Starting phenix.real_space_refine on Mon Jul 6 08:33:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ab6_15312/07_2026/8ab6_15312.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ab6_15312/07_2026/8ab6_15312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ab6_15312/07_2026/8ab6_15312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ab6_15312/07_2026/8ab6_15312.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ab6_15312/07_2026/8ab6_15312.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ab6_15312/07_2026/8ab6_15312.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ab6_15312/07_2026/8ab6_15312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ab6_15312/07_2026/8ab6_15312.cif" } resolution = 2.0 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= 0.009 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 20428 2.51 5 N 5128 2.21 5 O 7226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.04s 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: 32914 Number of models: 1 Model: "" Number of chains: 53 Chain: "C" Number of atoms: 3055 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Conformer: "B" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} bond proxies already assigned to first conformer: 3149 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: 481 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 63, 478 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Conformer: "B" Number of residues, atoms: 63, 478 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} bond proxies already assigned to first conformer: 483 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: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'LMT': 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: "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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} 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: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "E" 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: "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: "C" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 165 Classifications: {'water': 165} Link IDs: {None: 164} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "N" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 157 Classifications: {'water': 157} Link IDs: {None: 156} Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "O" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "S" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "T" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 7.53, per 1000 atoms: 0.23 Number of scatterers: 32914 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 7226 8.00 N 5128 7.00 C 20428 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=2.05 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.06 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=2.05 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: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7272 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 18 sheets defined 62.9% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 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: 3.744A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 removed outlier: 3.526A 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 202 Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 221 through 247 removed outlier: 6.912A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.844A 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: 3.783A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.837A 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: 4.113A 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: 3.593A 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: 3.627A 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: 3.516A 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: 4.308A 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: 3.598A 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 removed outlier: 3.520A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) 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 155 removed outlier: 4.033A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.545A 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: 3.525A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 4.002A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.565A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.898A 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: 3.684A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.276A 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: 3.657A 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: 3.593A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.745A 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: 3.579A 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: 3.836A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 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: 3.619A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.600A 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 'B' and resid 412 through 416 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: 4.432A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.716A 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: 3.507A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.569A 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: 3.785A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.653A 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: 3.736A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.559A 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 202 Proline residue: N 187 - end of helix Processing helix chain 'N' and resid 221 through 247 removed outlier: 6.932A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.846A 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: 3.772A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.842A 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: 4.112A 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: 3.681A 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: 3.631A 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: 3.522A 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: 4.302A 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: 3.602A 