Starting phenix.real_space_refine on Mon Jul 6 07:41:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ab9_15315/07_2026/8ab9_15315.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ab9_15315/07_2026/8ab9_15315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ab9_15315/07_2026/8ab9_15315.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ab9_15315/07_2026/8ab9_15315.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ab9_15315/07_2026/8ab9_15315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ab9_15315/07_2026/8ab9_15315.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ab9_15315/07_2026/8ab9_15315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ab9_15315/07_2026/8ab9_15315.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21031 2.51 5 N 5296 2.21 5 O 6073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.02s 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: 32540 Number of models: 1 Model: "" Number of chains: 32 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} 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: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} 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: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 298 Unusual residues: {'CDL': 2, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 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: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 29.983 52.027 37.153 1.00138.40 S ATOM 4207 SG CYS P 187 32.583 49.171 36.973 1.00126.56 S Time building chain proxies: 5.59, per 1000 atoms: 0.17 Number of scatterers: 32540 At special positions: 0 Unit cell: (118.833, 129.636, 163.707, 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 8 26.01 S 102 16.00 P 30 15.00 O 6073 8.00 N 5296 7.00 C 21031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.02 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=2.07 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.07 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: 2.10 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 21 sheets defined 61.4% alpha, 8.6% 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: 3.729A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 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: 6.806A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.781A 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: 3.759A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.832A 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: 4.052A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 382 Processing helix chain 'P' and resid 58 through 89 removed outlier: 3.590A 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 99 Processing helix chain 'P' and resid 131 through 139 Processing helix chain 'P' and resid 151 through 156 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 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 84 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: 4.183A 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: 3.565A 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: 3.507A 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: 4.000A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.571A 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 Processing helix chain 'A' and resid 311 through 317 removed outlier: 4.001A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.593A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.577A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.400A 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 467 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' 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: 3.577A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.837A 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: 3.583A 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 removed outlier: 3.526A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.806A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.800A pdb=" N VAL B 283 " --> pdb=" O GLN B 280 " (cutoff:3.500A) 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: 3.663A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.587A 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 removed outlier: 3.907A pdb=" N LEU D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 139 " --> pdb=" O TRP D 135 " (cutoff:3.500A) No H-bonds generated for '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 220 Processing helix chain 'D' and resid 266 through 283 Processing helix chain 'D' and resid 285 through 321 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 81 removed outlier: 4.381A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.699A 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 removed outlier: 3.500A pdb=" N ILE I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) 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: 3.566A pdb=" N TRP J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Proline residue: J 33 - end of helix Processing helix chain 'J' and resid 53 through 60 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 66 through 72 removed outlier: 3.747A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.712A 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: 3.716A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 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: 6.791A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.789A 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: 3.763A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.826A 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: 4.045A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 382 Processing helix chain 'E' and resid 58 through 89 removed outlier: 3.634A 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 99 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 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 84 Processing helix chain 'R' and resid 88 through 92 Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 4.172A 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: 3.567A 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 78 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: 