.17: 23203 3.17 - 4.03: 84155 4.03 - 4.90: 149555 Warning: very small nonbonded interaction distances. Nonbonded interactions: 257018 Sorted by model distance: nonbonded pdb=" CD GLN F 62 " pdb=" ND1 HIS I 372 " model vdw 0.571 2.680 nonbonded pdb=" SG CYS J 158 " pdb=" CD LYS J 160 " model vdw 0.596 3.800 nonbonded pdb=" CA ASP F 63 " pdb=" SD MET I 374 " model vdw 0.675 3.830 nonbonded pdb=" CB ASP F 63 " pdb=" CG MET I 374 " model vdw 0.856 3.840 nonbonded pdb=" OD1 ASP F 63 " pdb=" CA MET I 374 " model vdw 0.888 3.470 ... (remaining 257013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 40 or resid 67 through 225 or resid 234 through \ 319 or resid 321 through 342)) selection = (chain 'C' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 40 or resid 67 through 225 or resid 234 through 3 \ 19 or resid 321 through 342)) selection = (chain 'D' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 40 or resid 67 through 225 or resid 234 through 3 \ 19 or resid 321 through 342)) selection = (chain 'E' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 40 or resid 67 through 225 or resid 234 through 3 \ 19 or resid 321 through 342)) selection = (chain 'F' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 40 or resid 67 through 225 or resid 234 through 3 \ 19 or resid 321 through 342)) selection = (chain 'G' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 342)) } ncs_group { reference = (chain 'I' and resid 5 through 405) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.230 Set scattering table: 0.260 Process input model: 78.380 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.410 ------------------------------------------------------------------------------- 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 : 3.715 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: 1.4179 time to fit residues: 634.2494 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 : 3.465 ------------------------------------------------------------------------------- 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 = 0.126314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.067594 restraints weight = 69551.385| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.88 r_work: 0.2780 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8572 (tt) REVERT: A 147 TRP cc_start: 0.8666 (p90) cc_final: 0.8300 (p-90) REVERT: A 477 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8901 (tm-30) REVERT: A 567 MET cc_start: 0.9538 (ttp) cc_final: 0.9292 (ttp) REVERT: A 592 LEU cc_start: 0.9300 (mt) cc_final: 0.8931 (mt) REVERT: A 593 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7800 (mtm110) REVERT: A 682 MET cc_start: 0.8307 (ptm) cc_final: 0.8082 (ptm) REVERT: A 692 MET cc_start: 0.9354 (mmm) cc_final: 0.8960 (mmm) REVERT: B 340 MET cc_start: 0.9278 (mtm) cc_final: 0.9073 (mtm) REVERT: D 74 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8498 (mp0) REVERT: D 340 MET cc_start: 0.8623 (mtp) cc_final: 0.8394 (mtp) REVERT: E 74 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7987 (pt0) REVERT: G 236 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8387 (mt0) REVERT: G 297 GLN cc_start: 0.7861 (mm110) cc_final: 0.6944 (pt0) REVERT: H 5 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.7105 (p90) REVERT: I 25 VAL cc_start: 0.0409 (OUTLIER) cc_final: -0.0078 (p) REVERT: I 400 ASP cc_start: 0.8818 (m-30) cc_final: 0.8366 (p0) REVERT: J 46 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: J 162 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7319 (tp-100) REVERT: J 368 THR cc_start: 0.3227 (OUTLIER) cc_final: 0.2904 (p) REVERT: J 378 ILE cc_start: -0.0594 (OUTLIER) cc_final: -0.0890 (tt) outliers start: 70 outliers final: 22 residues processed: 221 average time/residue: 1.2411 time to fit residues: 334.1082 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 : 3.416 ------------------------------------------------------------------------------- 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: 0.0570 chunk 285 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 340 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 240 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 ASN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN G 83 HIS ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS I 66 HIS I 246 GLN I 253 ASN I 389 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.126342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068294 restraints weight = 69730.245| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.90 r_work: 0.2799 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 32660 Z= 0.132 Angle : 0.641 17.760 44739 Z= 0.335 Chirality : 0.043 0.594 4966 Planarity : 0.003 0.050 5358 Dihedral : 17.146 179.322 5478 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.75 % Favored : 95.79 % Rotamer: Outliers : 2.08 % Allowed : 9.96 % Favored : 87.96 % 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: -0.44 (0.13), residues: 3679 helix: 0.77 (0.14), residues: 1263 sheet: 0.34 (0.22), residues: 537 loop : -1.24 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 308 HIS 0.015 0.001 HIS I 372 PHE 0.016 0.001 PHE C 108 TYR 0.025 0.001 TYR H 181 ARG 0.005 0.000 ARG A 668 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 1023) hydrogen bonds : angle 4.45361 ( 2802) SS BOND : bond 0.00749 ( 9) SS BOND : angle 2.23168 ( 18) covalent geometry : bond 0.00274 (32647) covalent geometry : angle 0.63956 (44721) Misc. bond : bond 0.01810 ( 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 206 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 141 time to evaluate : 3.