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 removed outlier: 3.515A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) 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 155 removed outlier: 4.042A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 removed outlier: 5.031A pdb=" N ASN L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 156 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: 3.523A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 4.003A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 328 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.557A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.745A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.257A 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: 3.660A 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: 3.563A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.684A 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 141 Processing helix chain 'M' and resid 143 through 158 removed outlier: 3.570A 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: 3.831A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 331 Processing helix chain 'M' and resid 333 through 354 Processing helix chain 'M' and resid 354 through 367 removed outlier: 3.969A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.525A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 removed outlier: 3.503A pdb=" N LEU M 393 " --> pdb=" O ALA M 389 " (cutoff:3.500A) 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: 4.380A 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: 6.017A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.724A 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: 3.610A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.558A 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: 3.791A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.645A 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: 6.548A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU A 44 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 308 removed outlier: 3.927A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.792A 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: 4.186A 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 235 removed outlier: 6.617A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.598A 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: 6.548A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU L 44 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 306 through 308 removed outlier: 3.924A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.793A 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: 4.236A 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 removed outlier: 6.599A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) 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 1857 hydrogen bonds defined for protein. 5241 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: 6.96 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.35: 9758 1.35 - 1.54: 21936 1.54 - 1.73: 504 1.73 - 1.93: 174 1.93 - 2.12: 20 Bond restraints: 32392 Sorted by residual: bond pdb=" CB HIS A 433 " pdb=" CG HIS A 433 " ideal model delta sigma weight residual 1.497 1.368 0.129 1.40e-02 5.10e+03 8.51e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.470 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.470 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" CA HIS A 433 " pdb=" CB HIS A 433 " ideal model delta sigma weight residual 1.532 1.425 0.107 1.65e-02 3.67e+03 4.20e+01 bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.452 -0.124 2.00e-02 2.50e+03 3.82e+01 ... (remaining 32387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.03: 43470 5.03 - 10.05: 509 10.05 - 15.08: 43 15.08 - 20.11: 7 20.11 - 25.13: 1 Bond angle restraints: 44030 Sorted by residual: angle pdb=" N HIS A 433 " pdb=" CA HIS A 433 " pdb=" CB HIS A 433 " ideal model delta sigma weight residual 110.44 85.31 25.13 1.56e+00 4.11e-01 2.60e+02 angle pdb=" C HIS L 433 " pdb=" CA HIS L 433 " pdb=" CB HIS L 433 " ideal model delta sigma weight residual 110.85 91.10 19.75 1.70e+00 3.46e-01 1.35e+02 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 97.11 14.16 1.47e+00 4.63e-01 9.28e+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 91.97 20.03 2.20e+00 2.07e-01 8.29e+01 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 97.90 13.37 1.47e+00 4.63e-01 8.27e+01 ... (remaining 44025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.54: 17882 28.54 - 57.09: 897 57.09 - 85.63: 142 85.63 - 114.17: 11 114.17 - 142.72: 2 Dihedral angle restraints: 18934 sinusoidal: 7648 harmonic: 11286 Sorted by residual: dihedral pdb=" N HIS A 433 " pdb=" C HIS A 433 " pdb=" CA HIS A 433 " pdb=" CB HIS A 433 " ideal model delta harmonic sigma weight residual 122.80 93.92 28.88 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" C ASN L 379 " pdb=" N ASN L 379 " pdb=" CA ASN L 379 " pdb=" CB ASN L 379 " ideal model delta harmonic sigma weight residual -122.60 -145.78 23.18 0 2.50e+00 1.60e-01 8.60e+01 dihedral pdb=" N ASN L 379 " pdb=" C ASN L 379 " pdb=" CA ASN L 379 " pdb=" CB ASN L 379 " ideal model delta harmonic sigma weight residual 122.80 144.61 -21.81 0 2.50e+00 1.60e-01 7.61e+01 ... (remaining 18931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 4556 0.199 - 0.399: 249 0.399 - 0.598: 10 0.598 - 0.798: 4 0.798 - 0.997: 1 Chirality restraints: 4820 Sorted by residual: chirality pdb=" CA ASN L 379 " pdb=" N ASN L 379 " pdb=" C ASN L 379 " pdb=" CB ASN L 379 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CB4 CDL S 702 " pdb=" CB3 CDL S 702 " pdb=" CB6 CDL S 702 " pdb=" OB6 CDL S 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.86 -0.71 2.00e-01 2.50e+01 1.27e+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 1.24e+01 ... (remaining 4817 not shown) Planarity restraints: 5526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 433 " 0.105 2.00e-02 2.50e+03 7.86e-02 9.28e+01 pdb=" CG HIS A 433 " -0.084 2.00e-02 2.50e+03 pdb=" ND1 HIS A 433 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 HIS A 433 " -0.077 2.00e-02 2.50e+03 pdb=" CE1 HIS A 433 " 0.048 2.00e-02 2.50e+03 pdb=" NE2 HIS A 433 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 120 " -0.050 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR D 120 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 120 