3.997A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 160 removed outlier: 3.575A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 157 through 160' Processing helix chain 'L' and resid 161 through 175 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 Processing helix chain 'L' and resid 311 through 317 removed outlier: 3.998A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 329 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.607A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.631A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.417A 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 467 Processing helix chain 'L' and resid 468 through 470 No H-bonds generated for 'chain 'L' and resid 468 through 470' 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: 3.576A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR M 118 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 128 through 142 Processing helix chain 'M' and resid 143 through 158 removed outlier: 3.572A 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 removed outlier: 3.519A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.785A 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: 3.880A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.590A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 Processing helix chain 'M' and resid 406 through 410 Processing helix chain 'M' and resid 412 through 416 Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 109 through 123 Processing helix chain 'O' and resid 124 through 127 Processing helix chain 'O' and resid 134 through 139 removed outlier: 3.916A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL O 139 " --> pdb=" O TRP O 135 " (cutoff:3.500A) No H-bonds generated for '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 220 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 321 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.361A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.685A 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 removed outlier: 3.508A pdb=" N ILE T 53 " --> pdb=" O GLN T 49 " (cutoff:3.500A) 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: 3.564A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.569A 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: 3.764A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.717A 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 'P' and resid 103 through 106 Processing sheet with id=AA3, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.921A pdb=" N LYS P 114 " --> pdb=" O HIS P 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 176 through 177 removed outlier: 3.536A pdb=" N SER P 192 " --> pdb=" O CYS P 187 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG P 202 " --> pdb=" O HIS P 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AA6, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.470A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU A 44 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 306 through 308 removed outlier: 4.012A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE H 24 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.595A pdb=" N LYS B 24 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLY B 195 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA B 26 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.608A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 241 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 156 through 158 Processing sheet with id=AB2, first strand: chain 'D' and resid 236 through 237 Processing sheet with id=AB3, first strand: chain 'J' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'N' and resid 21 through 23 Processing sheet with id=AB6, first strand: chain 'L' and resid 31 through 34 removed outlier: 6.466A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU L 44 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 306 through 308 removed outlier: 3.939A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 16 through 20 removed outlier: 4.067A pdb=" N LYS M 24 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.610A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 156 through 158 Processing sheet with id=AC2, first strand: chain 'O' and resid 236 through 237 Processing sheet with id=AC3, first strand: chain 'U' and resid 19 through 20 1886 hydrogen bonds defined for protein. 5331 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: 4.95 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 13591 1.40 - 1.61: 19566 1.61 - 1.82: 166 1.82 - 2.03: 25 2.03 - 2.23: 19 Bond restraints: 33367 Sorted by residual: bond pdb=" N TYR H 9 " pdb=" CA TYR H 9 " ideal model delta sigma weight residual 1.458 1.632 -0.174 1.90e-02 2.77e+03 8.43e+01 bond pdb=" N TYR S 9 " pdb=" CA TYR S 9 " ideal model delta sigma weight residual 1.458 1.616 -0.158 1.90e-02 2.77e+03 6.91e+01 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.613 -0.155 1.90e-02 2.77e+03 6.66e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.604 -0.146 1.90e-02 2.77e+03 5.92e+01 bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.475 -0.147 2.00e-02 2.50e+03 5.39e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 42404 3.27 - 6.54: 2608 6.54 - 9.80: 295 9.80 - 13.07: 34 13.07 - 16.34: 11 Bond angle restraints: 45352 Sorted by residual: angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.56 12.77 1.14e+00 7.69e-01 1.25e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 92.13 12.20 1.20e+00 6.94e-01 1.03e+02 angle pdb=" C GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta sigma weight residual 109.64 94.44 15.20 1.77e+00 3.19e-01 7.38e+01 angle pdb=" C GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta sigma weight residual 109.64 94.62 15.02 1.77e+00 3.19e-01 7.20e+01 angle pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " pdb="FE2 FES P 301 " ideal model delta sigma weight residual 75.66 85.13 -9.47 1.14e+00 7.69e-01 6.90e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.95: 18472 31.95 - 63.90: 947 63.90 - 95.85: 94 95.85 - 127.81: 1 127.81 - 159.76: 1 Dihedral angle restraints: 19515 sinusoidal: 7896 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -103.89 -18.71 0 2.50e+00 1.60e-01 5.60e+01 dihedral pdb=" C GLN B 215 " pdb=" N GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta harmonic sigma weight residual -122.60 -104.26 -18.34 0 2.50e+00 1.60e-01 5.38e+01 dihedral pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " pdb=" CBB HEC D 401 " ideal model delta sinusoidal sigma weight residual 60.00 -4.73 64.73 2 1.00e+01 1.00e-02 3.93e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 4554 0.194 - 0.387: 388 0.387 - 0.581: 16 0.581 - 0.774: 0 0.774 - 0.968: 4 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB4 CDL N 506 " pdb=" CB3 CDL N 506 " pdb=" CB6 CDL N 506 " pdb=" OB6 CDL N 506 " both_signs ideal model delta sigma weight residual False -2.57 -1.61 -0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CB4 CDL O 402 " pdb=" CB3 CDL O 402 " pdb=" CB6 CDL O 402 " pdb=" OB6 CDL O 402 " both_signs ideal model delta sigma weight residual False -2.57 -1.68 -0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.74 -0.83 2.00e-01 2.50e+01 1.74e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC O 401 " -0.019 2.00e-02 2.50e+03 2.99e-02 2.01e+01 pdb=" C2C HEC O 401 " -0.014 2.00e-02 2.50e+03 pdb=" C3C HEC O 401 " 0.025 2.00e-02 2.50e+03 pdb=" C4C HEC O 401 " -0.010 2.00e-02 2.50e+03 pdb=" CAC HEC O 401 " 0.042 2.00e-02 2.50e+03 pdb=" CHC HEC O 401 " 0.050 2.00e-02 2.50e+03 pdb=" CHD HEC O 401 " -0.025 2.00e-02 2.50e+03 pdb=" CMC HEC O 401 " -0.042 2.00e-02 2.50e+03 pdb=" NC HEC O 401 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEC O 401 " 0.003 2.00e-02 2.50e+03 2.84e-02 1.81e+01 pdb=" C1B HEC O 401 " 0.006 2.00e-02 2.50e+03 pdb=" C2B HEC O 401 " -0.025 2.00e-02 2.50e+03 pdb=" C3B HEC O 401 " -0.027 2.00e-02 2.50e+03 pdb=" C4B HEC O 401 " 0.003 2.00e-02 2.50e+03 pdb=" CAB HEC O 401 " 0.059 2.00e-02 2.50e+03 pdb=" CHB HEC O 401 " 0.032 2.00e-02 2.50e+03 pdb=" CHC HEC O 401 " -0.027 2.00e-02 2.50e+03 pdb=" CMB HEC O 401 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 96 " -0.041 2.00e-02 2.50e+03 3.38e-02 1.72e+01 pdb=" CG HIS N 96 " 0.060 2.00e-02 2.50e+03 pdb=" ND1 HIS N 96 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS N 96 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS N 96 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS N 96 " -0.035 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 215 2.62 - 3.19: 28509 3.19 - 3.76: 53622 3.76 - 4.33: 79781 4.33 - 4.90: 122644 Nonbonded interactions: 284771 Sorted by model distance: nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.046 3.080 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.047 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.120 3.120 nonbonded pdb=" ND2 ASN C 149 " pdb=" O LEU P 171 " model vdw 2.126 3.120 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.149 3.080 ... (remaining 284766 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 503) selection = (chain 'N' and resid 1 through 503) } ncs_group { reference = chain 'D' selection = (chain 'O' and resid 85 through 401) } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and resid 9 through 93) 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 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: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 28.730 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9383 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 : 0.011 0.230 33382 Z= 0.664 Angle : 1.792 22.479 45365 Z= 1.122 Chirality : 0.114 0.968 4962 Planarity : 0.007 0.044 5700 Dihedral : 17.891 159.757 12014 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 3.82 % Allowed : 8.24 % Favored : 87.94 % Cbeta Deviations : 1.36 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.63 (0.12), residues: 3955 helix: -1.26 (0.09), residues: 2158 sheet: -0.08 (0.26), residues: 353 loop : -0.74 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG L 269 TYR 0.049 0.007 TYR H 9 PHE 0.045 0.007 PHE C 234 TRP 0.042 0.008 TRP A 474 HIS 0.026 0.005 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.01103 / 0.66 (33367) covalent geometry : angle 1.78583 / 1.12 (45352) SS BOND : bond 0.02817 / 1.70 ( 5) SS BOND : angle 2.37374 / 1.23 ( 10) hydrogen bonds : bond 0.18682 / 12.53 ( 1886) hydrogen bonds : angle 7.10356 / 5.11 ( 5331) metal coordination : bond 0.10868 / 5.53 ( 4) metal coordination : angle 18.51231 / 9.86 ( 3) Misc. bond : bond 0.13309 / 6.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 487 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9452 (tttt) cc_final: 0.8949 (tptt) REVERT: C 229 ASP cc_start: 0.9275 (m-30) cc_final: 0.8993 (m-30) REVERT: C 239 MET cc_start: 0.9118 (ttp) cc_final: 0.8668 (mmt) REVERT: C 309 ASP cc_start: 0.9348 (t0) cc_final: 0.9107 (t0) REVERT: P 74 MET cc_start: 0.9154 (ttp) cc_final: 0.8913 (tmm) REVERT: P 119 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8713 (ttmt) REVERT: P 123 LYS cc_start: 0.9096 (mttt) cc_final: 0.8841 (mttp) REVERT: P 150 GLN cc_start: 0.6698 (tt0) cc_final: 0.6173 (tt0) REVERT: P 154 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8238 (tp30) REVERT: P 222 LEU cc_start: 0.9527 (pp) cc_final: 0.9185 (tt) REVERT: G 9 LYS cc_start: 0.9409 (mttp) cc_final: 0.9095 (tttt) REVERT: F 80 ILE cc_start: 0.9263 (mt) cc_final: 0.9018 (tt) REVERT: F 109 GLN cc_start: 0.9413 (mt0) cc_final: 0.9118 (mt0) REVERT: F 114 TYR cc_start: 0.8543 (t80) cc_final: 0.7892 (t80) REVERT: F 126 GLU cc_start: 0.9166 (mp0) cc_final: 0.8899 (mp0) REVERT: A 87 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8119 (mtp85) REVERT: I 30 ASP cc_start: 0.9532 (t70) cc_final: 0.9234 (t0) REVERT: I 43 ARG cc_start: 0.9302 (mtm110) cc_final: 0.9017 (ttp80) REVERT: J 11 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8779 (ptpp) REVERT: J 55 ARG cc_start: 0.8926 (ttm-80) cc_final: 0.8316 (ttm-80) REVERT: N 288 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8523 (ttpt) REVERT: E 55 ASP cc_start: 0.9248 (OUTLIER) cc_final: 0.8704 (p0) REVERT: R 9 LYS cc_start: 0.9181 (mttp) cc_final: 0.8642 (pttm) REVERT: R 85 LYS cc_start: 0.9398 (mttm) cc_final: 0.9147 (mmtm) REVERT: Q 80 ILE cc_start: 0.9454 (mt) cc_final: 0.9177 (mt) REVERT: Q 113 ASP cc_start: 0.9250 (m-30) cc_final: 0.8960 (t0) REVERT: Q 122 ASP cc_start: 0.8745 (p0) cc_final: 0.8499 (p0) REVERT: Q 126 GLU cc_start: 0.9480 (mp0) cc_final: 0.9112 (mp0) REVERT: L 36 LYS cc_start: 