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8574 (tt) REVERT: A 147 TRP cc_start: 0.8544 (p90) cc_final: 0.8168 (p-90) REVERT: A 433 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7186 (m-70) REVERT: A 477 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8730 (tm-30) REVERT: A 567 MET cc_start: 0.9507 (ttp) cc_final: 0.9186 (ttp) REVERT: A 592 LEU cc_start: 0.9339 (mt) cc_final: 0.9052 (mt) REVERT: A 603 MET cc_start: 0.9377 (mmt) cc_final: 0.8864 (mmm) REVERT: A 639 MET cc_start: 0.9224 (ptt) cc_final: 0.8932 (pmt) REVERT: A 668 ARG cc_start: 0.8989 (mmm-85) cc_final: 0.8665 (tpp80) REVERT: A 682 MET cc_start: 0.8048 (ptm) cc_final: 0.7780 (ptm) REVERT: A 692 MET cc_start: 0.9189 (mmm) cc_final: 0.8850 (mmm) REVERT: B 227 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8558 (mmmm) REVERT: B 308 TRP cc_start: 0.8535 (t60) cc_final: 0.8221 (t60) REVERT: B 340 MET cc_start: 0.9152 (mtm) cc_final: 0.8851 (mtm) REVERT: C 28 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8728 (m-30) REVERT: C 153 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: D 58 ASN cc_start: 0.8947 (p0) cc_final: 0.8694 (p0) REVERT: D 74 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: E 74 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7741 (pt0) REVERT: E 226 ASP cc_start: 0.8723 (p0) cc_final: 0.8499 (p0) REVERT: G 236 GLN cc_start: 0.8571 (mt0) cc_final: 0.8322 (mt0) REVERT: G 297 GLN cc_start: 0.7928 (mm110) cc_final: 0.7075 (pt0) REVERT: G 340 MET cc_start: 0.7244 (ptp) cc_final: 0.7037 (ptp) REVERT: H 4 TYR cc_start: 0.8864 (m-80) cc_final: 0.8658 (m-80) REVERT: H 5 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.6999 (p90) REVERT: H 186 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8859 (t0) REVERT: I 25 VAL cc_start: 0.0968 (OUTLIER) cc_final: 0.0478 (p) REVERT: I 228 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6786 (ppp) REVERT: I 400 ASP cc_start: 0.8783 (m-30) cc_final: 0.8348 (OUTLIER) REVERT: J 47 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8714 (mt) REVERT: J 228 MET cc_start: -0.3459 (mmt) cc_final: -0.3855 (mpp) REVERT: J 307 GLN cc_start: 0.6732 (tm-30) cc_final: 0.6127 (mm-40) outliers start: 65 outliers final: 25 residues processed: 189 average time/residue: 1.2728 time to fit residues: 294.4288 Evaluate side-chains 151 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 3.545 ------------------------------------------------------------------------------- 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 28 ASP Chi-restraints excluded: chain C residue 153 GLU 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 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 341 PHE Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 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 47 LEU Chi-restraints excluded: chain J residue 92 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 279 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 281 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 313 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 345 optimal weight: 10.0000 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 438 HIS ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.124182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.069312 restraints weight = 70023.791| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.35 r_work: 0.2722 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 32660 Z= 0.205 Angle : 0.645 24.945 44739 Z= 0.334 Chirality : 0.043 0.465 4966 Planarity : 0.004 0.044 5358 Dihedral : 17.040 176.767 5471 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.64 % Favored : 96.00 % Rotamer: Outliers : 1.82 % Allowed : 11.14 % Favored : 87.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.16 (0.13), residues: 3679 helix: 1.06 (0.14), residues: 1264 sheet: 0.58 (0.22), residues: 509 loop : -1.13 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 308 HIS 0.022 0.001 HIS F 66 PHE 0.015 0.002 PHE A 163 TYR 0.016 0.001 TYR H 74 ARG 0.006 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 1023) hydrogen bonds : angle 4.33311 ( 2802) SS BOND : bond 0.00630 ( 9) SS BOND : angle 3.28100 ( 18) covalent geometry : bond 0.00462 (32647) covalent geometry : angle 0.64148 (44721) Misc. bond : bond 0.01209 ( 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 182 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 125 time to evaluate : 4.