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR D 120 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR D 120 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 120 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 120 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 120 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEC D 401 " 0.002 2.00e-02 2.50e+03 2.34e-02 1.23e+01 pdb=" C1B HEC D 401 " 0.004 2.00e-02 2.50e+03 pdb=" C2B HEC D 401 " 0.012 2.00e-02 2.50e+03 pdb=" C3B HEC D 401 " 0.007 2.00e-02 2.50e+03 pdb=" C4B HEC D 401 " -0.012 2.00e-02 2.50e+03 pdb=" CAB HEC D 401 " -0.043 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " -0.030 2.00e-02 2.50e+03 pdb=" CHC HEC D 401 " 0.031 2.00e-02 2.50e+03 pdb=" CMB HEC D 401 " 0.029 2.00e-02 2.50e+03 ... (remaining 5523 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 780 2.65 - 3.21: 31180 3.21 - 3.78: 58210 3.78 - 4.34: 84107 4.34 - 4.90: 126646 Nonbonded interactions: 300923 Sorted by model distance: nonbonded pdb=" OD2 ASP A 461 " pdb=" O HOH A3101 " model vdw 2.091 3.040 nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.100 3.080 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.103 3.080 nonbonded pdb=" OD2 ASP L 461 " pdb=" O HOH L3101 " model vdw 2.107 3.040 nonbonded pdb=" O2D HEM C 502 " pdb=" O HOH C 601 " model vdw 2.113 3.040 ... (remaining 300918 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' and (resid 1 through 321 or resid 323 through 506)) selection = (chain 'N' and (resid 1 through 321 or resid 323 through 506)) } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = (chain 'E' and (resid 39 through 64 or resid 66 through 101)) selection = (chain 'P' and (resid 39 through 64 or resid 66 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' and resid 8 through 82) 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=0.50 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 31.520 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 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 0.179 32402 Z= 0.596 Angle : 1.596 25.133 44038 Z= 0.996 Chirality : 0.105 0.997 4820 Planarity : 0.006 0.079 5526 Dihedral : 16.849 142.718 11650 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.32 % Favored : 97.65 % Rotamer: Outliers : 1.89 % Allowed : 5.99 % Favored : 92.12 % Cbeta Deviations : 0.77 % 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: -0.82 (0.12), residues: 3836 helix: -0.63 (0.10), residues: 2154 sheet: 0.44 (0.25), residues: 330 loop : -0.34 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG B 339 TYR 0.050 0.006 TYR D 120 PHE 0.047 0.006 PHE M 107 TRP 0.038 0.006 TRP O 280 HIS 0.029 0.004 HIS A 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00980 / 0.60 (32392) covalent geometry : angle 1.59597 / 1.00 (44030) SS BOND : bond 0.02248 / 1.11 ( 4) SS BOND : angle 2.25424 / 1.17 ( 8) hydrogen bonds : bond 0.18106 / 12.18 ( 1857) hydrogen bonds : angle 6.70834 / 4.82 ( 5241) Misc. bond : bond 0.10211 / 5.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 595 time to evaluate : 1.238 Fit side-chains REVERT: C 152 SER cc_start: 0.8240 (m) cc_final: 0.7994 (p) REVERT: C 159 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7086 (pm20) REVERT: C 165 LEU cc_start: 0.8315 (mt) cc_final: 0.8038 (tp) REVERT: C 250 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7801 (tppt) REVERT: C 288 LYS cc_start: 0.7116 (tttt) cc_final: 0.6817 (tttt) REVERT: G 9 LYS cc_start: 0.8010 (mttp) cc_final: 0.7520 (mmmt) REVERT: G 23 ILE cc_start: 0.7734 (mt) cc_final: 0.7407 (mm) REVERT: G 32 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8748 (t) REVERT: G 33 LYS cc_start: 0.8020 (tttt) cc_final: 0.7774 (tttt) REVERT: G 44 MET cc_start: 0.8839 (tmm) cc_final: 0.8620 (tmm) REVERT: G 66 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7859 (mm-30) REVERT: G 117 ASP cc_start: 0.7808 (m-30) cc_final: 0.7575 (m-30) REVERT: F 144 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6761 (mtt90) REVERT: A 29 LYS cc_start: 0.7058 (tttm) cc_final: 0.6856 (tttm) REVERT: A 32 THR cc_start: 0.8258 (m) cc_final: 0.7684 (p) REVERT: A 36 LYS cc_start: 0.6728 (mmtt) cc_final: 0.6523 (ttmm) REVERT: A 68 TYR cc_start: 0.6797 (m-80) cc_final: 0.6503 (m-80) REVERT: A 87 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7327 (ptp90) REVERT: A 93 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6626 (mt-10) REVERT: A 97 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6790 (mm-30) REVERT: A 98 ASN cc_start: 0.7429 (m-40) cc_final: 0.7220 (m-40) REVERT: A 125 LYS cc_start: 0.7152 (mttp) cc_final: 0.6567 (ttmm) REVERT: A 128 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7211 (tm-30) REVERT: A 147 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6531 (tp30) REVERT: A 149 GLU cc_start: 0.6053 (mt-10) cc_final: 0.5808 (tm-30) REVERT: A 153 ARG cc_start: 0.6223 (ttp-110) cc_final: 0.5864 (ttt90) REVERT: A 176 MET cc_start: 0.8871 (ttm) cc_final: 0.8670 (ttm) REVERT: A 198 GLU cc_start: 0.6813 (pt0) cc_final: 0.6085 (tp30) REVERT: A 201 LYS cc_start: 0.7864 (tttm) cc_final: 0.7614 (tttt) REVERT: A 220 VAL cc_start: 0.7956 (t) cc_final: 0.7640 (p) REVERT: A 231 LYS cc_start: 0.7355 (tttt) cc_final: 0.7033 (tttp) REVERT: A 292 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7109 (pm20) REVERT: A 390 LYS cc_start: 0.7331 (tptt) cc_final: 0.6641 (mtmt) REVERT: A 422 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6555 (mt-10) REVERT: A 426 LYS cc_start: 0.7906 (mttt) cc_final: 0.7705 (mmtp) REVERT: A 436 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8209 (mtm-85) REVERT: B 19 GLU cc_start: 0.7065 (tp30) cc_final: 0.6838 (mm-30) REVERT: B 72 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8590 (tpp-160) REVERT: B 83 LYS cc_start: 0.8315 (mmtm) cc_final: 0.8023 (mmmm) REVERT: B 139 LYS cc_start: 0.7454 (tttt) cc_final: 0.7125 (ttpt) REVERT: B 180 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6754 (tp30) REVERT: B 251 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5891 (pm20) REVERT: B 269 MET cc_start: 0.8072 (ttp) cc_final: 0.7749 (ttp) REVERT: B 339 ARG cc_start: 0.7520 (ttp80) cc_final: 0.7129 (ttp-110) REVERT: B 353 GLU cc_start: 0.6173 (mt-10) cc_final: 0.5838 (pp20) REVERT: B 354 ASN cc_start: 0.6159 (t0) cc_final: 0.5923 (t0) REVERT: B 364 MET cc_start: 0.7437 (tpp) cc_final: 0.7215 (tpp) REVERT: B 376 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6341 (pt0) REVERT: B 379 GLN cc_start: 0.6903 (tt0) cc_final: 0.6575 (tt0) REVERT: B 380 LYS cc_start: 0.7115 (tttm) cc_final: 0.6894 (tttt) REVERT: D 86 THR cc_start: 0.7638 (m) cc_final: 0.7159 (p) REVERT: D 89 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7835 (mt-10) REVERT: D 96 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7246 (mp0) REVERT: D 154 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7016 (pt0) REVERT: D 164 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6456 (mp0) REVERT: D 166 ASN cc_start: 0.7533 (m110) cc_final: 0.7327 (m-40) REVERT: D 224 GLU cc_start: 0.6941 (tt0) cc_final: 0.6691 (pm20) REVERT: D 230 VAL cc_start: 0.6979 (t) cc_final: 0.6666 (m) REVERT: H 35 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7780 (mtm110) REVERT: H 78 GLU cc_start: 0.7722 (tt0) cc_final: 0.7261 (mt-10) REVERT: J 10 LYS cc_start: 0.7271 (tttm) cc_final: 0.6543 (tptp) REVERT: J 11 LYS cc_start: 0.6085 (OUTLIER) cc_final: 0.5602 (mmtm) REVERT: J 20 PHE cc_start: 0.7586 (t80) cc_final: 0.7266 (t80) REVERT: J 55 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.7982 (ttp-110) REVERT: J 58 GLN cc_start: 0.7439 (tp40) cc_final: 0.7225 (tt0) REVERT: N 159 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7106 (pm20) REVERT: N 165 LEU cc_start: 0.8311 (mt) cc_final: 0.8036 (tp) REVERT: N 250 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7786 (tppt) REVERT: N 288 LYS cc_start: 0.6918 (tttt) cc_final: 0.6708 (tttm) REVERT: E 54 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7130 (mmpt) REVERT: R 9 LYS cc_start: 0.8042 (mttp) cc_final: 0.7544 (mmmt) REVERT: R 22 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5806 (ptpt) REVERT: R 23 ILE cc_start: 0.7817 (mt) cc_final: 0.7440 (mm) REVERT: R 33 LYS cc_start: 0.8021 (tttt) cc_final: 0.7765 (tttt) REVERT: R 66 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7845 (mm-30) REVERT: R 117 ASP cc_start: 0.7799 (m-30) cc_final: 0.7567 (m-30) REVERT: L 32 THR cc_start: 0.8230 (m) cc_final: 0.7663 (p) REVERT: L 36 LYS cc_start: 0.6724 (mmtt) cc_final: 0.6522 (ttmm) REVERT: L 68 TYR cc_start: 0.6787 (m-80) cc_final: 0.6495 (m-80) REVERT: L 93 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6623 (mt-10) REVERT: L 97 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6614 (mm-30) REVERT: L 98 ASN cc_start: 0.7444 (m-40) cc_final: 0.7112 (m-40) REVERT: L 120 LYS cc_start: 0.6574 (tttt) cc_final: 0.6210 (ptmt) REVERT: L 125 LYS cc_start: 0.7156 (mttp) cc_final: 0.6896 (mtmm) REVERT: L 128 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7182 (tm-30) REVERT: L 147 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6520 (tp30) REVERT: L 153 ARG cc_start: 0.6194 (ttp-110) cc_final: 0.5848 (ttt90) REVERT: L 176 MET cc_start: 0.8874 (ttm) cc_final: 0.8615 (ttm) REVERT: L 191 ILE cc_start: 0.7991 (mt) cc_final: 0.7784 (mp) REVERT: L 198 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6555 (tp30) REVERT: L 201 LYS cc_start: 0.7875 (tttm) cc_final: 0.7636 (tttt) REVERT: L 220 VAL cc_start: 0.7926 (t) cc_final: 0.7601 (p) REVERT: L 231 LYS cc_start: 0.7387 (tttt) cc_final: 0.7077 (tttp) REVERT: L 292 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7108 (pm20) REVERT: L 390 LYS cc_start: 0.7289 (tptt) cc_final: 0.6596 (mtpt) REVERT: L 422 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6555 (mt-10) REVERT: L 433 HIS cc_start: 0.7698 (m-70) cc_final: 0.6708 (t-90) REVERT: L 436 ARG cc_start: 0.8505 (mtp85) cc_final: 0.8235 (mtm-85) REVERT: M 24 LYS cc_start: 0.7420 (mttt) cc_final: 0.7101 (mmtp) REVERT: M 72 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8607 (tpp-160) REVERT: M 83 LYS cc_start: 0.8331 (mmtm) cc_final: 0.8044 (mmmm) REVERT: M 139 LYS cc_start: 0.7454 (tttt) cc_final: 0.7127 (ttpt) REVERT: M 180 GLU cc_start: 0.7065 (tp30) cc_final: 0.6856 (tp30) REVERT: M 269 MET cc_start: 0.8234 (ptt) cc_final: 0.7884 (ptt) REVERT: M 335 GLU cc_start: 0.6058 (tm-30) cc_final: 0.5672 (tp30) REVERT: M 379 GLN cc_start: 0.6896 (tt0) cc_final: 0.6569 (tt0) REVERT: M 380 LYS cc_start: 0.7114 (tttm) cc_final: 0.6865 (tttt) REVERT: O 164 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6451 (mp0) REVERT: O 166 ASN cc_start: 0.7536 (m110) cc_final: 0.7330 (m-40) REVERT: S 35 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7776 (mtm110) REVERT: S 53 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8147 (ttpp) REVERT: S 78 GLU cc_start: 0.7721 (tt0) cc_final: 0.7260 (mt-10) REVERT: U 10 LYS cc_start: 0.7451 (tttm) cc_final: 0.6655 (tptp) REVERT: U 20 PHE cc_start: 0.7613 (t80) cc_final: 0.7291 (t80) REVERT: U 58 GLN cc_start: 0.7472 (tp40) cc_final: 0.7253 (tt0) REVERT: U 73 ARG cc_start: 0.6244 (OUTLIER) cc_final: 0.5838 (mpt180) outliers start: 60 outliers final: 8 residues processed: 633 average time/residue: 0.8327 time to fit residues: 611.0407 Evaluate side-chains 466 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 448 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN C 14 ASN C 22 GLN C 173 ASN C 202 HIS C 332 ASN ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 ASN F 96 HIS A 74 HIS A 89 GLN A 222 HIS A 410 GLN B 319 HIS D 93 HIS I 55 HIS N 11 ASN N 14 ASN N 22 GLN N 202 HIS N 332 ASN ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN L 89 GLN L 192 GLN L 371 ASN L 410 GLN M 197 ASN M 241 ASN M 319 HIS M 354 ASN O 93 HIS T 55 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.118188 restraints weight = 21819.056| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 0.53 r_work: 0.3050 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work: 0.2685 rms_B_bonded: 4.99 restraints_weight: 0.1250 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.300 32402 Z= 0.198 Angle : 0.712 10.021 44038 Z= 0.370 Chirality : 0.046 0.168 4820 Planarity : 0.005 0.051 5526 Dihedral : 12.619 105.188 4730 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.49 % Allowed : 7.29 % Favored : 91.22 % 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: 1.18 (0.13), residues: 3836 helix: 1.15 (0.11), residues: 2152 sheet: 0.71 (0.25), residues: 336 loop : 0.41 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 283 TYR 0.025 0.003 TYR O 237 PHE 0.029 0.003 PHE L 334 TRP 0.021 0.003 TRP L 474 HIS 0.017 0.002 HIS A 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (32392) covalent geometry : angle 0.71225 / 0.37 (44030) SS BOND : bond 0.00379 / 0.19 ( 4) SS BOND : angle 0.39086 / 0.19 ( 8) hydrogen bonds : bond 0.06499 / 4.33 ( 1857) hydrogen bonds : angle 4.92596 / 3.59 ( 5241) Misc. bond : bond 0.24096 / 12.