0.9549 (mmtt) cc_final: 0.9345 (mmtt) REVERT: L 97 GLU cc_start: 0.9530 (OUTLIER) cc_final: 0.9323 (mt-10) REVERT: M 16 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8872 (p) REVERT: M 58 GLU cc_start: 0.9459 (OUTLIER) cc_final: 0.9241 (tm-30) REVERT: M 124 GLU cc_start: 0.9407 (mt-10) cc_final: 0.9164 (mt-10) REVERT: T 30 ASP cc_start: 0.9541 (t70) cc_final: 0.9187 (t0) REVERT: T 38 ASP cc_start: 0.9164 (m-30) cc_final: 0.8841 (t0) REVERT: U 13 SER cc_start: 0.9324 (t) cc_final: 0.8965 (p) REVERT: U 55 ARG cc_start: 0.8883 (ttm-80) cc_final: 0.8658 (ttm-80) REVERT: U 58 GLN cc_start: 0.9145 (tp40) cc_final: 0.8657 (mt0) REVERT: U 59 ASP cc_start: 0.9288 (m-30) cc_final: 0.9064 (m-30) REVERT: U 74 GLU cc_start: 0.8907 (mp0) cc_final: 0.8583 (pm20) REVERT: U 80 ASN cc_start: 0.9169 (t0) cc_final: 0.8439 (p0) outliers start: 127 outliers final: 21 residues processed: 570 average time/residue: 0.2283 time to fit residues: 201.7820 Evaluate side-chains 358 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 329 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 197 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 109 PRO Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 288 LYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 261 SER Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN C 14 ASN C 173 ASN C 202 HIS C 332 ASN P 85 GLN G 54 ASN A 64 ASN A 222 HIS A 371 ASN B 87 HIS N 11 ASN N 14 ASN N 202 HIS N 332 ASN ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 371 ASN M 87 HIS ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 ASN M 377 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.067377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.052882 restraints weight = 79823.530| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 2.06 r_work: 0.2576 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9239 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.466 33382 Z= 0.148 Angle : 0.634 18.748 45365 Z= 0.314 Chirality : 0.042 0.217 4962 Planarity : 0.004 0.041 5700 Dihedral : 11.992 129.610 4884 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.56 % Allowed : 10.53 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 0.71 (0.13), residues: 3955 helix: 0.92 (0.11), residues: 2153 sheet: 0.46 (0.27), residues: 363 loop : -0.03 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 199 TYR 0.018 0.002 TYR D 237 PHE 0.019 0.002 PHE L 334 TRP 0.027 0.001 TRP C 156 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (33367) covalent geometry : angle 0.62680 / 0.31 (45352) SS BOND : bond 0.00153 / 0.08 ( 5) SS BOND : angle 0.86486 / 0.46 ( 10) hydrogen bonds : bond 0.04851 / 3.22 ( 1886) hydrogen bonds : angle 4.85317 / 3.45 ( 5331) metal coordination : bond 0.01947 / 0.96 ( 4) metal coordination : angle 12.05712 / 6.22 ( 3) Misc. bond : bond 0.31619 / 19.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 350 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9380 (tttt) cc_final: 0.8784 (tptt) REVERT: P 154 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7991 (tp30) REVERT: P 155 ARG cc_start: 0.5861 (mtp85) cc_final: 0.5461 (mtp85) REVERT: P 199 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8628 (ptp-110) REVERT: P 222 LEU cc_start: 0.9002 (pp) cc_final: 0.8730 (tt) REVERT: G 120 ASP cc_start: 0.9053 (m-30) cc_final: 0.8710 (m-30) REVERT: F 109 GLN cc_start: 0.9265 (mt0) cc_final: 0.8985 (mt0) REVERT: A 87 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8556 (ptp90) REVERT: H 51 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8208 (ptm160) REVERT: I 30 ASP cc_start: 0.9270 (t70) cc_final: 0.9035 (t0) REVERT: J 51 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8586 (tm-30) REVERT: E 55 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.7922 (p0) REVERT: R 9 LYS cc_start: 0.8836 (mttp) cc_final: 0.8499 (tttm) REVERT: R 85 LYS cc_start: 0.9131 (mttm) cc_final: 0.8823 (mmtm) REVERT: Q 84 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8489 (mt-10) REVERT: Q 88 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8118 (mp0) REVERT: Q 96 HIS cc_start: 0.8822 (t-170) cc_final: 0.8490 (t70) REVERT: Q 103 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8321 (tm-30) REVERT: Q 107 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9102 (mtmm) REVERT: Q 122 ASP cc_start: 0.8476 (p0) cc_final: 0.7696 (p0) REVERT: Q 126 GLU cc_start: 0.9168 (mp0) cc_final: 0.8754 (mp0) REVERT: L 97 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8626 (mt-10) REVERT: M 58 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8719 (tm-30) REVERT: M 124 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8511 (mt-10) REVERT: S 51 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8646 (ptm160) REVERT: T 30 ASP cc_start: 0.9328 (t70) cc_final: 0.8902 (t0) REVERT: U 13 SER cc_start: 0.9332 (t) cc_final: 0.8908 (p) REVERT: U 58 GLN cc_start: 0.8804 (tp40) cc_final: 0.8432 (tp40) REVERT: U 59 ASP cc_start: 0.8792 (m-30) cc_final: 0.8523 (m-30) REVERT: U 80 ASN cc_start: 0.9099 (t0) cc_final: 0.8315 (p0) outliers start: 52 outliers final: 16 residues processed: 389 average time/residue: 0.2171 time to fit residues: 134.6973 Evaluate side-chains 326 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 199 ARG Chi-restraints excluded: chain P residue 214 TYR Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain U residue 56 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 275 optimal weight: 2.9990 chunk 317 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 377 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 292 optimal weight: 8.9990 chunk 384 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN A 317 GLN B 121 GLN B 316 GLN L 317 GLN ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 HIS ** M 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.067448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.053251 restraints weight = 79964.517| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.04 r_work: 0.2594 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9237 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.389 33382 Z= 0.134 Angle : 0.551 16.633 45365 Z= 0.267 Chirality : 0.041 0.185 4962 Planarity : 0.004 0.042 5700 Dihedral : 10.856 113.039 4843 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.17 % Allowed : 11.28 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.52 (0.13), residues: 3955 helix: 1.62 (0.11), residues: 2169 sheet: 0.72 (0.27), residues: 361 loop : 0.27 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 128 TYR 0.018 0.001 TYR F 114 PHE 0.015 0.001 PHE L 334 TRP 0.017 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (33367) covalent geometry : angle 0.54431 / 0.27 (45352) SS BOND : bond 0.00231 / 0.13 ( 5) SS BOND : angle 0.52564 / 0.25 ( 10) hydrogen bonds : bond 0.04160 / 2.75 ( 1886) hydrogen bonds : angle 4.47532 / 3.17 ( 5331) metal coordination : bond 0.01312 / 0.65 ( 4) metal coordination : angle 10.80328 / 5.58 ( 3) Misc. bond : bond 0.28345 / 16.