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8520 (tt) REVERT: A 433 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7409 (m-70) REVERT: A 477 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8825 (tm-30) REVERT: A 567 MET cc_start: 0.9507 (ttp) cc_final: 0.9113 (ttp) REVERT: A 587 GLN cc_start: 0.9145 (tt0) cc_final: 0.8611 (tp40) REVERT: A 592 LEU cc_start: 0.9285 (mt) cc_final: 0.9071 (mt) REVERT: A 603 MET cc_start: 0.9380 (mmt) cc_final: 0.8791 (mmm) REVERT: A 668 ARG cc_start: 0.9038 (mmm-85) cc_final: 0.8745 (tpp80) REVERT: A 682 MET cc_start: 0.8055 (ptm) cc_final: 0.7769 (ptm) REVERT: A 692 MET cc_start: 0.9294 (mmm) cc_final: 0.8920 (mmm) REVERT: B 113 GLU cc_start: 0.8601 (mp0) cc_final: 0.8331 (mm-30) REVERT: B 227 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8603 (mmmm) REVERT: B 340 MET cc_start: 0.9210 (mtm) cc_final: 0.8841 (mtm) REVERT: C 153 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: D 58 ASN cc_start: 0.9049 (p0) cc_final: 0.8808 (p0) REVERT: D 74 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8460 (mp0) REVERT: E 74 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7831 (pt0) REVERT: E 226 ASP cc_start: 0.8802 (p0) cc_final: 0.8544 (p0) REVERT: H 4 TYR cc_start: 0.9061 (m-80) cc_final: 0.8829 (m-80) REVERT: H 5 TYR cc_start: 0.7224 (p90) cc_final: 0.6851 (p90) REVERT: I 25 VAL cc_start: 0.0720 (OUTLIER) cc_final: 0.0222 (p) REVERT: I 400 ASP cc_start: 0.8937 (m-30) cc_final: 0.8568 (p0) REVERT: J 142 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: J 228 MET cc_start: -0.3328 (mmt) cc_final: -0.3769 (mpp) REVERT: J 307 GLN cc_start: 0.6596 (tm-30) cc_final: 0.6062 (mm-40) outliers start: 57 outliers final: 29 residues processed: 168 average time/residue: 1.6645 time to fit residues: 339.7066 Evaluate side-chains 149 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain 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 46 GLU 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 185 THR Chi-restraints excluded: chain J residue 203 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 70 optimal weight: 10.0000 chunk 303 optimal weight: 0.4980 chunk 368 optimal weight: 0.0870 chunk 175 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 334 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 86 optimal weight: 0.0020 chunk 191 optimal weight: 4.9990 overall best weight: 0.4768 ------------------------------------------------------------------------------- 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 ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 389 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.126123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.068924 restraints weight = 69704.666| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.88 r_work: 0.2810 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 32660 Z= 0.112 Angle : 0.572 12.422 44739 Z= 0.299 Chirality : 0.041 0.391 4966 Planarity : 0.003 0.043 5358 Dihedral : 16.937 176.336 5471 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.75 % Favored : 95.95 % Rotamer: Outliers : 1.50 % Allowed : 11.53 % Favored : 86.97 % 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: 0.10 (0.13), residues: 3679 helix: 1.28 (0.14), residues: 1264 sheet: 0.73 (0.23), residues: 505 loop : -0.97 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 308 HIS 0.021 0.001 HIS F 66 PHE 0.014 0.001 PHE D 332 TYR 0.015 0.001 TYR H 74 ARG 0.004 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 1023) hydrogen bonds : angle 4.10372 ( 2802) SS BOND : bond 0.00480 ( 9) SS BOND : angle 3.39236 ( 18) covalent geometry : bond 0.00238 (32647) covalent geometry : angle 0.56826 (44721) Misc. bond : bond 0.00966 ( 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 181 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.5883 (tpp) REVERT: A 44 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8512 (tt) REVERT: A 433 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7280 (m-70) REVERT: A 477 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8720 (tm-30) REVERT: A 567 MET cc_start: 0.9505 (ttp) cc_final: 0.9099 (ttp) REVERT: A 587 GLN cc_start: 0.9041 (tt0) cc_final: 0.8531 (tp40) REVERT: A 592 LEU cc_start: 0.9309 (mt) cc_final: 0.9063 (mt) REVERT: A 603 MET cc_start: 0.9390 (mmt) cc_final: 0.8965 (mmm) REVERT: A 639 MET cc_start: 0.9268 (ptt) cc_final: 0.8961 (pmt) REVERT: A 668 ARG cc_start: 0.9007 (mmm-85) cc_final: 0.8804 (tpp80) REVERT: A 682 MET cc_start: 0.7963 (ptm) cc_final: 0.7754 (ptm) REVERT: A 692 MET cc_start: 0.9240 (mmm) cc_final: 0.8850 (mmm) REVERT: B 113 GLU cc_start: 0.8576 (mp0) cc_final: 0.8275 (mm-30) REVERT: B 308 TRP cc_start: 0.8609 (t60) cc_final: 0.8296 (t60) REVERT: B 340 MET cc_start: 