Starting phenix.real_space_refine on Mon Jul 6 04:44:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8abl_15325/07_2026/8abl_15325.cif Found real_map, /net/cci-nas-00/data/ceres_data/8abl_15325/07_2026/8abl_15325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8abl_15325/07_2026/8abl_15325.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8abl_15325/07_2026/8abl_15325.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8abl_15325/07_2026/8abl_15325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8abl_15325/07_2026/8abl_15325.map" model { file = "/net/cci-nas-00/data/ceres_data/8abl_15325/07_2026/8abl_15325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8abl_15325/07_2026/8abl_15325.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 30 5.49 5 S 96 5.16 5 C 20480 2.51 5 N 5132 2.21 5 O 5916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31660 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 478 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 478 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 287 Unusual residues: {'AWB': 1, 'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'HEC': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 287 Unusual residues: {'AWB': 1, 'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "U" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.60, per 1000 atoms: 0.18 Number of scatterers: 31660 At special positions: 0 Unit cell: (119.691, 129.735, 164.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 96 16.00 P 30 15.00 O 5916 8.00 N 5132 7.00 C 20480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.07 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.06 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 Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.3 seconds 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7268 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 18 sheets defined 62.9% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 7 through 18 Processing helix chain 'C' and resid 27 through 30 Processing helix chain 'C' and resid 31 through 52 Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 74 through 103 removed outlier: 3.750A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 removed outlier: 3.545A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 149 Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 172 through 203 Proline residue: C 187 - end of helix removed outlier: 4.006A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 247 removed outlier: 6.874A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 275 through 285 removed outlier: 3.798A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.834A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'C' and resid 347 through 365 removed outlier: 4.088A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 383 Processing helix chain 'P' and resid 58 through 89 removed outlier: 3.627A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 92 No H-bonds generated for 'chain 'P' and resid 90 through 92' Processing helix chain 'P' and resid 94 through 100 removed outlier: 3.663A pdb=" N MET P 100 " --> pdb=" O ASP P 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 17 Processing helix chain 'G' and resid 17 through 36 Proline residue: G 26 - end of helix removed outlier: 3.547A pdb=" N GLY G 36 " --> pdb=" O VAL G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 63 through 83 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 102 through 120 Processing helix chain 'F' and resid 77 through 89 removed outlier: 4.260A pdb=" N ALA F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 111 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 138 through 145 removed outlier: 3.581A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 122 through 136 Processing helix chain 'A' and resid 140 through 156 removed outlier: 3.973A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.556A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.537A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 4.012A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.561A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.509A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.647A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 69 through 80 Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.557A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.580A pdb=" N THR B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.814A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 333 through 354 Processing helix chain 'B' and resid 354 through 368 removed outlier: 3.639A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.557A pdb=" N VAL B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 266 through 283 Processing helix chain 'D' and resid 285 through 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 81 removed outlier: 4.398A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 49 through 54 Processing helix chain 'I' and resid 55 through 57 No H-bonds generated for 'chain 'I' and resid 55 through 57' Processing helix chain 'J' and resid 25 through 50 removed outlier: 3.509A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Proline residue: J 33 - end of helix Processing helix chain 'J' and resid 53 through 60 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 66 through 72 removed outlier: 3.747A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.662A pdb=" N ASN J 80 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 18 Processing helix chain 'N' and resid 27 through 30 Processing helix chain 'N' and resid 31 through 52 Processing helix chain 'N' and resid 60 through 71 Processing helix chain 'N' and resid 74 through 103 removed outlier: 3.751A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.545A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 149 Processing helix chain 'N' and resid 150 through 154 Processing helix chain 'N' and resid 157 through 167 Processing helix chain 'N' and resid 172 through 203 Proline residue: N 187 - end of helix removed outlier: 4.005A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 247 removed outlier: 6.873A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 258 Processing helix chain 'N' and resid 272 through 274 No H-bonds generated for 'chain 'N' and resid 272 through 274' Processing helix chain 'N' and resid 275 through 285 removed outlier: 3.797A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.833A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 309 Processing helix chain 'N' and resid 319 through 340 Processing helix chain 'N' and resid 347 through 365 removed outlier: 4.087A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 383 Processing helix chain 'E' and resid 58 through 89 removed outlier: 3.617A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 94 through 100 removed outlier: 3.665A pdb=" N MET E 100 " --> pdb=" O ASP E 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 17 Processing helix chain 'R' and resid 17 through 36 Proline residue: R 26 - end of helix removed outlier: 3.545A pdb=" N GLY R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 41 Processing helix chain 'R' and resid 43 through 48 Processing helix chain 'R' and resid 52 through 61 Processing helix chain 'R' and resid 63 through 83 Processing helix chain 'R' and resid 88 through 92 Processing helix chain 'R' and resid 94 through 98 Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 4.236A pdb=" N ALA Q 81 " --> pdb=" O ASP Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 