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 331 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 222 LEU cc_start: 0.8890 (pp) cc_final: 0.8527 (tt) REVERT: G 115 GLU cc_start: 0.9140 (tt0) cc_final: 0.8873 (tt0) REVERT: G 120 ASP cc_start: 0.9048 (m-30) cc_final: 0.8682 (m-30) REVERT: F 80 ILE cc_start: 0.9264 (mt) cc_final: 0.8969 (tt) REVERT: F 114 TYR cc_start: 0.8891 (t80) cc_final: 0.8476 (t80) REVERT: I 30 ASP cc_start: 0.9259 (t70) cc_final: 0.8984 (t0) REVERT: J 51 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8703 (tm-30) REVERT: N 283 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8608 (mtm180) REVERT: N 369 MET cc_start: 0.8453 (mmp) cc_final: 0.8223 (mtt) REVERT: E 55 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.7788 (p0) REVERT: E 92 SER cc_start: 0.9544 (t) cc_final: 0.9326 (p) REVERT: R 85 LYS cc_start: 0.9120 (mttm) cc_final: 0.8826 (mmtm) REVERT: R 110 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8571 (mm-30) REVERT: Q 84 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8555 (mt-10) REVERT: Q 88 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8131 (mp0) REVERT: Q 96 HIS cc_start: 0.8862 (t-170) cc_final: 0.8594 (t70) REVERT: Q 100 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8572 (mt-10) REVERT: Q 103 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8145 (tm-30) REVERT: Q 107 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.8910 (mtmm) REVERT: Q 113 ASP cc_start: 0.8400 (t0) cc_final: 0.8192 (t70) REVERT: L 97 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8620 (mt-10) REVERT: M 170 TYR cc_start: 0.7895 (p90) cc_final: 0.7664 (p90) REVERT: T 30 ASP cc_start: 0.9284 (t70) cc_final: 0.8876 (t0) REVERT: T 39 ASN cc_start: 0.8977 (m-40) cc_final: 0.8773 (m-40) REVERT: U 13 SER cc_start: 0.9302 (t) cc_final: 0.9037 (t) REVERT: U 55 ARG cc_start: 0.8888 (ttm-80) cc_final: 0.8571 (ttm-80) REVERT: U 58 GLN cc_start: 0.8812 (tp40) cc_final: 0.8445 (tp40) REVERT: U 59 ASP cc_start: 0.8770 (m-30) cc_final: 0.8499 (m-30) REVERT: U 80 ASN cc_start: 0.9114 (t0) cc_final: 0.8287 (p0) outliers start: 39 outliers final: 16 residues processed: 358 average time/residue: 0.2069 time to fit residues: 118.0295 Evaluate side-chains 320 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 267 GLU 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: 392 random chunks: chunk 364 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 295 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 220 optimal weight: 0.0870 chunk 384 optimal weight: 10.0000 chunk 337 optimal weight: 10.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 GLN ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 HIS F 109 GLN F 116 HIS F 137 ASN ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.066293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.052108 restraints weight = 80749.658| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.04 r_work: 0.2568 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2432 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9258 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.363 33382 Z= 0.171 Angle : 0.563 19.698 45365 Z= 0.267 Chirality : 0.041 0.161 4962 Planarity : 0.004 0.044 5700 Dihedral : 10.330 99.761 4827 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.47 % Allowed : 11.82 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.81 (0.14), residues: 3955 helix: 1.89 (0.11), residues: 2157 sheet: 0.73 (0.27), residues: 361 loop : 0.40 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 128 TYR 0.018 0.001 TYR N 225 PHE 0.014 0.001 PHE N 90 TRP 0.018 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (33367) covalent geometry : angle 0.55464 / 0.27 (45352) SS BOND : bond 0.00248 / 0.14 ( 5) SS BOND : angle 0.62178 / 0.32 ( 10) hydrogen bonds : bond 0.04045 / 2.67 ( 1886) hydrogen bonds : angle 4.39140 / 3.11 ( 5331) metal coordination : bond 0.01110 / 0.54 ( 4) metal coordination : angle 12.13514 / 6.19 ( 3) Misc. bond : bond 0.27008 / 15.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 308 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 341 GLN cc_start: 0.9218 (pp30) cc_final: 0.8987 (pp30) REVERT: P 222 LEU cc_start: 0.8916 (pp) cc_final: 0.8579 (tt) REVERT: G 120 ASP cc_start: 0.9041 (m-30) cc_final: 0.8680 (m-30) REVERT: F 80 ILE cc_start: 0.9296 (mt) cc_final: 0.8994 (tt) REVERT: F 114 TYR cc_start: 0.8938 (t80) cc_final: 0.8459 (t80) REVERT: I 30 ASP cc_start: 0.9276 (t70) cc_final: 0.9013 (t0) REVERT: I 34 GLU cc_start: 0.8841 (tt0) cc_final: 0.8606 (tt0) REVERT: J 51 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8751 (tm-30) REVERT: N 369 MET cc_start: 0.8470 (mmp) cc_final: 0.8241 (mtt) REVERT: E 55 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8158 (p0) REVERT: E 92 SER cc_start: 0.9547 (t) cc_final: 0.9318 (p) REVERT: R 85 LYS cc_start: 0.9173 (mttm) cc_final: 0.8873 (mmtm) REVERT: R 110 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8502 (mm-30) REVERT: R 112 GLU cc_start: 0.8806 (tt0) cc_final: 0.8460 (tt0) REVERT: Q 84 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8534 (mt-10) REVERT: Q 88 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8125 (mp0) REVERT: Q 96 HIS cc_start: 0.8869 (t-170) cc_final: 0.8489 (t70) REVERT: Q 100 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8672 (mm-30) REVERT: Q 103 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8455 (tm-30) REVERT: Q 107 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9005 (mtmm) REVERT: Q 114 TYR cc_start: 0.8172 (t80) cc_final: 0.7857 (t80) REVERT: Q 126 GLU cc_start: 0.9013 (mp0) cc_final: 0.8559 (mp0) REVERT: Q 131 GLN cc_start: 0.9138 (tp40) cc_final: 0.8420 (mp10) REVERT: L 97 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8621 (mt-10) REVERT: O 104 MET cc_start: 0.8506 (mtt) cc_final: 0.8281 (mtm) REVERT: S 51 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8639 (ptm160) REVERT: T 30 ASP cc_start: 0.9296 (t70) cc_final: 0.8901 (t0) REVERT: U 13 SER cc_start: 0.9338 (t) cc_final: 0.9053 (t) REVERT: U 55 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8551 (ttm-80) REVERT: U 58 GLN cc_start: 0.8826 (tp40) cc_final: 0.8458 (tp40) REVERT: U 59 ASP cc_start: 0.8744 (m-30) cc_final: 0.8472 (m-30) REVERT: U 80 ASN cc_start: 0.9115 (t0) cc_final: 0.8285 (p0) outliers start: 49 outliers final: 26 residues processed: 347 average time/residue: 0.2129 time to fit residues: 119.2690 Evaluate side-chains 327 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain U residue 56 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 99 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 287 optimal weight: 0.5980 chunk 275 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 chunk 369 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 321 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS N 177 GLN ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.067350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.053271 restraints weight = 80208.931| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.05 r_work: 0.2599 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9234 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.384 33382 Z= 0.118 Angle : 0.520 16.905 45365 Z= 0.248 Chirality : 0.040 0.149 4962 Planarity : 0.004 0.045 5700 Dihedral : 9.788 89.160 4825 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.23 % Allowed : 12.18 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.11 (0.14), residues: 3955 helix: 2.10 (0.11), residues: 2150 sheet: 0.83 (0.27), residues: 361 loop : 0.59 (0.18), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 144 TYR 0.018 0.001 TYR L 106 PHE 0.017 0.001 PHE P 126 TRP 0.015 0.001 TRP C 142 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (33367) covalent geometry : angle 0.51260 / 0.25 (45352) SS BOND : bond 0.00218 / 0.13 ( 5) SS BOND : angle 0.57420 / 0.30 ( 10) hydrogen bonds : bond 0.03724 / 2.45 ( 1886) hydrogen bonds : angle 4.27038 / 3.02 ( 5331) metal coordination : bond 0.00660 / 0.33 ( 4) metal coordination : angle 10.73424 / 5.54 ( 3) Misc. bond : bond 0.26070 / 13.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 317 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 341 GLN cc_start: 0.9182 (pp30) cc_final: 0.8675 (pp30) REVERT: P 68 MET cc_start: 0.9089 (mmm) cc_final: 0.8883 (tpp) REVERT: P 222 LEU cc_start: 0.8907 (pp) cc_final: 0.8573 (tt) REVERT: G 115 GLU cc_start: 0.9118 (tt0) cc_final: 0.8855 (tt0) REVERT: G 120 ASP cc_start: 0.9045 (m-30) cc_final: 0.8677 (m-30) REVERT: F 80 ILE cc_start: 0.9265 (mt) cc_final: 0.9063 (tt) REVERT: F 103 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8580 (mp0) REVERT: F 114 TYR cc_start: 0.8902 (t80) cc_final: 0.8412 (t80) REVERT: I 30 ASP cc_start: 0.9240 (t70) cc_final: 0.8981 (t0) REVERT: I 34 GLU cc_start: 0.8808 (tt0) cc_final: 0.8588 (tt0) REVERT: J 51 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8755 (tm-30) REVERT: N 186 MET cc_start: 0.9282 (tpp) cc_final: 0.9005 (mmt) REVERT: E 55 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8161 (p0) REVERT: E 92 SER cc_start: 0.9535 (t) cc_final: 0.9305 (p) REVERT: R 85 LYS cc_start: 0.9160 (mttm) cc_final: 0.8871 (mmtm) REVERT: R 112 GLU cc_start: 0.8811 (tt0) cc_final: 0.8599 (tp30) REVERT: Q 84 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8552 (mt-10) REVERT: Q 88 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8130 (mp0) REVERT: Q 96 HIS cc_start: 0.8869 (t-170) cc_final: 0.8648 (t70) REVERT: Q 100 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8691 (mt-10) REVERT: Q 107 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9210 (mttm) REVERT: Q 114 TYR cc_start: 0.8016 (t80) cc_final: 0.7736 (t80) REVERT: Q 131 GLN cc_start: 0.9122 (tp40) cc_final: 0.8430 (mp10) REVERT: L 97 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8588 (mt-10) REVERT: O 104 MET cc_start: 0.8461 (mtt) cc_final: 0.8234 (mtm) REVERT: T 30 ASP cc_start: 0.9282 (t70) cc_final: 0.8909 (t0) REVERT: U 13 SER cc_start: 0.9334 (t) cc_final: 0.9056 (t) REVERT: U 55 ARG cc_start: 0.8892 (ttm-80) cc_final: 0.8579 (ttm-80) REVERT: U 59 ASP cc_start: 0.8733 (m-30) cc_final: 0.8464 (m-30) REVERT: U 80 ASN cc_start: 0.9104 (t0) cc_final: 0.8273 (p0) outliers start: 41 outliers final: 22 residues processed: 348 average time/residue: 0.1974 time to fit residues: 110.9823 Evaluate side-chains 327 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 302 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 309 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 297 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 352 optimal weight: 0.0040 chunk 153 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 289 optimal weight: 0.9980 chunk 176 optimal weight: 8.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 343 HIS B 354 ASN R 84 HIS ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN M 408 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.067841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.053768 restraints weight = 80260.118| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.05 r_work: 0.2613 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9229 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.325 33382 Z= 0.116 Angle : 0.513 16.500 45365 Z= 0.244 Chirality : 0.040 0.142 4962 Planarity : 0.004 0.045 5700 Dihedral : 9.460 87.943 4823 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.26 % Allowed : 12.39 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.24 (0.14), residues: 3955 helix: 2.22 (0.11), residues: 2146 sheet: 0.79 (0.26), residues: 371 loop : 0.66 (0.18), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 201 TYR 0.027 0.001 TYR G 31 PHE 0.013 0.001 PHE A 334 TRP 0.011 0.001 TRP N 142 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (33367) covalent geometry : angle 0.50511 / 0.24 (45352) SS BOND : bond 0.00320 / 0.19 ( 5) SS BOND : angle 0.89736 / 0.47 ( 10) hydrogen bonds : bond 0.03654 / 2.41 ( 1886) hydrogen bonds : angle 4.19944 / 2.97 ( 5331) metal coordination : bond 0.00492 / 0.25 ( 4) metal coordination : angle 10.90522 / 5.68 ( 3) Misc. bond : bond 0.23898 / 13.