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 498 time to evaluate : 1.031 Fit side-chains REVERT: P 47 ASP cc_start: 0.9004 (t0) cc_final: 0.8788 (t0) REVERT: A 32 THR cc_start: 0.8552 (m) cc_final: 0.8139 (p) REVERT: A 50 GLN cc_start: 0.7344 (mm-40) cc_final: 0.7089 (mm-40) REVERT: A 68 TYR cc_start: 0.6995 (m-80) cc_final: 0.6707 (m-80) REVERT: B 19 GLU cc_start: 0.7019 (tp30) cc_final: 0.6796 (mm-30) REVERT: B 28 GLN cc_start: 0.7967 (tt0) cc_final: 0.7552 (tt0) REVERT: B 364 MET cc_start: 0.7953 (tpp) cc_final: 0.7737 (tpp) REVERT: B 379 GLN cc_start: 0.6836 (tt0) cc_final: 0.6634 (tt0) REVERT: D 96 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7874 (mp0) REVERT: D 230 VAL cc_start: 0.7460 (t) cc_final: 0.7148 (m) REVERT: D 256 VAL cc_start: 0.8649 (m) cc_final: 0.8382 (p) REVERT: J 10 LYS cc_start: 0.7773 (tttm) cc_final: 0.7509 (tptp) REVERT: J 55 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8386 (ttp-170) REVERT: R 23 ILE cc_start: 0.8470 (mt) cc_final: 0.8255 (mm) REVERT: L 32 THR cc_start: 0.8552 (m) cc_final: 0.8133 (p) REVERT: L 50 GLN cc_start: 0.7302 (mm-40) cc_final: 0.7018 (mm-40) REVERT: L 68 TYR cc_start: 0.7011 (m-80) cc_final: 0.6718 (m-80) REVERT: L 93 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7201 (mt-10) REVERT: M 28 GLN cc_start: 0.7968 (tt0) cc_final: 0.7550 (tt0) REVERT: M 269 MET cc_start: 0.8515 (ptt) cc_final: 0.8274 (ptt) REVERT: O 96 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7845 (mp0) REVERT: O 230 VAL cc_start: 0.7464 (t) cc_final: 0.7130 (m) REVERT: O 256 VAL cc_start: 0.8654 (m) cc_final: 0.8392 (p) REVERT: U 10 LYS cc_start: 0.7866 (tttm) cc_final: 0.7540 (tptp) REVERT: U 55 ARG cc_start: 0.8678 (ttm-80) cc_final: 0.8438 (ttp-170) outliers start: 47 outliers final: 17 residues processed: 525 average time/residue: 0.7384 time to fit residues: 450.7873 Evaluate side-chains 450 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 433 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 332 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 121 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 298 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 369 optimal weight: 0.8980 chunk 371 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN A 98 ASN A 192 GLN A 329 ASN B 319 HIS D 93 HIS H 15 HIS J 58 GLN ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 ASN L 329 ASN M 205 GLN M 319 HIS O 93 HIS S 15 HIS U 58 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.139305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119561 restraints weight = 28088.290| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 0.58 r_work: 0.3053 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 1.78 restraints_weight: 0.2500 r_work: 0.2712 rms_B_bonded: 4.77 restraints_weight: 0.1250 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.304 32402 Z= 0.186 Angle : 0.681 11.001 44038 Z= 0.350 Chirality : 0.045 0.159 4820 Planarity : 0.005 0.064 5526 Dihedral : 12.255 97.155 4699 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.36 % Allowed : 8.59 % Favored : 90.04 % 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: 1.64 (0.13), residues: 3836 helix: 1.52 (0.11), residues: 2138 sheet: 0.71 (0.26), residues: 340 loop : 0.69 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 55 TYR 0.023 0.003 TYR D 237 PHE 0.028 0.003 PHE A 334 TRP 0.019 0.002 TRP A 474 HIS 0.011 0.002 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (32392) covalent geometry : angle 0.68138 / 0.35 (44030) SS BOND : bond 0.00418 / 0.21 ( 4) SS BOND : angle 0.55562 / 0.30 ( 8) hydrogen bonds : bond 0.06125 / 4.08 ( 1857) hydrogen bonds : angle 4.80405 / 3.50 ( 5241) Misc. bond : bond 0.25199 / 13.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 466 time to evaluate : 1.148 Fit side-chains REVERT: P 47 ASP cc_start: 0.8982 (t0) cc_final: 0.8751 (t0) REVERT: A 32 THR cc_start: 0.8668 (m) cc_final: 0.8290 (p) REVERT: A 34 ASN cc_start: 0.8281 (m110) cc_final: 0.7997 (m-40) REVERT: A 68 TYR cc_start: 0.7078 (m-80) cc_final: 0.6804 (m-80) REVERT: B 307 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.8036 (pttp) REVERT: D 96 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7867 (mp0) REVERT: D 230 VAL cc_start: 0.7503 (t) cc_final: 0.7174 (m) REVERT: D 256 VAL cc_start: 0.8619 (m) cc_final: 0.8385 (p) REVERT: E 47 ASP cc_start: 0.8910 (t0) cc_final: 0.8647 (t0) REVERT: R 23 ILE cc_start: 0.8502 (mt) cc_final: 0.8294 (mm) REVERT: L 32 THR cc_start: 0.8622 (m) cc_final: 0.8246 (p) REVERT: L 34 ASN cc_start: 0.8269 (m110) cc_final: 0.7988 (m-40) REVERT: L 50 GLN cc_start: 0.7286 (mm-40) cc_final: 0.6978 (mm-40) REVERT: L 68 TYR cc_start: 0.7038 (m-80) cc_final: 0.6752 (m-80) REVERT: L 94 LEU cc_start: 0.7432 (mp) cc_final: 0.7223 (mp) REVERT: O 96 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7859 (mp0) REVERT: O 230 VAL cc_start: 0.7501 (t) cc_final: 0.7160 (m) REVERT: O 256 VAL cc_start: 0.8626 (m) cc_final: 0.8371 (p) outliers start: 43 outliers final: 18 residues processed: 499 average time/residue: 0.7647 time to fit residues: 448.3254 Evaluate side-chains 461 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 442 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 352 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 312 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 375 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN A 192 GLN A 329 ASN B 205 GLN B 316 GLN B 319 HIS B 406 GLN N 202 HIS ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 ASN L 329 ASN M 205 GLN M 316 GLN M 319 HIS U 58 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.141784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121990 restraints weight = 28228.841| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 0.56 r_work: 0.3094 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work: 0.2746 rms_B_bonded: 4.95 restraints_weight: 0.1250 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.337 32402 Z= 0.134 Angle : 0.587 13.469 44038 Z= 0.296 Chirality : 0.041 0.157 4820 Planarity : 0.004 0.038 5526 Dihedral : 11.620 89.881 4695 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.33 % Allowed : 8.81 % Favored : 89.86 % 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: 2.00 (0.14), residues: 3836 helix: 1.83 (0.11), residues: 2132 sheet: 0.85 (0.26), residues: 340 loop : 0.82 (0.18), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 61 TYR 0.020 0.002 TYR D 237 PHE 0.023 0.002 PHE A 334 TRP 0.017 0.002 TRP C 156 HIS 0.011 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (32392) covalent geometry : angle 0.58661 / 0.30 (44030) SS BOND : bond 0.00249 / 0.12 ( 4) SS BOND : angle 0.38644 / 0.22 ( 8) hydrogen bonds : bond 0.05170 / 3.45 ( 1857) hydrogen bonds : angle 4.56391 / 3.33 ( 5241) Misc. bond : bond 0.27173 / 14.