111 Processing helix chain 'Q' and resid 123 through 137 Processing helix chain 'Q' and resid 138 through 145 removed outlier: 3.582A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 71 through 80 Processing helix chain 'L' and resid 88 through 100 Processing helix chain 'L' and resid 122 through 136 Processing helix chain 'L' and resid 140 through 156 removed outlier: 3.746A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU L 156 " --> pdb=" O THR L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 160 removed outlier: 3.521A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 157 through 160' Processing helix chain 'L' and resid 161 through 175 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 removed outlier: 3.536A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 4.013A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 329 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.523A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.796A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU L 394 " --> pdb=" O LYS L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 414 Processing helix chain 'L' and resid 419 through 429 Processing helix chain 'L' and resid 431 through 443 Processing helix chain 'L' and resid 461 through 468 removed outlier: 3.641A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 48 Processing helix chain 'M' and resid 52 through 60 Processing helix chain 'M' and resid 69 through 80 Processing helix chain 'M' and resid 103 through 118 removed outlier: 3.552A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR M 118 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 128 through 142 Processing helix chain 'M' and resid 143 through 158 removed outlier: 3.577A pdb=" N THR M 147 " --> pdb=" O ASP M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 163 Processing helix chain 'M' and resid 174 through 186 Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'M' and resid 199 through 211 Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.786A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 331 removed outlier: 3.608A pdb=" N GLU M 331 " --> pdb=" O ASP M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 333 through 354 Processing helix chain 'M' and resid 354 through 367 removed outlier: 3.909A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.562A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 Processing helix chain 'M' and resid 406 through 410 Processing helix chain 'M' and resid 412 through 416 Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 109 through 123 Processing helix chain 'O' and resid 124 through 127 Processing helix chain 'O' and resid 134 through 139 Processing helix chain 'O' and resid 144 through 154 Processing helix chain 'O' and resid 184 through 191 Processing helix chain 'O' and resid 210 through 219 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 320 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.398A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 85 through 93 Processing helix chain 'T' and resid 5 through 12 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 49 through 54 Processing helix chain 'T' and resid 55 through 57 No H-bonds generated for 'chain 'T' and resid 55 through 57' Processing helix chain 'U' and resid 25 through 50 removed outlier: 3.534A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP U 31 " --> pdb=" O THR U 27 " (cutoff:3.500A) Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 53 through 60 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 66 through 72 removed outlier: 3.744A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.663A pdb=" N ASN U 80 " --> pdb=" O ALA U 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.520A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A 44 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 308 removed outlier: 3.948A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE H 24 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.157A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 232 removed outlier: 6.178A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 241 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 156 through 158 Processing sheet with id=AA8, first strand: chain 'D' and resid 236 through 237 Processing sheet with id=AA9, first strand: chain 'J' and resid 14 through 16 Processing sheet with id=AB1, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AB2, first strand: chain 'N' and resid 21 through 23 Processing sheet with id=AB3, first strand: chain 'L' and resid 31 through 34 removed outlier: 6.483A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU L 44 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 307 through 308 removed outlier: 3.942A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 16 through 20 removed outlier: 4.151A pdb=" N LYS M 24 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 231 through 235 Processing sheet with id=AB7, first strand: chain 'O' and resid 156 through 158 Processing sheet with id=AB8, first strand: chain 'O' and resid 236 through 237 Processing sheet with id=AB9, first strand: chain 'U' and resid 19 through 20 1866 hydrogen bonds defined for protein. 5253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.27 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.30: 5046 1.30 - 1.51: 14789 1.51 - 1.71: 12435 1.71 - 1.91: 174 1.91 - 2.12: 20 Bond restraints: 32464 Sorted by residual: bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.459 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.464 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.464 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C18 XP4 A3003 " pdb=" O7 XP4 A3003 " ideal model delta sigma weight residual 1.328 1.454 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C23 AWB N 507 " pdb=" O7 AWB N 507 " ideal model delta sigma weight residual 1.354 1.477 -0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 32459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 42866 4.10 - 8.21: 1119 8.21 - 12.31: 114 12.31 - 16.41: 19 16.41 - 20.52: 6 Bond angle restraints: 44124 Sorted by residual: angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 95.71 15.56 1.47e+00 4.63e-01 1.12e+02 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 95.94 15.33 1.47e+00 4.63e-01 1.09e+02 angle pdb=" CG ARG B 90 " pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " ideal model delta sigma weight residual 112.00 91.48 20.52 2.20e+00 2.07e-01 8.70e+01 angle pdb=" CG ARG O 289 " pdb=" CD ARG O 289 " pdb=" NE ARG O 289 " ideal model delta sigma weight residual 112.00 91.85 20.15 2.20e+00 2.07e-01 8.39e+01 angle pdb=" CG ARG D 289 " pdb=" CD ARG D 289 " pdb=" NE ARG D 289 " ideal model delta sigma weight residual 112.00 91.86 20.14 2.20e+00 2.07e-01 8.38e+01 ... (remaining 44119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.96: 17893 29.96 - 59.91: 1006 59.91 - 89.87: 118 89.87 - 119.82: 1 119.82 - 149.78: 2 Dihedral angle restraints: 19020 sinusoidal: 7742 harmonic: 11278 Sorted by residual: dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -104.77 -17.83 0 2.50e+00 1.60e-01 5.09e+01 dihedral pdb=" C GLU D 283 " pdb=" N GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta harmonic sigma weight residual -122.60 -105.09 -17.51 0 2.50e+00 1.60e-01 4.91e+01 dihedral pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " pdb=" CBB HEC D 401 " ideal model delta sinusoidal sigma weight residual 60.00 -0.83 60.83 2 1.00e+01 1.00e-02 