0.9132 (mtm) cc_final: 0.8808 (mtm) REVERT: C 153 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: D 58 ASN cc_start: 0.8914 (p0) cc_final: 0.8654 (p0) REVERT: D 74 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: D 303 PHE cc_start: 0.9648 (OUTLIER) cc_final: 0.8789 (t80) REVERT: E 62 GLN cc_start: 0.7650 (pp30) cc_final: 0.7270 (tm130) REVERT: E 74 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7719 (pt0) REVERT: E 226 ASP cc_start: 0.8762 (p0) cc_final: 0.8521 (p0) REVERT: G 297 GLN cc_start: 0.8356 (mm110) cc_final: 0.7662 (pt0) REVERT: H 4 TYR cc_start: 0.8953 (m-80) cc_final: 0.8745 (m-80) REVERT: H 5 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.6802 (p90) REVERT: I 25 VAL cc_start: 0.0584 (OUTLIER) cc_final: 0.0145 (p) REVERT: I 400 ASP cc_start: 0.8809 (m-30) cc_final: 0.8430 (OUTLIER) REVERT: J 43 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8894 (mm-30) REVERT: J 173 TYR cc_start: 0.9093 (m-80) cc_final: 0.8822 (m-80) REVERT: J 228 MET cc_start: -0.3698 (mmt) cc_final: -0.4049 (mpp) REVERT: J 307 GLN cc_start: 0.6361 (tm-30) cc_final: 0.5949 (mm-40) outliers start: 47 outliers final: 23 residues processed: 168 average time/residue: 1.2155 time to fit residues: 250.5925 Evaluate side-chains 149 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 3.461 ------------------------------------------------------------------------------- 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 249 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 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 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 115 VAL Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 37 optimal weight: 0.1980 chunk 312 optimal weight: 30.0000 chunk 159 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 332 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 374 optimal weight: 30.0000 chunk 354 optimal weight: 10.0000 chunk 48 optimal weight: 50.0000 chunk 91 optimal weight: 0.9990 chunk 270 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 67 ASN F 216 GLN G 319 ASN H 2 GLN ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.124975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.067345 restraints weight = 70172.546| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.85 r_work: 0.2780 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32660 Z= 0.145 Angle : 0.576 15.523 44739 Z= 0.299 Chirality : 0.041 0.367 4966 Planarity : 0.003 0.043 5358 Dihedral : 16.843 176.091 5468 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.59 % Favored : 96.14 % Rotamer: Outliers : 1.56 % Allowed : 12.23 % Favored : 86.21 % 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 (0.13), residues: 3679 helix: 1.42 (0.15), residues: 1265 sheet: 0.78 (0.23), residues: 504 loop : -0.91 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 308 HIS 0.013 0.001 HIS F 66 PHE 0.016 0.001 PHE B 332 TYR 0.014 0.001 TYR H 74 ARG 0.003 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 1023) hydrogen bonds : angle 4.04247 ( 2802) SS BOND : bond 0.00539 ( 9) SS BOND : angle 2.82002 ( 18) covalent geometry : bond 0.00325 (32647) covalent geometry : angle 0.57328 (44721) Misc. bond : bond 0.00760 ( 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 170 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8494 (tt) REVERT: A 433 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7492 (m-70) REVERT: A 477 GLU cc_start: 0.9210 (tm-30) cc_final: 0.8888 (tm-30) REVERT: A 567 MET cc_start: 0.9541 (ttp) cc_final: 0.9145 (ttp) REVERT: A 587 GLN cc_start: 0.9121 (tt0) cc_final: 0.8612 (tp40) REVERT: A 592 LEU cc_start: 0.9326 (mt) cc_final: 0.9104 (mt) REVERT: A 603 MET cc_start: 0.9455 (mmt) cc_final: 0.8968 (mmm) REVERT: A 639 MET cc_start: 0.9367 (ptt) cc_final: 0.9040 (pmt) REVERT: A 668 ARG cc_start: 0.9067 (mmm-85) cc_final: 0.8792 (tpp80) REVERT: A 692 MET cc_start: 0.9295 (mmm) cc_final: 0.8924 (mmm) REVERT: B 113 GLU cc_start: 0.8726 (mp0) cc_final: 0.8425 (mm-30) REVERT: B 308 TRP cc_start: 0.8768 (t60) cc_final: 0.8455 (t60) REVERT: B 340 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.9025 (mtm) REVERT: C 153 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: D 58 ASN cc_start: 0.9129 (p0) cc_final: 0.8894 (p0) REVERT: D 74 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8602 (mp0) REVERT: D 303 PHE cc_start: 0.9668 (OUTLIER) cc_final: 0.8832 (t80) REVERT: E 62 GLN cc_start: 0.7758 (pp30) cc_final: 0.7289 (tm130) REVERT: E 74 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8057 (pt0) REVERT: E 226 ASP cc_start: 0.8912 (p0) cc_final: 0.8674 (p0) REVERT: G 297 GLN cc_start: 0.8444 (mm110) cc_final: 0.7706 (pt0) REVERT: H 4 TYR cc_start: 0.8901 (m-80) cc_final: 0.8637 (m-80) REVERT: H 5 TYR cc_start: 0.7242 (p90) cc_final: 0.6799 (p90) REVERT: H 186 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8630 (t0) REVERT: I 228 MET cc_start: 0.7654 (pp-130) cc_final: 