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 316 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 341 GLN cc_start: 0.9135 (pp30) cc_final: 0.8637 (pp30) REVERT: P 222 LEU cc_start: 0.8854 (pp) cc_final: 0.8582 (tt) REVERT: G 120 ASP cc_start: 0.9050 (m-30) cc_final: 0.8672 (m-30) REVERT: F 114 TYR cc_start: 0.8872 (t80) cc_final: 0.8573 (t80) REVERT: A 63 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8658 (ttt180) REVERT: I 30 ASP cc_start: 0.9230 (t70) cc_final: 0.8964 (t0) REVERT: I 34 GLU cc_start: 0.8772 (tt0) cc_final: 0.8545 (tt0) REVERT: J 51 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8812 (tm-30) REVERT: E 55 ASP cc_start: 0.8463 (m-30) cc_final: 0.8215 (p0) REVERT: E 92 SER cc_start: 0.9517 (t) cc_final: 0.9301 (p) REVERT: R 85 LYS cc_start: 0.9184 (mttm) cc_final: 0.8943 (mmtm) REVERT: Q 84 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8534 (mt-10) REVERT: Q 88 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8119 (mp0) REVERT: Q 96 HIS cc_start: 0.8838 (t-170) cc_final: 0.8553 (t70) REVERT: Q 100 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8104 (mt-10) REVERT: Q 103 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8543 (pp20) REVERT: Q 107 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9188 (mttp) REVERT: Q 114 TYR cc_start: 0.7725 (t80) cc_final: 0.7419 (t80) REVERT: Q 122 ASP cc_start: 0.8183 (p0) cc_final: 0.7929 (p0) REVERT: Q 131 GLN cc_start: 0.9130 (tp40) cc_final: 0.8457 (mp10) REVERT: L 97 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8607 (mt-10) REVERT: M 339 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8905 (ttp-110) REVERT: O 104 MET cc_start: 0.8498 (mtt) cc_final: 0.8285 (mtm) REVERT: T 30 ASP cc_start: 0.9290 (t70) cc_final: 0.8950 (t0) REVERT: U 13 SER cc_start: 0.9335 (t) cc_final: 0.9060 (t) REVERT: U 55 ARG cc_start: 0.8908 (ttm-80) cc_final: 0.8547 (ttm-80) REVERT: U 59 ASP cc_start: 0.8677 (m-30) cc_final: 0.8460 (m-30) REVERT: U 80 ASN cc_start: 0.9104 (t0) cc_final: 0.8279 (p0) outliers start: 42 outliers final: 25 residues processed: 348 average time/residue: 0.2162 time to fit residues: 121.7338 Evaluate side-chains 327 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 298 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain M residue 339 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 132 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 332 ASN C 343 HIS P 193 HIS D 90 HIS E 85 GLN ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.064981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.050844 restraints weight = 81888.323| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.06 r_work: 0.2535 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9282 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.405 33382 Z= 0.239 Angle : 0.604 19.356 45365 Z= 0.283 Chirality : 0.043 0.148 4962 Planarity : 0.004 0.047 5700 Dihedral : 9.562 89.503 4821 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.32 % Allowed : 12.96 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.15 (0.14), residues: 3955 helix: 2.13 (0.11), residues: 2159 sheet: 0.72 (0.27), residues: 371 loop : 0.66 (0.18), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 144 TYR 0.024 0.002 TYR M 170 PHE 0.019 0.002 PHE N 90 TRP 0.017 0.001 TRP C 142 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (33367) covalent geometry : angle 0.59418 / 0.28 (45352) SS BOND : bond 0.00360 / 0.21 ( 5) SS BOND : angle 0.76663 / 0.39 ( 10) hydrogen bonds : bond 0.04130 / 2.73 ( 1886) hydrogen bonds : angle 4.33280 / 3.08 ( 5331) metal coordination : bond 0.01190 / 0.59 ( 4) metal coordination : angle 13.09292 / 6.81 ( 3) Misc. bond : bond 0.29471 / 16.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 222 LEU cc_start: 0.8885 (pp) cc_final: 0.8535 (tt) REVERT: G 120 ASP cc_start: 0.9050 (m-30) cc_final: 0.8653 (m-30) REVERT: F 114 TYR cc_start: 0.8921 (t80) cc_final: 0.8667 (t80) REVERT: A 63 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8602 (ttt180) REVERT: H 51 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8618 (ptm160) REVERT: I 30 ASP cc_start: 0.9330 (t70) cc_final: 0.9096 (t0) REVERT: J 51 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8831 (tm-30) REVERT: N 159 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8545 (mm-30) REVERT: E 55 ASP cc_start: 0.8487 (m-30) cc_final: 0.8248 (p0) REVERT: E 92 SER cc_start: 0.9538 (t) cc_final: 0.9329 (p) REVERT: R 85 LYS cc_start: 0.9224 (mttm) cc_final: 0.8941 (mmtm) REVERT: Q 84 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8482 (mt-10) REVERT: Q 88 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8156 (mp0) REVERT: Q 96 HIS cc_start: 0.8882 (t-170) cc_final: 0.8481 (t70) REVERT: Q 100 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8241 (mm-30) REVERT: Q 103 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8511 (pp20) REVERT: Q 107 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9133 (mttp) REVERT: Q 131 GLN cc_start: 0.9222 (tp40) cc_final: 0.8448 (mp10) REVERT: M 339 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8855 (ttp-110) REVERT: T 30 ASP cc_start: 0.9293 (t70) cc_final: 0.8923 (t0) REVERT: U 13 SER cc_start: 0.9356 (t) cc_final: 0.9085 (t) REVERT: U 55 ARG cc_start: 0.8917 (ttm-80) cc_final: 0.8547 (ttm-80) REVERT: U 59 ASP cc_start: 0.8680 (m-30) cc_final: 0.8436 (m-30) REVERT: U 80 ASN cc_start: 0.9164 (t0) cc_final: 0.8270 (p0) outliers start: 44 outliers final: 29 residues processed: 331 average time/residue: 0.2175 time to fit residues: 116.2015 Evaluate side-chains 322 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 133 GLU Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain M residue 339 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 344 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 389 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 307 