3.66e+01 ... (remaining 19017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 4143 0.152 - 0.303: 627 0.303 - 0.455: 51 0.455 - 0.606: 3 0.606 - 0.758: 4 Chirality restraints: 4828 Sorted by residual: chirality pdb=" CB4 CDL N 505 " pdb=" CB3 CDL N 505 " pdb=" CB6 CDL N 505 " pdb=" OB6 CDL N 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.82 -0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.82 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CB4 CDL H 702 " pdb=" CB3 CDL H 702 " pdb=" CB6 CDL H 702 " pdb=" OB6 CDL H 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.87 -0.71 2.00e-01 2.50e+01 1.26e+01 ... (remaining 4825 not shown) Planarity restraints: 5536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 AWB C 507 " 0.049 2.00e-02 2.50e+03 5.64e-02 3.18e+01 pdb=" C21 AWB C 507 " -0.063 2.00e-02 2.50e+03 pdb=" N1 AWB C 507 " -0.048 2.00e-02 2.50e+03 pdb=" O5 AWB C 507 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 76 " -0.129 9.50e-02 1.11e+02 7.20e-02 2.49e+01 pdb=" NE ARG G 76 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG G 76 " -0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG G 76 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG G 76 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 76 " 0.130 9.50e-02 1.11e+02 7.22e-02 2.45e+01 pdb=" NE ARG R 76 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG R 76 " 0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG R 76 " -0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG R 76 " -0.021 2.00e-02 2.50e+03 ... (remaining 5533 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 268 2.63 - 3.20: 27725 3.20 - 3.76: 52614 3.76 - 4.33: 76968 4.33 - 4.90: 118768 Nonbonded interactions: 276343 Sorted by model distance: nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.060 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.062 3.120 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.072 3.080 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.162 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEM C 502 " model vdw 2.202 3.080 ... (remaining 276338 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 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'N' } ncs_group { reference = (chain 'D' and resid 85 through 401) selection = chain 'O' } ncs_group { reference = chain 'E' selection = (chain 'P' and resid 39 through 101) } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.100 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 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 : 0.010 0.199 32474 Z= 0.624 Angle : 1.687 20.515 44132 Z= 1.039 Chirality : 0.109 0.758 4828 Planarity : 0.008 0.072 5536 Dihedral : 17.814 149.779 11740 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.76 % Rotamer: Outliers : 4.41 % Allowed : 7.57 % Favored : 88.02 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 3834 helix: -0.60 (0.10), residues: 2142 sheet: -0.19 (0.26), residues: 338 loop : -0.47 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.083 0.003 ARG G 76 TYR 0.053 0.008 TYR O 237 PHE 0.051 0.007 PHE B 107 TRP 0.041 0.008 TRP L 438 HIS 0.021 0.005 HIS L 171 Details of bonding type rmsd/Z covalent geometry : bond 0.01021 / 0.62 (32464) covalent geometry : angle 1.68655 / 1.04 (44124) SS BOND : bond 0.03153 / 1.57 ( 4) SS BOND : angle 2.49303 / 1.24 ( 8) hydrogen bonds : bond 0.17828 / 11.85 ( 1866) hydrogen bonds : angle 6.68445 / 4.79 ( 5253) Misc. bond : bond 0.11603 / 5.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 652 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.8624 (tttt) cc_final: 0.8417 (ttpt) REVERT: C 139 MET cc_start: 0.9132 (mmm) cc_final: 0.8915 (mmm) REVERT: C 165 LEU cc_start: 0.8446 (mt) cc_final: 0.8194 (tp) REVERT: C 186 MET cc_start: 0.8897 (tpp) cc_final: 0.8662 (tpp) REVERT: C 288 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7713 (ttpp) REVERT: C 295 MET cc_start: 0.8840 (ttp) cc_final: 0.8398 (ttp) REVERT: F 107 LYS cc_start: 0.7304 (tttt) cc_final: 0.6985 (ttmt) REVERT: F 126 GLU cc_start: 0.8605 (mp0) cc_final: 0.8388 (mp0) REVERT: F 138 THR cc_start: 0.8571 (m) cc_final: 0.8212 (p) REVERT: A 68 TYR cc_start: 0.7696 (m-80) cc_final: 0.7472 (m-80) REVERT: A 97 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: A 99 MET cc_start: 0.7265 (ttp) cc_final: 0.7034 (tmm) REVERT: A 128 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7927 (tm-30) REVERT: A 149 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7119 (pp20) REVERT: A 153 ARG cc_start: 0.7163 (ttp-110) cc_final: 0.6568 (ttt-90) REVERT: A 160 LYS cc_start: 0.6283 (tptp) cc_final: 0.5956 (mmtp) REVERT: A 188 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7449 (ttm-80) REVERT: A 196 ASN cc_start: 0.8155 (p0) cc_final: 0.7745 (p0) REVERT: A 212 MET cc_start: 0.9114 (mtp) cc_final: 0.8613 (mtp) REVERT: A 275 MET cc_start: 0.9114 (mtp) cc_final: 0.8903 (mtp) REVERT: A 320 ARG cc_start: 0.8729 (tpt170) cc_final: 0.8358 (tpt170) REVERT: A 390 LYS cc_start: 0.8245 (tptt) cc_final: 0.7850 (mtmm) REVERT: A 433 HIS cc_start: 0.8006 (t70) cc_final: 0.7714 (m90) REVERT: B 31 GLN cc_start: 0.7433 (mt0) cc_final: 0.7060 (mm-40) REVERT: B 139 LYS cc_start: 0.8218 (tttt) cc_final: 0.7906 (ttpt) REVERT: B 215 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: B 239 THR cc_start: 0.6283 (OUTLIER) cc_final: 0.5992 (t) REVERT: B 251 GLU cc_start: 0.7179 (mp0) cc_final: 0.6819 (pm20) REVERT: B 289 VAL cc_start: 0.8892 (t) cc_final: 0.8624 (p) REVERT: B 309 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7027 (m-30) REVERT: B 313 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 364 MET cc_start: 0.8099 (tpp) cc_final: 0.7852 (tpt) REVERT: B 373 ILE cc_start: 0.7600 (mm) cc_final: 0.7384 (mp) REVERT: B 376 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7100 (pt0) REVERT: D 86 THR cc_start: 0.8377 (m) cc_final: 0.8072 (p) REVERT: D 160 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7290 (mm-30) REVERT: D 164 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7280 (mp0) REVERT: D 166 ASN cc_start: 0.8206 (m110) cc_final: 0.7977 (m-40) REVERT: D 185 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7795 (tt0) REVERT: H 41 VAL cc_start: 0.8419 (t) cc_final: 0.8182 (t) REVERT: H 51 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8710 (mtp180) REVERT: H 78 GLU cc_start: 0.8341 (tt0) cc_final: 0.8128 (tt0) REVERT: H 88 GLU cc_start: 0.7478 (mp0) cc_final: 0.7265 (mm-30) REVERT: I 30 ASP cc_start: 0.8336 (t70) cc_final: 0.8080 (t0) REVERT: I 43 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7407 (ttm170) REVERT: J 10 LYS cc_start: 0.7810 (tttm) cc_final: 0.7551 (tmtp) REVERT: J 11 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6978 (mttm) REVERT: J 30 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8329 (mmtm) REVERT: N 6 LYS cc_start: 0.8626 (tttt) cc_final: 0.8417 (ttpt) REVERT: N 139 MET cc_start: 0.9137 (mmm) cc_final: 0.8847 (mmm) REVERT: N 165 LEU cc_start: 0.8433 (mt) cc_final: 0.8169 (tp) REVERT: N 178 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8968 (ptp-170) REVERT: N 186 MET cc_start: 0.8891 (tpp) cc_final: 0.8660 (tpp) REVERT: N 288 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7714 (ttpp) REVERT: N 295 MET cc_start: 0.8837 (ttp) cc_final: 0.8395 (ttp) REVERT: E 54 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7982 (mmpt) REVERT: E 55 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6851 (p0) REVERT: E 91 MET cc_start: 0.8770 (mtp) cc_final: 0.8569 (mtm) REVERT: Q 126 GLU cc_start: 