0.7324 (pp-130) REVERT: I 400 ASP cc_start: 0.8793 (m-30) cc_final: 0.8419 (OUTLIER) REVERT: J 173 TYR cc_start: 0.9046 (m-80) cc_final: 0.8743 (m-80) REVERT: J 228 MET cc_start: -0.3808 (mmt) cc_final: -0.4169 (mpp) REVERT: J 307 GLN cc_start: 0.6415 (tm-30) cc_final: 0.6023 (mm-40) outliers start: 49 outliers final: 27 residues processed: 160 average time/residue: 1.2170 time to fit residues: 239.7379 Evaluate side-chains 149 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 3.403 ------------------------------------------------------------------------------- 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 333 SER Chi-restraints excluded: chain H residue 56 ILE 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 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 115 VAL Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 357 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 74 optimal weight: 0.1980 chunk 64 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 50.0000 chunk 295 optimal weight: 20.0000 chunk 266 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 355 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 GLN ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.125782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.068779 restraints weight = 69978.611| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.87 r_work: 0.2805 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 32660 Z= 0.111 Angle : 0.555 12.723 44739 Z= 0.287 Chirality : 0.040 0.333 4966 Planarity : 0.003 0.043 5358 Dihedral : 16.791 177.271 5463 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.78 % Favored : 95.98 % Rotamer: Outliers : 1.31 % Allowed : 12.74 % Favored : 85.95 % 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: 0.36 (0.14), residues: 3679 helix: 1.51 (0.15), residues: 1265 sheet: 0.85 (0.23), residues: 505 loop : -0.82 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 308 HIS 0.011 0.001 HIS F 66 PHE 0.013 0.001 PHE D 332 TYR 0.013 0.001 TYR H 74 ARG 0.003 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 1023) hydrogen bonds : angle 3.92679 ( 2802) SS BOND : bond 0.00356 ( 9) SS BOND : angle 2.61689 ( 18) covalent geometry : bond 0.00239 (32647) covalent geometry : angle 0.55286 (44721) Misc. bond : bond 0.00777 ( 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 169 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 8.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7043 (mtp) cc_final: 0.5953 (tpp) REVERT: A 44 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8432 (tt) REVERT: A 238 GLU cc_start: 0.8743 (tt0) cc_final: 0.8178 (tm-30) REVERT: A 433 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7299 (m-70) REVERT: A 477 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8682 (tm-30) REVERT: A 567 MET cc_start: 0.9490 (ttp) cc_final: 0.9086 (ttp) REVERT: A 587 GLN cc_start: 0.9032 (tt0) cc_final: 0.8540 (tp40) REVERT: A 592 LEU cc_start: 0.9312 (mt) cc_final: 0.9111 (mt) REVERT: A 603 MET cc_start: 0.9408 (mmt) cc_final: 0.8894 (mmm) REVERT: A 639 MET cc_start: 0.9253 (ptt) cc_final: 0.8969 (pmt) REVERT: A 668 ARG cc_start: 0.9015 (mmm-85) cc_final: 0.8728 (tpp80) REVERT: A 692 MET cc_start: 0.9249 (mmm) cc_final: 0.8868 (mmm) REVERT: B 113 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8218 (mm-30) REVERT: B 308 TRP cc_start: 0.8680 (t60) cc_final: 0.8350 (t60) REVERT: B 321 ASN cc_start: 0.8675 (p0) cc_final: 0.8376 (p0) REVERT: B 340 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8873 (mtm) REVERT: C 153 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: D 58 ASN cc_start: 0.9022 (p0) cc_final: 0.8767 (p0) REVERT: D 74 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: D 303 PHE cc_start: 0.9611 (OUTLIER) cc_final: 0.8818 (t80) REVERT: E 62 GLN cc_start: 0.7794 (pp30) cc_final: 0.7293 (tm130) REVERT: E 74 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7780 (pt0) REVERT: E 226 ASP cc_start: 0.8761 (p0) cc_final: 0.8534 (p0) REVERT: F 323 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8721 (mppt) REVERT: G 297 GLN cc_start: 0.8364 (mm110) cc_final: 0.7826 (pt0) REVERT: H 4 TYR cc_start: 0.8903 (m-80) cc_final: 0.8637 (m-80) REVERT: H 5 TYR cc_start: 0.7252 (p90) cc_final: 0.6798 (p90) REVERT: I 400 ASP cc_start: 0.8835 (m-30) cc_final: 0.8476 (p0) REVERT: J 23 ARG cc_start: 0.7641 (ttt-90) cc_final: 0.7287 (ptt-90) REVERT: J 173 TYR cc_start: 0.9063 (m-80) cc_final: 0.8784 (m-80) REVERT: J 228 MET cc_start: -0.4235 (mmt) cc_final: -0.4562 (mpp) REVERT: J 307 GLN cc_start: 0.6370 (tm-30) cc_final: 0.5961 (mm-40) outliers start: 41 outliers final: 23 residues processed: 161 average time/residue: 1.3783 time to fit residues: 275.5174 Evaluate side-chains 145 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 3.882 ------------------------------------------------------------------------------- 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 