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 458 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 47 ASP cc_start: 0.9023 (t0) cc_final: 0.8790 (t0) REVERT: A 32 THR cc_start: 0.8625 (m) cc_final: 0.8226 (p) REVERT: A 34 ASN cc_start: 0.8245 (m110) cc_final: 0.7974 (m-40) REVERT: A 68 TYR cc_start: 0.6942 (m-80) cc_final: 0.6657 (m-80) REVERT: A 198 GLU cc_start: 0.7224 (tp30) cc_final: 0.6913 (tp30) REVERT: B 236 ARG cc_start: 0.6924 (ttp-170) cc_final: 0.6573 (ttm-80) REVERT: D 256 VAL cc_start: 0.8582 (m) cc_final: 0.8342 (p) REVERT: E 47 ASP cc_start: 0.8966 (t0) cc_final: 0.8742 (t0) REVERT: L 32 THR cc_start: 0.8612 (m) cc_final: 0.8211 (p) REVERT: L 34 ASN cc_start: 0.8261 (m110) cc_final: 0.8002 (m-40) REVERT: L 50 GLN cc_start: 0.7345 (mm-40) cc_final: 0.7004 (mm-40) REVERT: L 68 TYR cc_start: 0.6948 (m-80) cc_final: 0.6664 (m-80) REVERT: O 230 VAL cc_start: 0.7508 (t) cc_final: 0.7189 (m) REVERT: O 256 VAL cc_start: 0.8582 (m) cc_final: 0.8324 (p) outliers start: 42 outliers final: 17 residues processed: 488 average time/residue: 0.8004 time to fit residues: 458.1320 Evaluate side-chains 444 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 427 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 138 LYS 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 273 VAL Chi-restraints excluded: chain U residue 55 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 176 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 342 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 372 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 361 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN A 192 GLN B 316 GLN B 319 HIS N 202 HIS N 343 HIS L 98 ASN M 319 HIS U 58 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.140247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.120529 restraints weight = 28193.461| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 0.58 r_work: 0.3068 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work: 0.2725 rms_B_bonded: 4.89 restraints_weight: 0.1250 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.309 32402 Z= 0.159 Angle : 0.634 12.443 44038 Z= 0.322 Chirality : 0.043 0.154 4820 Planarity : 0.004 0.045 5526 Dihedral : 11.613 89.257 4694 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.33 % Allowed : 9.37 % Favored : 89.30 % 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: 1.92 (0.14), residues: 3836 helix: 1.75 (0.11), residues: 2142 sheet: 0.80 (0.26), residues: 340 loop : 0.81 (0.18), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 56 TYR 0.021 0.002 TYR O 237 PHE 0.026 0.002 PHE L 334 TRP 0.015 0.002 TRP A 474 HIS 0.012 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (32392) covalent geometry : angle 0.63403 / 0.32 (44030) SS BOND : bond 0.00289 / 0.14 ( 4) SS BOND : angle 0.44287 / 0.24 ( 8) hydrogen bonds : bond 0.05662 / 3.78 ( 1857) hydrogen bonds : angle 4.65776 / 3.40 ( 5241) Misc. bond : bond 0.25593 / 13.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 435 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 47 ASP cc_start: 0.8991 (t0) cc_final: 0.8724 (t0) REVERT: A 32 THR cc_start: 0.8626 (m) cc_final: 0.8265 (p) REVERT: A 34 ASN cc_start: 0.8278 (m110) cc_final: 0.8016 (m-40) REVERT: A 68 TYR cc_start: 0.6931 (m-80) cc_final: 0.6662 (m-80) REVERT: A 198 GLU cc_start: 0.7162 (tp30) cc_final: 0.6878 (tp30) REVERT: B 236 ARG cc_start: 0.6923 (ttp-170) cc_final: 0.6598 (ttm-80) REVERT: D 158 ASP cc_start: 0.8279 (m-30) cc_final: 0.8025 (m-30) REVERT: D 256 VAL cc_start: 0.8579 (m) cc_final: 0.8359 (p) REVERT: E 47 ASP cc_start: 0.8950 (t0) cc_final: 0.8673 (t0) REVERT: L 32 THR cc_start: 0.8634 (m) cc_final: 0.8265 (p) REVERT: L 34 ASN cc_start: 0.8289 (m110) cc_final: 0.8043 (m-40) REVERT: L 68 TYR cc_start: 0.6939 (m-80) cc_final: 0.6676 (m-80) REVERT: O 158 ASP cc_start: 0.8287 (m-30) cc_final: 0.8020 (m-30) REVERT: O 256 VAL cc_start: 0.8601 (m) cc_final: 0.8363 (p) outliers start: 42 outliers final: 18 residues processed: 464 average time/residue: 0.8237 time to fit residues: 447.5407 Evaluate side-chains 443 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 425 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain U residue 55 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 237 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 334 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 283 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 319 HIS N 202 HIS N 343 HIS L 379 ASN M 319 HIS M 406 GLN M 408 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.141387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.121883 restraints weight = 31885.970| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.61 r_work: 0.3080 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.320 32402 Z= 0.141 Angle : 0.600 13.054 44038 Z= 0.303 Chirality : 0.042 0.157 4820 Planarity : 0.004 0.039 5526 Dihedral : 11.448 89.309 4694 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.21 % Allowed : 9.55 % Favored : 89.24 % 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: 2.03 (0.14), residues: 3836 helix: 1.84 (0.11), residues: 2132 sheet: 0.85 (0.26), residues: 342 loop : 0.87 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 61 TYR 0.020 0.002 TYR D 237 PHE 0.024 0.002 PHE L 334 TRP 0.012 0.002 TRP L 474 HIS 0.012 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (32392) covalent geometry : angle 0.59958 / 0.30 (44030) SS BOND : bond 0.00269 / 0.13 ( 4) SS BOND : angle 0.36630 / 0.20 ( 8) hydrogen bonds : bond 0.05286 / 3.53 ( 1857) hydrogen bonds : angle 4.57526 / 3.34 ( 5241) Misc. bond : bond 0.26030 / 14.