0.8597 (mp0) cc_final: 0.8306 (mp0) REVERT: Q 138 THR cc_start: 0.8572 (m) cc_final: 0.8210 (p) REVERT: L 44 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8024 (tm-30) REVERT: L 94 LEU cc_start: 0.7935 (mt) cc_final: 0.7680 (mm) REVERT: L 122 ASP cc_start: 0.7540 (m-30) cc_final: 0.7277 (m-30) REVERT: L 141 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: L 146 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7239 (mtp85) REVERT: L 160 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.5523 (mmtp) REVERT: L 196 ASN cc_start: 0.7314 (p0) cc_final: 0.7033 (p0) REVERT: L 198 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7092 (tp30) REVERT: L 212 MET cc_start: 0.9037 (mtp) cc_final: 0.8688 (mtp) REVERT: L 231 LYS cc_start: 0.8105 (tttt) cc_final: 0.7779 (tptm) REVERT: L 275 MET cc_start: 0.9112 (mtp) cc_final: 0.8902 (mtp) REVERT: L 320 ARG cc_start: 0.8711 (tpt170) cc_final: 0.8315 (tpt170) REVERT: L 390 LYS cc_start: 0.8127 (tptt) cc_final: 0.7911 (mtmm) REVERT: L 426 LYS cc_start: 0.8489 (mmtp) cc_final: 0.8255 (mttt) REVERT: M 31 GLN cc_start: 0.7589 (mt0) cc_final: 0.7006 (mt0) REVERT: M 139 LYS cc_start: 0.8229 (tttt) cc_final: 0.7909 (ttpt) REVERT: M 170 TYR cc_start: 0.7613 (p90) cc_final: 0.7113 (p90) REVERT: M 215 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: M 236 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7073 (ttm-80) REVERT: M 238 SER cc_start: 0.7529 (m) cc_final: 0.7096 (p) REVERT: M 251 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7182 (pm20) REVERT: M 269 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8608 (ptt) REVERT: M 288 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8438 (p) REVERT: M 309 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: M 379 GLN cc_start: 0.7476 (tt0) cc_final: 0.7237 (tt0) REVERT: O 160 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7282 (mm-30) REVERT: O 164 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7292 (mp0) REVERT: O 166 ASN cc_start: 0.8110 (m110) cc_final: 0.7871 (m-40) REVERT: O 185 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7794 (tt0) REVERT: O 288 GLU cc_start: 0.8499 (tp30) cc_final: 0.7829 (mp0) REVERT: S 41 VAL cc_start: 0.8416 (t) cc_final: 0.8177 (t) REVERT: S 78 GLU cc_start: 0.8347 (tt0) cc_final: 0.8135 (tt0) REVERT: S 88 GLU cc_start: 0.7483 (mp0) cc_final: 0.7276 (mm-30) REVERT: T 30 ASP cc_start: 0.8342 (t70) cc_final: 0.8057 (t0) REVERT: T 43 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7356 (ttm170) REVERT: U 11 LYS cc_start: 0.7251 (tttt) cc_final: 0.6879 (mttm) REVERT: U 15 LYS cc_start: 0.8723 (pttt) cc_final: 0.8521 (pttt) REVERT: U 21 LEU cc_start: 0.8388 (mt) cc_final: 0.8187 (mt) outliers start: 142 outliers final: 13 residues processed: 722 average time/residue: 0.6996 time to fit residues: 585.9479 Evaluate side-chains 474 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 440 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 288 LYS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 146 ARG Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 215 GLN Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain M residue 333 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 173 ASN C 332 ASN C 343 HIS P 90 ASN G 54 ASN G 84 HIS A 74 HIS A 222 HIS A 371 ASN B 87 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 241 ASN B 354 ASN B 392 GLN D 186 GLN D 269 GLN J 58 GLN N 14 ASN N 332 ASN E 90 ASN R 84 HIS L 46 ASN L 98 ASN L 433 HIS M 87 HIS M 205 GLN M 215 GLN M 241 ASN M 316 GLN M 354 ASN O 90 HIS O 186 GLN U 58 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.096347 restraints weight = 31027.660| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 0.74 r_work: 0.2956 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.371 32474 Z= 0.156 Angle : 0.642 14.651 44132 Z= 0.323 Chirality : 0.043 0.165 4828 Planarity : 0.004 0.061 5536 Dihedral : 12.751 117.090 4866 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.92 % Allowed : 10.34 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.13), residues: 3834 helix: 1.31 (0.11), residues: 2142 sheet: 0.34 (0.27), residues: 342 loop : 0.40 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 55 TYR 0.023 0.002 TYR N 16 PHE 0.024 0.002 PHE A 334 TRP 0.027 0.002 TRP C 156 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (32464) covalent geometry : angle 0.64203 / 0.32 (44124) SS BOND : bond 0.00175 / 0.08 ( 4) SS BOND : angle 0.53967 / 0.27 ( 8) hydrogen bonds : bond 0.05644 / 3.74 ( 1866) hydrogen bonds : angle 4.69170 / 3.34 ( 5253) Misc. bond : bond 0.28893 / 14.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 455 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: C 288 LYS cc_start: 0.8112 (tttp) cc_final: 0.7899 (ttpp) REVERT: C 295 MET cc_start: 0.9047 (ttp) cc_final: 0.8746 (ttp) REVERT: F 77 ASP cc_start: 0.8180 (t0) cc_final: 0.7596 (t70) REVERT: F 138 THR cc_start: 0.8535 (m) cc_final: 0.8327 (p) REVERT: A 128 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 153 ARG cc_start: 0.7188 (ttp-110) cc_final: 0.6910 (ttt-90) REVERT: A 188 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7185 (ttm-80) REVERT: A 212 MET cc_start: 0.9095 (mtp) cc_final: 0.8755 (mtp) REVERT: A 236 LEU cc_start: 0.8286 (mt) cc_final: 0.8007 (mt) REVERT: A 320 ARG cc_start: 0.8547 (tpt170) cc_final: 0.8286 (tpt170) REVERT: A 424 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: B 31 GLN cc_start: 0.7503 (mt0) cc_final: 0.6983 (mp-120) REVERT: B 236 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7316 (ttm-80) REVERT: B 239 THR cc_start: 0.6360 (OUTLIER) cc_final: 0.6132 (t) REVERT: B 289 VAL cc_start: 0.8910 (t) cc_final: 0.8693 (p) REVERT: B 313 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7783 (mt-10) REVERT: D 160 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7299 (mm-30) REVERT: D 166 ASN cc_start: 0.8377 (m110) cc_final: 0.8171 (m-40) REVERT: N 288 LYS cc_start: 0.8139 (tttp) cc_final: 0.7924 (ttpp) REVERT: N 295 MET cc_start: 0.9038 (ttp) cc_final: 0.8741 (ttp) REVERT: E 91 MET cc_start: 0.8945 (mtp) cc_final: 0.8738 (mtm) REVERT: Q 77 ASP cc_start: 0.8200 (t0) cc_final: 0.7612 (t70) REVERT: Q 126 GLU cc_start: 0.8786 (mp0) cc_final: 0.8581 (mp0) REVERT: L 44 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8184 (tp30) REVERT: L 99 MET cc_start: 0.7387 (tmm) cc_final: 0.6875 (tmm) REVERT: L 212 MET cc_start: 0.9081 (mtp) cc_final: 0.8591 (mtp) REVERT: M 31 GLN cc_start: 0.7600 (mt0) cc_final: 0.7055 (mp-120) REVERT: M 236 ARG cc_start: 0.7437 (mtt90) cc_final: 0.7192 (ttm-80) REVERT: M 238 SER cc_start: 0.7556 (m) cc_final: 0.7119 (p) REVERT: M 309 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6824 (m-30) REVERT: O 160 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7231 (mm-30) outliers start: 62 outliers final: 15 residues processed: 498 average time/residue: 0.6954 time to fit residues: 401.9285 Evaluate side-chains 418 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 399 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain L residue 43 SER Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 309 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 122 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 361 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS P 85 GLN A 64 ASN A 98 ASN A 371 ASN E 85 GLN L 64 ASN L 90 HIS M 354 ASN O 90 HIS O 269 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.091383 restraints weight = 30920.065| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 0.88 r_work: 0.2895 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.328 32474 Z= 0.252 Angle : 0.743 14.130 44132 Z= 0.373 Chirality : 0.048 0.249 4828 Planarity : 0.005 0.050 5536 Dihedral : 12.355 102.252 4793 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.17 % Allowed : 10.02 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.13), residues: 3834 helix: 1.39 (0.11), residues: 2146 sheet: 0.57 (0.27), residues: 340 loop : 0.66 (0.18), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 61 TYR 0.025 0.003 TYR N 16 PHE 0.028 0.003 PHE N 240 TRP 0.018 0.003 TRP L 474 HIS 0.012 0.002 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 (32464) covalent geometry : angle 0.74312 / 0.37 (44124) SS BOND : bond 0.00626 / 0.31 ( 4) SS BOND : angle 0.59515 / 0.30 ( 8) hydrogen bonds : bond 0.06637 / 4.40 ( 1866) hydrogen bonds : angle 4.75175 / 3.39 ( 5253) Misc. bond : bond 0.27084 / 13.