249 VAL Chi-restraints excluded: chain B residue 340 MET 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 323 LYS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 79 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 118 optimal weight: 0.0970 chunk 111 optimal weight: 2.9990 chunk 364 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 377 optimal weight: 30.0000 chunk 251 optimal weight: 0.0010 chunk 23 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.124976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.068043 restraints weight = 69856.395| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.83 r_work: 0.2783 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32660 Z= 0.139 Angle : 0.557 12.374 44739 Z= 0.288 Chirality : 0.041 0.358 4966 Planarity : 0.003 0.044 5358 Dihedral : 16.769 176.909 5463 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.81 % Favored : 95.98 % Rotamer: Outliers : 1.44 % Allowed : 13.09 % 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: 0.41 (0.14), residues: 3679 helix: 1.57 (0.15), residues: 1267 sheet: 0.80 (0.23), residues: 507 loop : -0.78 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 308 HIS 0.008 0.001 HIS F 66 PHE 0.013 0.001 PHE B 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 0.03421 ( 1023) hydrogen bonds : angle 3.89760 ( 2802) SS BOND : bond 0.00337 ( 9) SS BOND : angle 2.38209 ( 18) covalent geometry : bond 0.00310 (32647) covalent geometry : angle 0.55515 (44721) Misc. bond : bond 0.00763 ( 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 163 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.5838 (tpp) REVERT: A 44 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8442 (tt) REVERT: A 238 GLU cc_start: 0.8855 (tt0) cc_final: 0.8381 (tm-30) REVERT: A 433 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7452 (m-70) REVERT: A 477 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8896 (tm-30) REVERT: A 567 MET cc_start: 0.9547 (ttp) cc_final: 0.9172 (ttp) REVERT: A 587 GLN cc_start: 0.9123 (tt0) cc_final: 0.8617 (tp40) REVERT: A 603 MET cc_start: 0.9449 (mmt) cc_final: 0.8980 (mmm) REVERT: A 639 MET cc_start: 0.9375 (ptt) cc_final: 0.9079 (pmt) REVERT: A 668 ARG cc_start: 0.9067 (mmm-85) cc_final: 0.8778 (tpp80) REVERT: A 692 MET cc_start: 0.9361 (mmm) cc_final: 0.9003 (mmm) REVERT: B 113 GLU cc_start: 0.8765 (mp0) cc_final: 0.8452 (mm-30) REVERT: B 308 TRP cc_start: 0.8801 (t60) cc_final: 0.8499 (t60) REVERT: B 340 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.9055 (mtm) REVERT: C 153 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: D 58 ASN cc_start: 0.9178 (p0) cc_final: 0.8940 (p0) REVERT: D 74 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8584 (mp0) REVERT: D 303 PHE cc_start: 0.9656 (OUTLIER) cc_final: 0.8929 (t80) REVERT: E 62 GLN cc_start: 0.7903 (pp30) cc_final: 0.7358 (tm130) REVERT: E 74 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8030 (pt0) REVERT: E 226 ASP cc_start: 0.8857 (p0) cc_final: 0.8631 (p0) REVERT: F 323 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8753 (mppt) REVERT: G 297 GLN cc_start: 0.8339 (mm110) cc_final: 0.7811 (pt0) REVERT: H 4 TYR cc_start: 0.8899 (m-80) cc_final: 0.8639 (m-80) REVERT: H 5 TYR cc_start: 0.7168 (p90) cc_final: 0.6754 (p90) REVERT: H 152 MET cc_start: 0.6238 (tmt) cc_final: 0.5984 (ppp) REVERT: I 228 MET cc_start: 0.8048 (pp-130) cc_final: 0.7509 (pp-130) REVERT: I 279 MET cc_start: 0.7711 (mmm) cc_final: 0.6791 (mpt) REVERT: I 400 ASP cc_start: 0.8812 (m-30) cc_final: 0.8462 (OUTLIER) REVERT: J 23 ARG cc_start: 0.7774 (ttt-90) cc_final: 0.7439 (ptt-90) REVERT: J 173 TYR cc_start: 0.9091 (m-80) cc_final: 0.8785 (m-80) REVERT: J 228 MET cc_start: -0.4236 (mmt) cc_final: -0.4518 (mpp) REVERT: J 307 GLN cc_start: 0.6197 (tm-30) cc_final: 0.5830 (mm-40) outliers start: 45 outliers final: 32 residues processed: 156 average time/residue: 1.2562 time to fit residues: 241.4959 Evaluate side-chains 150 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 3.934 ------------------------------------------------------------------------------- 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 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 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 98 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 341 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain 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 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: 5.9990 chunk 77 optimal weight: 0.8980 chunk 342 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 332 optimal weight: 7.9990 chunk 198 optimal weight: 0.9980 chunk 303 optimal weight: 0.9990 chunk 285 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 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 = 0.4062 r_free = 0.4062 target = 0.124995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067964 restraints weight = 