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 437 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 47 ASP cc_start: 0.8805 (t0) cc_final: 0.8542 (t0) REVERT: A 32 THR cc_start: 0.8368 (m) cc_final: 0.8024 (p) REVERT: A 34 ASN cc_start: 0.7984 (m110) cc_final: 0.7724 (m-40) REVERT: A 198 GLU cc_start: 0.6985 (tp30) cc_final: 0.6682 (tp30) REVERT: D 158 ASP cc_start: 0.7998 (m-30) cc_final: 0.7690 (m-30) REVERT: E 47 ASP cc_start: 0.8789 (t0) cc_final: 0.8521 (t0) REVERT: L 32 THR cc_start: 0.8398 (m) cc_final: 0.8050 (p) REVERT: L 34 ASN cc_start: 0.8003 (m110) cc_final: 0.7755 (m-40) REVERT: O 158 ASP cc_start: 0.8007 (m-30) cc_final: 0.7683 (m-30) outliers start: 38 outliers final: 17 residues processed: 466 average time/residue: 0.7902 time to fit residues: 431.7400 Evaluate side-chains 430 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 413 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain U residue 55 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 83 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 313 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 333 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS J 58 GLN N 202 HIS N 343 HIS L 379 ASN M 319 HIS M 406 GLN M 408 HIS U 58 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.140635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.120734 restraints weight = 23396.983| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 0.52 r_work: 0.3083 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work: 0.2754 rms_B_bonded: 4.59 restraints_weight: 0.1250 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.317 32402 Z= 0.145 Angle : 0.609 13.187 44038 Z= 0.308 Chirality : 0.042 0.152 4820 Planarity : 0.004 0.039 5526 Dihedral : 11.423 89.581 4693 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.24 % Allowed : 9.93 % Favored : 88.83 % 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: 2.03 (0.14), residues: 3836 helix: 1.82 (0.11), residues: 2134 sheet: 0.84 (0.26), residues: 342 loop : 0.90 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 61 TYR 0.020 0.002 TYR O 237 PHE 0.024 0.002 PHE L 334 TRP 0.012 0.002 TRP L 474 HIS 0.012 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (32392) covalent geometry : angle 0.60916 / 0.31 (44030) SS BOND : bond 0.00272 / 0.13 ( 4) SS BOND : angle 0.34796 / 0.19 ( 8) hydrogen bonds : bond 0.05369 / 3.58 ( 1857) hydrogen bonds : angle 4.57285 / 3.34 ( 5241) Misc. bond : bond 0.26297 / 14.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 427 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 47 ASP cc_start: 0.8983 (t0) cc_final: 0.8696 (t0) REVERT: A 32 THR cc_start: 0.8531 (m) cc_final: 0.8132 (p) REVERT: A 34 ASN cc_start: 0.8214 (m110) cc_final: 0.7971 (m-40) REVERT: A 198 GLU cc_start: 0.7179 (tp30) cc_final: 0.6849 (tp30) REVERT: D 158 ASP cc_start: 0.8212 (m-30) cc_final: 0.7960 (m-30) REVERT: E 47 ASP cc_start: 0.8969 (t0) cc_final: 0.8677 (t0) REVERT: L 32 THR cc_start: 0.8553 (m) cc_final: 0.8157 (p) REVERT: L 34 ASN cc_start: 0.8206 (m110) cc_final: 0.7999 (m-40) REVERT: O 158 ASP cc_start: 0.8232 (m-30) cc_final: 0.7965 (m-30) outliers start: 39 outliers final: 24 residues processed: 457 average time/residue: 0.8123 time to fit residues: 434.6054 Evaluate side-chains 436 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 412 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 152 THR 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 273 VAL Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain M residue 388 GLU Chi-restraints excluded: chain U residue 55 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 225 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS C 343 HIS A 90 HIS B 205 GLN B 286 HIS B 319 HIS J 58 GLN N 202 HIS N 343 HIS M 205 GLN M 319 HIS M 408 HIS U 58 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.140924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.121203 restraints weight = 34353.621| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 0.58 r_work: 0.3075 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.316 32402 Z= 0.144 Angle : 0.608 12.982 44038 Z= 0.308 Chirality : 0.042 0.152 4820 Planarity : 0.004 0.039 5526 Dihedral : 11.391 89.949 4693 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.30 % Allowed : 9.99 % Favored : 88.71 % 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: 2.03 (0.14), residues: 3836 helix: 1.82 (0.11), residues: 2134 sheet: 0.81 (0.26), residues: 342 loop : 0.91 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 61 TYR 0.020 0.002 TYR O 237 PHE 0.024 0.002 PHE L 334 TRP 0.012 0.002 TRP L 474 HIS 0.011 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (32392) covalent geometry : angle 0.60853 / 0.31 (44030) SS BOND : bond 0.00261 / 0.13 ( 4) SS BOND : angle 0.31440 / 0.17 ( 8) hydrogen bonds : bond 0.05331 / 3.55 ( 1857) hydrogen bonds : angle 4.56374 / 3.34 ( 5241) Misc. bond : bond 0.26381 / 14.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 425 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 47 ASP cc_start: 0.8799 (t0) cc_final: 0.8514 (t0) REVERT: A 32 THR cc_start: 0.8387 (m) cc_final: 0.8039 (p) REVERT: A 34 ASN cc_start: 0.7982 (m110) cc_final: 0.7744 (m-40) REVERT: A 198 GLU cc_start: 0.7035 (tp30) cc_final: 0.6770 (tp30) REVERT: D 158 ASP cc_start: 0.7958 (m-30) cc_final: 0.7652 (m-30) REVERT: E 47 ASP cc_start: 0.8792 (t0) cc_final: 0.8499 (t0) REVERT: L 32 THR cc_start: 0.8399 (m) cc_final: 0.8049 (p) REVERT: L 34 ASN cc_start: 0.7992 (m110) cc_final: 0.7780 (m-40) REVERT: O 158 ASP cc_start: 0.7995 (m-30) cc_final: 0.7673 (m-30) outliers start: 41 outliers final: 24 residues processed: 457 average time/residue: 0.8324 time to fit residues: 445.7126 Evaluate side-chains 436 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 412 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 152 THR 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 273 VAL Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain M residue 388 GLU Chi-restraints excluded: chain U residue 55 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 323 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 266 optimal weight: 0.8980 chunk 319 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS C 343 HIS G 39 GLN B 92 HIS B 319 HIS N 202 HIS N 343 HIS R 39 GLN Q 96 HIS M 92 HIS M 286 HIS M 319 HIS M 408 HIS U 58 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.138835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.118743 restraints weight = 25718.567| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 