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 411 time to evaluate : 1.142 Fit side-chains REVERT: C 1 MET cc_start: 0.8360 (ttm) cc_final: 0.8107 (ttm) REVERT: C 288 LYS cc_start: 0.8218 (tttp) cc_final: 0.7936 (ttpp) REVERT: F 138 THR cc_start: 0.8559 (m) cc_final: 0.8351 (p) REVERT: A 36 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8024 (mptm) REVERT: A 90 HIS cc_start: 0.7648 (t70) cc_final: 0.7434 (t70) REVERT: A 153 ARG cc_start: 0.7256 (ttp-110) cc_final: 0.6977 (ttt-90) REVERT: A 188 ARG cc_start: 0.7519 (ttm-80) cc_final: 0.7259 (ttm-80) REVERT: A 212 MET cc_start: 0.9077 (mtp) cc_final: 0.8656 (mtp) REVERT: A 236 LEU cc_start: 0.8262 (mt) cc_final: 0.7966 (mt) REVERT: B 31 GLN cc_start: 0.7601 (mt0) cc_final: 0.7014 (mp-120) REVERT: B 289 VAL cc_start: 0.8947 (t) cc_final: 0.8706 (p) REVERT: D 160 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7290 (mm-30) REVERT: D 166 ASN cc_start: 0.8436 (m110) cc_final: 0.8223 (m-40) REVERT: N 288 LYS cc_start: 0.8217 (tttp) cc_final: 0.7941 (ttpp) REVERT: Q 126 GLU cc_start: 0.8805 (mp0) cc_final: 0.8497 (mp0) REVERT: L 90 HIS cc_start: 0.7573 (t-90) cc_final: 0.7288 (t-170) REVERT: L 99 MET cc_start: 0.7397 (tmm) cc_final: 0.7086 (tmm) REVERT: L 146 ARG cc_start: 0.7506 (ttm110) cc_final: 0.7036 (mtm110) REVERT: L 212 MET cc_start: 0.9053 (mtp) cc_final: 0.8620 (mtp) REVERT: M 31 GLN cc_start: 0.7594 (mt0) cc_final: 0.6999 (mp-120) REVERT: M 236 ARG cc_start: 0.7647 (mtt90) cc_final: 0.7253 (ttm-80) REVERT: M 309 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7084 (m-30) REVERT: M 316 GLN cc_start: 0.7683 (tt0) cc_final: 0.7282 (tt0) REVERT: M 352 PHE cc_start: 0.7904 (t80) cc_final: 0.7700 (t80) REVERT: M 366 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8676 (mt) REVERT: M 414 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7561 (p0) REVERT: O 160 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7277 (mm-30) outliers start: 70 outliers final: 31 residues processed: 464 average time/residue: 0.6729 time to fit residues: 362.9634 Evaluate side-chains 429 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 394 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain L residue 43 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 400 THR Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain M residue 366 LEU Chi-restraints excluded: chain M residue 414 ASP Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 74 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 132 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 330 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 299 optimal weight: 0.9980 chunk 373 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 HIS L 410 GLN M 354 ASN O 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.094168 restraints weight = 31070.799| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 0.88 r_work: 0.2950 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.356 32474 Z= 0.137 Angle : 0.582 13.880 44132 Z= 0.289 Chirality : 0.042 0.163 4828 Planarity : 0.004 0.049 5536 Dihedral : 11.607 95.517 4789 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.14 % Allowed : 10.58 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.14), residues: 3834 helix: 1.82 (0.11), residues: 2128 sheet: 0.69 (0.27), residues: 340 loop : 0.82 (0.18), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 55 TYR 0.018 0.002 TYR N 16 PHE 0.023 0.002 PHE L 334 TRP 0.015 0.001 TRP C 156 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (32464) covalent geometry : angle 0.58250 / 0.29 (44124) SS BOND : bond 0.00301 / 0.15 ( 4) SS BOND : angle 0.40631 / 0.20 ( 8) hydrogen bonds : bond 0.05132 / 3.39 ( 1866) hydrogen bonds : angle 4.45120 / 3.17 ( 5253) Misc. bond : bond 0.27536 / 13.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 426 time to evaluate : 1.152 Fit side-chains REVERT: C 1 MET cc_start: 0.8358 (ttm) cc_final: 0.8113 (ttm) REVERT: C 288 LYS cc_start: 0.8094 (tttp) cc_final: 0.7832 (ttpp) REVERT: A 90 HIS cc_start: 0.7628 (t70) cc_final: 0.7378 (t70) REVERT: A 120 LYS cc_start: 0.7639 (mtpt) cc_final: 0.7436 (mtpm) REVERT: A 128 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7946 (tm-30) REVERT: A 144 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8248 (mm) REVERT: A 153 ARG cc_start: 0.7197 (ttp-110) cc_final: 0.6866 (ttt-90) REVERT: A 188 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.7197 (ttm-80) REVERT: A 212 MET cc_start: 0.9069 (mtp) cc_final: 0.8610 (mtp) REVERT: A 292 GLU cc_start: 0.8003 (mp0) cc_final: 0.7786 (mp0) REVERT: B 31 GLN cc_start: 0.7581 (mt0) cc_final: 0.7036 (mp-120) REVERT: B 117 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8100 (mm-30) REVERT: B 236 ARG cc_start: 0.7776 (ttm170) cc_final: 0.7228 (ttm-80) REVERT: B 289 VAL cc_start: 0.8891 (t) cc_final: 0.8664 (p) REVERT: D 85 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7378 (mtp) REVERT: D 160 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7244 (mm-30) REVERT: D 166 ASN cc_start: 0.8349 (m110) cc_final: 0.8127 (m-40) REVERT: N 1 MET cc_start: 0.8366 (ttm) cc_final: 0.8114 (ttm) REVERT: N 288 LYS cc_start: 0.8089 (tttp) cc_final: 0.7821 (ttpp) REVERT: R 66 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8149 (mm-30) REVERT: Q 96 HIS cc_start: 0.7405 (t-90) cc_final: 0.7119 (t-90) REVERT: Q 126 GLU cc_start: 0.8724 (mp0) cc_final: 0.8474 (mp0) REVERT: L 146 ARG cc_start: 0.7488 (ttm110) cc_final: 0.7175 (mtm110) REVERT: L 212 MET cc_start: 0.9048 (mtp) cc_final: 0.8559 (mtp) REVERT: L 292 GLU cc_start: 0.7994 (mp0) cc_final: 0.7776 (mp0) REVERT: M 31 GLN cc_start: 0.7555 (mt0) cc_final: 0.6964 (mp-120) REVERT: M 117 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: M 180 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7377 (tm-30) REVERT: M 236 ARG cc_start: 0.7519 (mtt90) cc_final: 0.7188 (ttm-80) REVERT: M 309 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7079 (m-30) REVERT: M 414 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7653 (p0) REVERT: O 160 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7246 (mm-30) REVERT: S 86 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7371 (mtm110) outliers start: 69 outliers final: 35 residues processed: 472 average time/residue: 0.6906 time to fit residues: 379.0112 Evaluate side-chains 448 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 404 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 180 GLU Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 414 ASP Chi-restraints excluded: chain S residue 86 ARG Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 74 