69812.491| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.88 r_work: 0.2782 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32660 Z= 0.137 Angle : 0.577 13.059 44739 Z= 0.298 Chirality : 0.041 0.437 4966 Planarity : 0.003 0.044 5358 Dihedral : 16.772 176.846 5463 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.81 % Favored : 96.00 % Rotamer: Outliers : 1.44 % Allowed : 13.19 % Favored : 85.38 % 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: 0.45 (0.14), residues: 3679 helix: 1.59 (0.14), residues: 1267 sheet: 0.86 (0.24), residues: 500 loop : -0.76 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP G 308 HIS 0.062 0.001 HIS F 66 PHE 0.012 0.001 PHE B 332 TYR 0.019 0.001 TYR I 381 ARG 0.004 0.000 ARG I 371 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 1023) hydrogen bonds : angle 3.87229 ( 2802) SS BOND : bond 0.00320 ( 9) SS BOND : angle 2.28781 ( 18) covalent geometry : bond 0.00306 (32647) covalent geometry : angle 0.57562 (44721) Misc. bond : bond 0.01515 ( 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 161 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.5718 (tpp) REVERT: A 44 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8405 (tt) REVERT: A 238 GLU cc_start: 0.8633 (tt0) cc_final: 0.8253 (tm-30) REVERT: A 433 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7370 (m-70) REVERT: A 477 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 567 MET cc_start: 0.9504 (ttp) cc_final: 0.9137 (ttp) REVERT: A 587 GLN cc_start: 0.9160 (tt0) cc_final: 0.8643 (tp40) REVERT: A 603 MET cc_start: 0.9415 (mmt) cc_final: 0.8939 (mmm) REVERT: A 639 MET cc_start: 0.9252 (ptt) cc_final: 0.8954 (pmt) REVERT: A 668 ARG cc_start: 0.9025 (mmm-85) cc_final: 0.8753 (tpp80) REVERT: A 692 MET cc_start: 0.9317 (mmm) cc_final: 0.8944 (mmm) REVERT: B 113 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8256 (mm-30) REVERT: B 308 TRP cc_start: 0.8710 (t60) cc_final: 0.8401 (t60) REVERT: B 340 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8926 (mtm) REVERT: C 153 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: D 58 ASN cc_start: 0.9019 (p0) cc_final: 0.8765 (p0) REVERT: D 74 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: D 232 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: D 303 PHE cc_start: 0.9622 (OUTLIER) cc_final: 0.8868 (t80) REVERT: E 62 GLN cc_start: 0.7863 (pp30) cc_final: 0.7313 (tm130) REVERT: E 74 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7759 (pt0) REVERT: E 226 ASP cc_start: 0.8784 (p0) cc_final: 0.8556 (p0) REVERT: F 323 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8793 (mppt) REVERT: G 297 GLN cc_start: 0.8342 (mm110) cc_final: 0.7826 (pt0) REVERT: H 4 TYR cc_start: 0.8896 (m-80) cc_final: 0.8630 (m-80) REVERT: H 5 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6671 (p90) REVERT: I 228 MET cc_start: 0.7942 (pp-130) cc_final: 0.7360 (pp-130) REVERT: I 279 MET cc_start: 0.7616 (mmm) cc_final: 0.6715 (mpp) REVERT: I 400 ASP cc_start: 0.8830 (m-30) cc_final: 0.8491 (OUTLIER) REVERT: J 173 TYR cc_start: 0.9111 (m-80) cc_final: 0.8850 (m-80) REVERT: J 228 MET cc_start: -0.4278 (mmt) cc_final: -0.4559 (mpp) REVERT: J 307 GLN cc_start: 0.6203 (tm-30) cc_final: 0.5829 (mm-40) outliers start: 45 outliers final: 31 residues processed: 152 average time/residue: 1.2560 time to fit residues: 234.0969 Evaluate side-chains 152 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 3.516 ------------------------------------------------------------------------------- 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 C residue 303 PHE Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 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 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 201 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 356 optimal weight: 0.2980 chunk 332 optimal weight: 30.0000 chunk 135 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 368 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 284 optimal weight: 30.0000 chunk 74 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 H 29 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.123874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.065684 restraints weight = 70122.898| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.88 r_work: 0.2740 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 32660 Z= 0.187 Angle : 0.597 16.618 44739 Z= 0.308 Chirality : 0.042 0.385 4966 Planarity : 0.003 0.044 5358 Dihedral : 16.758 174.952 5463 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.89 % Favored : 95.95 % Rotamer: Outliers : 1.40 % Allowed : 13.28 % Favored : 85.31 % 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: 0.42 (0.14), residues: 3679 helix: 1.58 (0.14), residues: 1268 sheet: 0.79 (0.24), residues: 499 loop : -0.76 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP G 308 HIS 0.040 0.001 HIS F 66 PHE 0.015 0.001 PHE B 332 TYR 0.012 0.001 TYR G 219 ARG 0.003 