0.56 r_work: 0.3051 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.289 32402 Z= 0.213 Angle : 0.721 10.552 44038 Z= 0.369 Chirality : 0.046 0.162 4820 Planarity : 0.005 0.066 5526 Dihedral : 11.952 93.542 4693 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.12 % Allowed : 10.45 % Favored : 88.43 % 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: 1.72 (0.13), residues: 3836 helix: 1.54 (0.11), residues: 2140 sheet: 0.68 (0.26), residues: 342 loop : 0.83 (0.18), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 283 TYR 0.025 0.003 TYR N 224 PHE 0.031 0.003 PHE L 334 TRP 0.016 0.003 TRP A 474 HIS 0.013 0.002 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (32392) covalent geometry : angle 0.72152 / 0.37 (44030) SS BOND : bond 0.00454 / 0.23 ( 4) SS BOND : angle 0.50835 / 0.26 ( 8) hydrogen bonds : bond 0.06341 / 4.23 ( 1857) hydrogen bonds : angle 4.82103 / 3.52 ( 5241) Misc. bond : bond 0.23402 / 12.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 423 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 47 ASP cc_start: 0.8753 (t0) cc_final: 0.8518 (t0) REVERT: A 32 THR cc_start: 0.8395 (m) cc_final: 0.8056 (p) REVERT: A 34 ASN cc_start: 0.8004 (m110) cc_final: 0.7755 (m-40) REVERT: D 158 ASP cc_start: 0.8041 (m-30) cc_final: 0.7724 (m-30) REVERT: E 47 ASP cc_start: 0.8759 (t0) cc_final: 0.8518 (t0) REVERT: L 32 THR cc_start: 0.8409 (m) cc_final: 0.8059 (p) REVERT: L 34 ASN cc_start: 0.8008 (m110) cc_final: 0.7784 (m-40) REVERT: O 158 ASP cc_start: 0.8111 (m-30) cc_final: 0.7789 (m-30) outliers start: 35 outliers final: 22 residues processed: 450 average time/residue: 0.8201 time to fit residues: 432.4776 Evaluate side-chains 429 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 407 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain M residue 388 GLU Chi-restraints excluded: chain U residue 55 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 108 optimal weight: 20.0000 chunk 254 optimal weight: 20.0000 chunk 345 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 206 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 281 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 106 optimal weight: 0.3980 chunk 238 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN C 202 HIS C 343 HIS A 90 HIS B 319 HIS N 11 ASN N 202 HIS N 343 HIS R 39 GLN L 90 HIS M 319 HIS M 408 HIS U 58 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.139464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.119339 restraints weight = 31766.259| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 0.56 r_work: 0.3060 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.2707 rms_B_bonded: 4.97 restraints_weight: 0.1250 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.275 32402 Z= 0.189 Angle : 0.681 10.791 44038 Z= 0.350 Chirality : 0.045 0.156 4820 Planarity : 0.005 0.053 5526 Dihedral : 11.876 91.779 4693 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.93 % Allowed : 10.86 % Favored : 88.21 % 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: 1.73 (0.13), residues: 3836 helix: 1.56 (0.11), residues: 2140 sheet: 0.68 (0.26), residues: 342 loop : 0.82 (0.18), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 55 TYR 0.022 0.003 TYR N 224 PHE 0.028 0.003 PHE L 334 TRP 0.016 0.002 TRP L 474 HIS 0.012 0.002 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (32392) covalent geometry : angle 0.68153 / 0.35 (44030) SS BOND : bond 0.00385 / 0.19 ( 4) SS BOND : angle 0.49277 / 0.26 ( 8) hydrogen bonds : bond 0.05984 / 3.99 ( 1857) hydrogen bonds : angle 4.75116 / 3.47 ( 5241) Misc. bond : bond 0.22763 / 12.47 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 417 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: P 47 ASP cc_start: 0.8964 (t0) cc_final: 0.8717 (t0) REVERT: A 32 THR cc_start: 0.8609 (m) cc_final: 0.8204 (p) REVERT: A 34 ASN cc_start: 0.8267 (m110) cc_final: 0.8021 (m-40) REVERT: A 153 ARG cc_start: 0.6835 (ttt180) cc_final: 0.6623 (ttp-110) REVERT: A 198 GLU cc_start: 0.7278 (tp30) cc_final: 0.6949 (tp30) REVERT: D 158 ASP cc_start: 0.8366 (m-30) cc_final: 0.8114 (m-30) REVERT: E 47 ASP cc_start: 0.8965 (t0) cc_final: 0.8723 (t0) REVERT: L 32 THR cc_start: 0.8593 (m) cc_final: 0.8202 (p) REVERT: L 34 ASN cc_start: 0.8244 (m110) cc_final: 0.8020 (m-40) REVERT: L 270 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8725 (mt) REVERT: O 158 ASP cc_start: 0.8361 (m-30) cc_final: 0.8106 (m-30) outliers start: 29 outliers final: 21 residues processed: 439 average time/residue: 0.7717 time to fit residues: 397.3803 Evaluate side-chains 433 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 411 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 270 LEU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain M residue 388 GLU Chi-restraints excluded: chain U residue 55 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 118 optimal weight: 3.9990 chunk 283 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 320 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS C 343 HIS B 319 HIS N 202 HIS N 343 HIS R 39 GLN L 90 HIS M 319 HIS M 408 HIS U 58 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.140611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.121343 restraints weight = 23036.086| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 0.50 r_work: 0.3085 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.316 32402 Z= 0.150 Angle : 0.625 12.951 44038 Z= 0.318 Chirality : 0.043 0.157 4820 Planarity : 0.004 0.038 5526 Dihedral : 11.599 89.896 4693 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.87 % Allowed : 10.86 % Favored : 88.28 % 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: 1.95 (0.14), residues: 3836 helix: 1.75 (0.11), residues: 2130 sheet: 0.73 (0.26), residues: 342 loop : 0.90 (0.18), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 283 TYR 0.020 0.002 TYR O 237 PHE 0.024 0.002 PHE A 334 TRP 0.013 0.002 TRP L 474 HIS 0.011 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (32392) covalent geometry : angle 0.62534 / 0.32 (44030) SS BOND : bond 0.00280 / 0.14 ( 4) SS BOND : angle 0.47813 / 0.26 ( 8) hydrogen bonds : bond 0.05443 / 3.63 ( 1857) hydrogen bonds : angle 4.63013 / 3.39 ( 5241) Misc. bond : bond 0.25184 / 14.02 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16717.48 seconds wall clock time: 284 minutes 47.54 seconds (17087.54 seconds total)