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 314 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 304 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 301 optimal weight: 0.9980 chunk 298 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 235 HIS B 205 GLN E 85 GLN L 90 HIS ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 HIS M 316 GLN M 354 ASN O 90 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.092877 restraints weight = 30911.426| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 0.88 r_work: 0.2934 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.339 32474 Z= 0.164 Angle : 0.619 14.401 44132 Z= 0.307 Chirality : 0.043 0.169 4828 Planarity : 0.004 0.047 5536 Dihedral : 11.571 97.195 4785 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.27 % Allowed : 10.40 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.14), residues: 3834 helix: 1.76 (0.11), residues: 2142 sheet: 0.72 (0.27), residues: 340 loop : 0.84 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 55 TYR 0.021 0.002 TYR N 16 PHE 0.024 0.002 PHE L 334 TRP 0.012 0.002 TRP D 280 HIS 0.012 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (32464) covalent geometry : angle 0.61862 / 0.31 (44124) SS BOND : bond 0.00409 / 0.20 ( 4) SS BOND : angle 0.47638 / 0.24 ( 8) hydrogen bonds : bond 0.05571 / 3.68 ( 1866) hydrogen bonds : angle 4.49229 / 3.20 ( 5253) Misc. bond : bond 0.27340 / 13.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 408 time to evaluate : 0.991 Fit side-chains REVERT: C 1 MET cc_start: 0.8351 (ttm) cc_final: 0.8095 (ttm) REVERT: C 288 LYS cc_start: 0.8134 (tttp) cc_final: 0.7871 (ttpp) REVERT: A 120 LYS cc_start: 0.7637 (mtpt) cc_final: 0.7433 (mtpm) REVERT: A 128 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 144 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8241 (mm) REVERT: A 146 ARG cc_start: 0.7517 (ttm110) cc_final: 0.7011 (mtm110) REVERT: A 153 ARG cc_start: 0.7140 (ttp-110) cc_final: 0.6793 (ttt-90) REVERT: B 31 GLN cc_start: 0.7635 (mt0) cc_final: 0.7029 (mp-120) REVERT: B 289 VAL cc_start: 0.8896 (t) cc_final: 0.8676 (p) REVERT: D 85 MET cc_start: 0.7554 (mtp) cc_final: 0.7254 (mtp) REVERT: D 160 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7186 (mm-30) REVERT: D 166 ASN cc_start: 0.8362 (m110) cc_final: 0.8117 (m-40) REVERT: N 288 LYS cc_start: 0.8128 (tttp) cc_final: 0.7865 (ttpp) REVERT: R 66 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8161 (mm-30) REVERT: Q 96 HIS cc_start: 0.7372 (t-90) cc_final: 0.7112 (t-90) REVERT: Q 126 GLU cc_start: 0.8764 (mp0) cc_final: 0.8518 (mp0) REVERT: L 205 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: L 212 MET cc_start: 0.9043 (mtp) cc_final: 0.8576 (mtp) REVERT: M 31 GLN cc_start: 0.7532 (mt0) cc_final: 0.6830 (mp10) REVERT: M 236 ARG cc_start: 0.7545 (mtt90) cc_final: 0.7107 (mtp85) REVERT: M 309 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7245 (m-30) REVERT: M 414 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7597 (p0) REVERT: O 160 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7206 (mm-30) REVERT: O 283 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: S 86 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7265 (mtm110) outliers start: 73 outliers final: 36 residues processed: 462 average time/residue: 0.6932 time to fit residues: 372.4093 Evaluate side-chains 445 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 402 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 414 ASP Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 283 GLU Chi-restraints excluded: chain S residue 86 ARG Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 74 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 353 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 301 optimal weight: 0.9980 chunk 308 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 334 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 354 ASN O 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.095216 restraints weight = 30730.783| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 0.88 r_work: 0.2958 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.350 32474 Z= 0.123 Angle : 0.557 13.952 44132 Z= 0.274 Chirality : 0.041 0.165 4828 Planarity : 0.004 0.048 5536 Dihedral : 11.131 88.991 4785 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.74 % Allowed : 10.96 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.14), residues: 3834 helix: 1.97 (0.11), residues: 2130 sheet: 0.75 (0.27), residues: 340 loop : 0.95 (0.18), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG U 55 TYR 0.017 0.002 TYR N 16 PHE 0.022 0.002 PHE A 334 TRP 0.013 0.001 TRP C 156 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (32464) covalent geometry : angle 0.55725 / 0.27 (44124) SS BOND : bond 0.00283 / 0.14 ( 4) SS BOND : angle 0.43115 / 0.21 ( 8) hydrogen bonds : bond 0.04811 / 3.17 ( 1866) hydrogen bonds : angle 4.34536 / 3.10 ( 5253) Misc. bond : bond 0.27343 / 13.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 418 time to evaluate : 1.072 Fit side-chains REVERT: C 288 LYS cc_start: 0.8089 (tttp) cc_final: 0.7800 (ttpp) REVERT: A 90 HIS cc_start: 0.7611 (t70) cc_final: 0.7347 (t70) REVERT: A 128 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 144 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8212 (mm) REVERT: A 153 ARG cc_start: 0.7127 (ttp-110) cc_final: 0.6798 (ttt-90) REVERT: B 31 GLN cc_start: 0.7591 (mt0) cc_final: 0.6965 (mp-120) REVERT: B 236 ARG cc_start: 0.7667 (ttm170) cc_final: 0.6894 (ttm-80) REVERT: B 289 VAL cc_start: 0.8869 (t) cc_final: 0.8649 (p) REVERT: D 85 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7082 (mtp) REVERT: D 160 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7199 (mm-30) REVERT: D 166 ASN cc_start: 0.8380 (m110) cc_final: 0.8132 (m-40) REVERT: N 288 LYS cc_start: 0.8051 (tttp) cc_final: 0.7766 (ttpp) REVERT: R 66 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8150 (mm-30) REVERT: Q 126 GLU cc_start: 0.8725 (mp0) cc_final: 0.8504 (mp0) REVERT: L 146 ARG cc_start: 0.7493 (ttm110) cc_final: 0.7035 (mtm110) REVERT: L 205 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: L 212 MET cc_start: 0.9031 (mtp) cc_final: 0.8548 (mtp) REVERT: M 31 GLN cc_start: 0.7551 (mt0) cc_final: 0.6841 (mp10) REVERT: M 236 ARG cc_start: 0.7512 (mtt90) cc_final: 0.7108 (ttm-80) REVERT: M 313 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7766 (mt-10) REVERT: M 414 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7631 (p0) REVERT: O 160 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7198 (mm-30) outliers start: 56 outliers final: 29 residues processed: 460 average time/residue: 0.6847 time to fit residues: 366.6983 Evaluate side-chains 442 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 408 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 414 ASP Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 74 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 181 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 282 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 377 optimal weight: 0.4980 chunk 336 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 280 GLN N 11 ASN E 85 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 354 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.096138 restraints weight = 30922.293| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 0.74 r_work: 0.2949 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.327 32474 Z= 0.159 Angle : 0.609 14.345 44132 Z= 0.301 Chirality : 0.043 0.157 4828 Planarity : 0.004 0.047 5536 Dihedral : 11.286 89.894 4782 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.61 % Allowed : 11.42 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.14), residues: 3834 helix: 1.85 (0.11), residues: 2144 sheet: 0.73 (0.27), residues: 340 loop : 0.93 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 55 TYR 0.021 0.002 TYR N 16 PHE 0.025 0.002 PHE L 334 TRP 0.012 0.002 TRP O 280 HIS 0.011 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (32464) covalent geometry : angle 0.60854 / 0.30 (44124) SS BOND : bond 0.00362 / 0.18 ( 4) SS BOND : angle 0.49179 / 0.25 ( 8) hydrogen bonds : bond 0.05417 / 3.57 ( 1866) hydrogen bonds : angle 4.42912 / 3.16 ( 5253) Misc. bond : bond 0.26867 / 12.