0.000 ARG D 87 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 1023) hydrogen bonds : angle 3.93592 ( 2802) SS BOND : bond 0.00327 ( 9) SS BOND : angle 2.24760 ( 18) covalent geometry : bond 0.00426 (32647) covalent geometry : angle 0.59504 (44721) Misc. bond : bond 0.01295 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.5572 (tpp) REVERT: A 44 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8392 (tt) REVERT: A 238 GLU cc_start: 0.8624 (tt0) cc_final: 0.8238 (tm-30) REVERT: A 433 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7440 (m-70) REVERT: A 477 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8685 (tm-30) REVERT: A 567 MET cc_start: 0.9505 (ttp) cc_final: 0.9133 (ttp) REVERT: A 587 GLN cc_start: 0.9234 (tt0) cc_final: 0.8715 (tp40) REVERT: A 603 MET cc_start: 0.9460 (mmt) cc_final: 0.8990 (mmm) REVERT: A 668 ARG cc_start: 0.9082 (mmm-85) cc_final: 0.8686 (tpp80) REVERT: A 692 MET cc_start: 0.9365 (mmm) cc_final: 0.8964 (mmm) REVERT: B 113 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: B 227 LYS cc_start: 0.8747 (mtmp) cc_final: 0.8264 (ptpp) REVERT: B 308 TRP cc_start: 0.8758 (t60) cc_final: 0.8452 (t60) REVERT: B 340 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8841 (mtm) REVERT: C 153 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: D 58 ASN cc_start: 0.9030 (p0) cc_final: 0.8794 (p0) REVERT: D 74 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8484 (mp0) REVERT: D 232 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: D 303 PHE cc_start: 0.9697 (OUTLIER) cc_final: 0.8897 (t80) REVERT: E 62 GLN cc_start: 0.7843 (pp30) cc_final: 0.7320 (tm130) REVERT: E 74 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7705 (pt0) REVERT: F 323 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8850 (mppt) REVERT: G 297 GLN cc_start: 0.8350 (mm110) cc_final: 0.7793 (pt0) REVERT: G 342 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6423 (tp40) REVERT: H 4 TYR cc_start: 0.8896 (m-80) cc_final: 0.8638 (m-80) REVERT: H 5 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6756 (p90) REVERT: H 152 MET cc_start: 0.6267 (ppp) cc_final: 0.5999 (ppp) REVERT: I 228 MET cc_start: 0.7830 (pp-130) cc_final: 0.7179 (pp-130) REVERT: I 279 MET cc_start: 0.7551 (mmm) cc_final: 0.6680 (mpp) REVERT: I 400 ASP cc_start: 0.8823 (m-30) cc_final: 0.8497 (OUTLIER) REVERT: J 173 TYR cc_start: 0.9113 (m-80) cc_final: 0.8840 (m-80) REVERT: J 228 MET cc_start: -0.4340 (mmt) cc_final: -0.4629 (mpp) REVERT: J 307 GLN cc_start: 0.6187 (tm-30) cc_final: 0.5815 (mm-40) outliers start: 44 outliers final: 29 residues processed: 148 average time/residue: 1.3252 time to fit residues: 239.5961 Evaluate side-chains 147 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 3.510 ------------------------------------------------------------------------------- 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 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 C residue 303 PHE Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain E residue 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 G residue 342 GLN Chi-restraints excluded: chain H residue 5 TYR Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 374 MET Chi-restraints excluded: chain I residue 378 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 106 optimal weight: 5.9990 chunk 349 optimal weight: 8.9990 chunk 371 optimal weight: 9.9990 chunk 240 optimal weight: 0.7980 chunk 300 optimal weight: 50.0000 chunk 186 optimal weight: 0.0870 chunk 311 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 315 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 GLN H 29 HIS ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.123894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.065969 restraints weight = 69640.425| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.86 r_work: 0.2766 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 32660 Z= 0.193 Angle : 0.705 59.188 44739 Z= 0.382 Chirality : 0.042 0.378 4966 Planarity : 0.003 0.043 5358 Dihedral : 16.755 175.035 5463 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.91 % Favored : 95.90 % Rotamer: Outliers : 1.34 % Allowed : 13.31 % Favored : 85.34 % Cbeta Deviations : 0.03 % 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: 0.43 (0.14), residues: 3679 helix: 1.58 (0.14), residues: 1268 sheet: 0.79 (0.24), residues: 499 loop : -0.76 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP G 308 HIS 0.033 0.001 HIS F 66 PHE 0.015 0.001 PHE B 332 TYR 0.012 0.001 TYR H 74 ARG 0.003 0.000 ARG I 371 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 1023) hydrogen bonds : angle 3.93445 ( 2802) SS BOND : bond 0.00325 ( 9) SS BOND : angle 2.24318 ( 18) covalent geometry : bond 0.00427 (32647) covalent geometry : angle 0.70387 (44721) Misc. bond : bond 0.01135 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36302.99 seconds wall clock time: 630 minutes 0.59 seconds (37800.59 seconds total)