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 411 time to evaluate : 1.121 Fit side-chains REVERT: C 1 MET cc_start: 0.8362 (ttm) cc_final: 0.8089 (ttm) REVERT: C 288 LYS cc_start: 0.8086 (tttp) cc_final: 0.7843 (ttpp) REVERT: G 66 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8105 (mm-30) REVERT: A 90 HIS cc_start: 0.7637 (t70) cc_final: 0.7396 (t70) REVERT: A 128 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7973 (tm-30) REVERT: A 144 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8238 (mm) REVERT: A 153 ARG cc_start: 0.7121 (ttp-110) cc_final: 0.6840 (ttt-90) REVERT: B 31 GLN cc_start: 0.7557 (mt0) cc_final: 0.6990 (mp-120) REVERT: B 289 VAL cc_start: 0.8882 (t) cc_final: 0.8673 (p) REVERT: D 85 MET cc_start: 0.7443 (mtp) cc_final: 0.7122 (mtp) REVERT: D 160 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7191 (mm-30) REVERT: D 166 ASN cc_start: 0.8415 (m110) cc_final: 0.8151 (m-40) REVERT: N 1 MET cc_start: 0.8369 (ttm) cc_final: 0.8097 (ttm) REVERT: N 288 LYS cc_start: 0.8078 (tttp) cc_final: 0.7835 (ttpp) REVERT: R 66 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: Q 126 GLU cc_start: 0.8743 (mp0) cc_final: 0.8534 (mp0) REVERT: L 141 GLU cc_start: 0.6923 (tt0) cc_final: 0.6595 (tt0) REVERT: L 146 ARG cc_start: 0.7509 (ttm110) cc_final: 0.7051 (mtm110) REVERT: L 205 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: L 212 MET cc_start: 0.9031 (mtp) cc_final: 0.8582 (mtp) REVERT: L 424 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: M 31 GLN cc_start: 0.7540 (mt0) cc_final: 0.6857 (mp10) REVERT: M 236 ARG cc_start: 0.7490 (mtt90) cc_final: 0.7098 (mtp85) REVERT: M 313 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7766 (mt-10) REVERT: M 414 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7589 (p0) REVERT: O 160 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7180 (mm-30) REVERT: O 283 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7884 (mt-10) outliers start: 52 outliers final: 32 residues processed: 451 average time/residue: 0.7216 time to fit residues: 377.7475 Evaluate side-chains 447 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 408 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 424 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 414 ASP Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 283 GLU Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 74 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 42 optimal weight: 5.9990 chunk 291 optimal weight: 4.9990 chunk 308 optimal weight: 0.8980 chunk 266 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 367 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN L 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.094589 restraints weight = 30878.046| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 0.88 r_work: 0.2944 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.339 32474 Z= 0.135 Angle : 0.575 14.228 44132 Z= 0.283 Chirality : 0.041 0.163 4828 Planarity : 0.004 0.049 5536 Dihedral : 11.096 89.596 4782 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.58 % Allowed : 11.48 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.14), residues: 3834 helix: 1.98 (0.11), residues: 2124 sheet: 0.75 (0.27), residues: 340 loop : 1.00 (0.18), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 55 TYR 0.018 0.002 TYR N 16 PHE 0.023 0.002 PHE L 334 TRP 0.013 0.001 TRP C 156 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (32464) covalent geometry : angle 0.57461 / 0.28 (44124) SS BOND : bond 0.00302 / 0.15 ( 4) SS BOND : angle 0.44404 / 0.22 ( 8) hydrogen bonds : bond 0.05011 / 3.30 ( 1866) hydrogen bonds : angle 4.36666 / 3.12 ( 5253) Misc. bond : bond 0.26897 / 12.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 409 time to evaluate : 1.143 Fit side-chains REVERT: C 288 LYS cc_start: 0.8078 (tttp) cc_final: 0.7789 (ttpp) REVERT: G 66 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8098 (mm-30) REVERT: A 90 HIS cc_start: 0.7619 (t70) cc_final: 0.7397 (t70) REVERT: A 128 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7964 (tm-30) REVERT: A 144 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8211 (mm) REVERT: A 146 ARG cc_start: 0.7595 (ttm110) cc_final: 0.7076 (mtm110) REVERT: A 153 ARG cc_start: 0.7139 (ttp-110) cc_final: 0.6866 (ttt-90) REVERT: A 292 GLU cc_start: 0.8014 (mp0) cc_final: 0.7757 (mp0) REVERT: B 31 GLN cc_start: 0.7553 (mt0) cc_final: 0.6958 (mp-120) REVERT: B 289 VAL cc_start: 0.8857 (t) cc_final: 0.8657 (p) REVERT: D 85 MET cc_start: 0.7381 (mtp) cc_final: 0.6991 (mtp) REVERT: D 160 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7198 (mm-30) REVERT: D 166 ASN cc_start: 0.8406 (m110) cc_final: 0.8119 (m-40) REVERT: N 288 LYS cc_start: 0.8031 (tttp) cc_final: 0.7776 (ttpp) REVERT: R 66 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8146 (mm-30) REVERT: Q 126 GLU cc_start: 0.8718 (mp0) cc_final: 0.8515 (mp0) REVERT: L 141 GLU cc_start: 0.6970 (tt0) cc_final: 0.6556 (tt0) REVERT: L 146 ARG cc_start: 0.7494 (ttm110) cc_final: 0.7037 (mtm110) REVERT: L 205 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: L 212 MET cc_start: 0.9034 (mtp) cc_final: 0.8550 (mtp) REVERT: L 292 GLU cc_start: 0.8022 (mp0) cc_final: 0.7765 (mp0) REVERT: L 424 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: M 236 ARG cc_start: 0.7437 (mtt90) cc_final: 0.7007 (ttm-80) REVERT: M 313 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7768 (mt-10) REVERT: M 414 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7625 (p0) REVERT: O 160 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7192 (mm-30) REVERT: O 283 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7877 (mt-10) outliers start: 51 outliers final: 34 residues processed: 448 average time/residue: 0.6969 time to fit residues: 362.6594 Evaluate side-chains 446 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 405 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 424 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 414 ASP Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 283 GLU Chi-restraints excluded: chain T residue 51 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 28 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 260 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 chunk 206 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 174 optimal weight: 0.8980 chunk 339 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 202 HIS E 85 GLN L 98 ASN M 354 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.096204 restraints weight = 30805.504| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 0.73 r_work: 0.2938 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.330 32474 Z= 0.160 Angle : 0.611 14.447 44132 Z= 0.302 Chirality : 0.043 0.159 4828 Planarity : 0.004 0.048 5536 Dihedral : 11.184 89.864 4782 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.64 % Allowed : 11.61 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.14), residues: 3834 helix: 1.86 (0.11), residues: 2138 sheet: 0.72 (0.27), residues: 340 loop : 0.98 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 55 TYR 0.020 0.002 TYR C 16 PHE 0.025 0.002 PHE L 334 TRP 0.012 0.002 TRP I 50 HIS 0.011 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (32464) covalent geometry : angle 0.61119 / 0.30 (44124) SS BOND : bond 0.00386 / 0.19 ( 4) SS BOND : angle 0.48087 / 0.24 ( 8) hydrogen bonds : bond 0.05423 / 3.58 ( 1866) hydrogen bonds : angle 4.43657 / 3.17 ( 5253) Misc. bond : bond 0.26983 / 12.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 403 time to evaluate : 0.974 Fit side-chains REVERT: C 1 MET cc_start: 0.8356 (ttm) cc_final: 0.8079 (ttm) REVERT: C 288 LYS cc_start: 0.8079 (tttp) cc_final: 0.7834 (ttpp) REVERT: G 66 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8100 (mm-30) REVERT: A 128 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 144 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8240 (mm) REVERT: A 146 ARG cc_start: 0.7589 (ttm110) cc_final: 0.7116 (mtm110) REVERT: A 153 ARG cc_start: 0.7138 (ttp-110) cc_final: 0.6910 (ttt-90) REVERT: B 31 GLN cc_start: 0.7499 (mt0) cc_final: 0.6978 (mp-120) REVERT: D 85 MET cc_start: 0.7373 (mtp) cc_final: 0.6960 (mtp) REVERT: D 160 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7183 (mm-30) REVERT: D 166 ASN cc_start: 0.8425 (m110) cc_final: 0.8139 (m-40) REVERT: N 1 MET cc_start: 0.8356 (ttm) cc_final: 0.8082 (ttm) REVERT: N 288 LYS cc_start: 0.8065 (tttp) cc_final: 0.7818 (ttpp) REVERT: R 66 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8137 (mm-30) REVERT: Q 126 GLU cc_start: 0.8730 (mp0) cc_final: 0.8527 (mp0) REVERT: L 141 GLU cc_start: 0.6945 (tt0) cc_final: 0.6592 (tt0) REVERT: L 146 ARG cc_start: 0.7480 (ttm110) cc_final: 0.7027 (mtm110) REVERT: L 205 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: L 212 MET cc_start: 0.9031 (mtp) cc_final: 0.8580 (mtp) REVERT: L 424 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: M 19 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: M 236 ARG cc_start: 0.7376 (mtt90) cc_final: 0.7039 (ttm-80) REVERT: M 313 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7763 (mt-10) REVERT: M 414 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7528 (p0) REVERT: O 160 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7170 (mm-30) REVERT: O 283 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7897 (mt-10) outliers start: 53 outliers final: 38 residues processed: 444 average time/residue: 0.6937 time to fit residues: 357.7880 Evaluate side-chains 446 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 400 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 400 THR Chi-restraints excluded: chain L residue 424 GLU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 414 ASP Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 283 GLU Chi-restraints excluded: chain T residue 51 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 203 optimal weight: 9.9990 chunk 372 optimal weight: 6.9990 chunk 276 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 249 optimal weight: 0.0770 chunk 326 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 ASN A 410 GLN E 85 GLN L 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.099472 restraints weight = 30938.143| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 0.81 r_work: 0.2979 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.332 32474 Z= 0.110 Angle : 0.531 13.079 44132 Z= 0.261 Chirality : 0.040 0.174 4828 Planarity : 0.004 0.045 5536 Dihedral : 10.562 89.445 4782 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.27 % Allowed : 12.14 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.14), residues: 3834 helix: 2.09 (0.11), residues: 2132 sheet: 0.85 (0.27), residues: 340 loop : 1.06 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 55 TYR 0.014 0.001 TYR O 117 PHE 0.019 0.001 PHE A 334 TRP 0.015 0.001 TRP C 156 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (32464) covalent geometry : angle 0.53135 / 0.26 (44124) SS BOND : bond 0.00208 / 0.10 ( 4) SS BOND : angle 0.41378 / 0.21 ( 8) hydrogen bonds : bond 0.04378 / 2.88 ( 1866) hydrogen bonds : angle 4.25922 / 3.04 ( 5253) Misc. bond : bond 0.25822 / 12.29 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 404 time to evaluate : 1.144 Fit side-chains REVERT: C 288 LYS cc_start: 0.8051 (tttp) cc_final: 0.7821 (ttpp) REVERT: G 66 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8075 (mm-30) REVERT: A 90 HIS cc_start: 0.7627 (t70) cc_final: 0.7163 (t-170) REVERT: A 128 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 144 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8210 (mm) REVERT: A 146 ARG cc_start: 0.7635 (ttm110) cc_final: 0.7166 (mtm110) REVERT: A 153 ARG cc_start: 0.7153 (ttp-110) cc_final: 0.6865 (ttt-90) REVERT: B 236 ARG cc_start: 0.7503 (ttm170) cc_final: 0.6888 (ttt180) REVERT: D 85 MET cc_start: 0.7261 (mtp) cc_final: 0.6793 (mtp) REVERT: D 160 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7245 (mm-30) REVERT: D 166 ASN cc_start: 0.8404 (m110) cc_final: 0.8116 (m-40) REVERT: N 288 LYS cc_start: 0.8048 (tttp) cc_final: 0.7812 (ttpp) REVERT: L 141 GLU cc_start: 0.6927 (tt0) cc_final: 0.6594 (tt0) REVERT: L 146 ARG cc_start: 0.7514 (ttm110) cc_final: 0.7063 (mtm110) REVERT: L 205 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: L 212 MET cc_start: 0.9047 (mtp) cc_final: 0.8544 (mtp) REVERT: L 422 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7434 (pt0) REVERT: M 236 ARG cc_start: 0.7325 (mtt90) cc_final: 0.7031 (mtp85) REVERT: M 414 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7668 (p0) REVERT: O 160 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7258 (mm-30) outliers start: 41 outliers final: 20 residues processed: 434 average time/residue: 0.7242 time to fit residues: 364.2667 Evaluate side-chains 420 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 396 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 414 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 83 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 268 optimal weight: 0.0670 chunk 214 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 ASN E 85 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.097918 restraints weight = 30960.065| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 0.74 r_work: 0.2967 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.330 32474 Z= 0.131 Angle : 0.572 14.597 44132 Z= 0.281 Chirality : 0.041 0.163 4828 Planarity : 0.004 0.050 5536 Dihedral : 10.664 89.419 4782 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.06 % Allowed : 12.69 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.14), residues: 3834 helix: 2.05 (0.11), residues: 2132 sheet: 0.85 (0.27), residues: 340 loop : 1.05 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 339 TYR 0.019 0.002 TYR C 16 PHE 0.023 0.002 PHE L 334 TRP 0.025 0.001 TRP B 271 HIS 0.011 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (32464) covalent geometry : angle 0.57220 / 0.28 (44124) SS BOND : bond 0.00307 / 0.15 ( 4) SS BOND : angle 0.46509 / 0.24 ( 8) hydrogen bonds : bond 0.04912 / 3.24 ( 1866) hydrogen bonds : angle 4.32040 / 3.08 ( 5253) Misc. bond : bond 0.26500 / 12.64 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13869.20 seconds wall clock time: 235 minutes 51.51 seconds (14151.51 seconds total)