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 chunk 286 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 343 HIS ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.066834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.052672 restraints weight = 80839.534| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.06 r_work: 0.2582 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9253 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.378 33382 Z= 0.137 Angle : 0.533 17.283 45365 Z= 0.254 Chirality : 0.040 0.142 4962 Planarity : 0.004 0.048 5700 Dihedral : 9.298 88.177 4818 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.05 % Allowed : 13.29 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.26 (0.14), residues: 3955 helix: 2.23 (0.11), residues: 2149 sheet: 0.73 (0.27), residues: 371 loop : 0.71 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 144 TYR 0.026 0.001 TYR M 170 PHE 0.017 0.001 PHE P 126 TRP 0.013 0.001 TRP C 142 HIS 0.013 0.001 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (33367) covalent geometry : angle 0.52522 / 0.25 (45352) SS BOND : bond 0.00303 / 0.18 ( 5) SS BOND : angle 0.73896 / 0.38 ( 10) hydrogen bonds : bond 0.03796 / 2.51 ( 1886) hydrogen bonds : angle 4.24781 / 3.02 ( 5331) metal coordination : bond 0.00409 / 0.21 ( 4) metal coordination : angle 11.40381 / 5.92 ( 3) Misc. bond : bond 0.26895 / 15.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 295 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: P 68 MET cc_start: 0.9093 (mmm) cc_final: 0.8868 (tpp) REVERT: P 130 ARG cc_start: 0.6421 (mtp-110) cc_final: 0.5945 (mmt90) REVERT: P 222 LEU cc_start: 0.8867 (pp) cc_final: 0.8549 (tt) REVERT: G 120 ASP cc_start: 0.9065 (m-30) cc_final: 0.8684 (m-30) REVERT: F 114 TYR cc_start: 0.8912 (t80) cc_final: 0.8649 (t80) REVERT: A 63 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8674 (ttt180) REVERT: I 30 ASP cc_start: 0.9308 (t70) cc_final: 0.9050 (t0) REVERT: J 51 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8852 (tm-30) REVERT: N 159 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8531 (mm-30) REVERT: E 55 ASP cc_start: 0.8484 (m-30) cc_final: 0.8248 (p0) REVERT: R 85 LYS cc_start: 0.9230 (mttm) cc_final: 0.8985 (mmtm) REVERT: Q 84 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8553 (mt-10) REVERT: Q 88 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8120 (mp0) REVERT: Q 96 HIS cc_start: 0.8862 (t-170) cc_final: 0.8450 (t70) REVERT: Q 100 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8280 (mm-30) REVERT: Q 103 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8523 (pp20) REVERT: Q 107 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9148 (mttp) REVERT: Q 131 GLN cc_start: 0.9165 (tp40) cc_final: 0.8467 (mp10) REVERT: M 339 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8850 (ttp-110) REVERT: T 30 ASP cc_start: 0.9305 (t70) cc_final: 0.8965 (t0) REVERT: U 13 SER cc_start: 0.9343 (t) cc_final: 0.9078 (t) REVERT: U 55 ARG cc_start: 0.8939 (ttm-80) cc_final: 0.8603 (ttm-80) REVERT: U 59 ASP cc_start: 0.8685 (m-30) cc_final: 0.8475 (m-30) REVERT: U 80 ASN cc_start: 0.9148 (t0) cc_final: 0.8257 (p0) outliers start: 35 outliers final: 27 residues processed: 321 average time/residue: 0.2150 time to fit residues: 111.8225 Evaluate side-chains 320 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 290 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 157 GLN Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain M residue 339 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 266 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 36 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 255 optimal weight: 0.6980 chunk 362 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 93 HIS ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.054237 restraints weight = 79899.972| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.05 r_work: 0.2627 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9219 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.339 33382 Z= 0.101 Angle : 0.503 15.628 45365 Z= 0.242 Chirality : 0.039 0.139 4962 Planarity : 0.004 0.050 5700 Dihedral : 8.996 88.690 4818 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.87 % Allowed : 13.56 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.38 (0.14), residues: 3955 helix: 2.34 (0.11), residues: 2148 sheet: 0.81 (0.27), residues: 371 loop : 0.74 (0.18), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 201 TYR 0.034 0.001 TYR G 31 PHE 0.019 0.001 PHE P 126 TRP 0.011 0.001 TRP C 142 HIS 0.005 0.001 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (33367) covalent geometry : angle 0.49540 / 0.24 (45352) SS BOND : bond 0.00296 / 0.19 ( 5) SS BOND : angle 0.84628 / 0.43 ( 10) hydrogen bonds : bond 0.03533 / 2.34 ( 1886) hydrogen bonds : angle 4.14760 / 2.94 ( 5331) metal coordination : bond 0.00862 / 0.45 ( 4) metal coordination : angle 10.40059 / 5.41 ( 3) Misc. bond : bond 0.26345 / 14.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 312 time to evaluate : 1.340 Fit side-chains REVERT: C 229 ASP cc_start: 0.8430 (m-30) cc_final: 0.8154 (m-30) REVERT: C 272 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8224 (mm-30) REVERT: P 128 ARG cc_start: 0.6425 (tpt90) cc_final: 0.6197 (tpt90) REVERT: P 130 ARG cc_start: 0.6406 (mtp-110) cc_final: 0.5872 (mmt90) REVERT: P 222 LEU cc_start: 0.8842 (pp) cc_final: 0.8567 (tt) REVERT: G 112 GLU cc_start: 0.8780 (tt0) cc_final: 0.8483 (tt0) REVERT: G 120 ASP cc_start: 0.9046 (m-30) cc_final: 0.8664 (m-30) REVERT: F 80 ILE cc_start: 0.8980 (tt) cc_final: 0.8780 (tt) REVERT: F 110 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8200 (pt0) REVERT: F 114 TYR cc_start: 0.8897 (t80) cc_final: 0.8637 (t80) REVERT: A 63 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8884 (ttt180) REVERT: I 30 ASP cc_start: 0.9270 (t70) cc_final: 0.9001 (t0) REVERT: J 51 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8842 (tm-30) REVERT: N 159 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8523 (mm-30) REVERT: E 55 ASP cc_start: 0.8452 (m-30) cc_final: 0.8201 (p0) REVERT: R 85 LYS cc_start: 0.9213 (mttm) cc_final: 0.8981 (mtmm) REVERT: Q 84 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8534 (mt-10) REVERT: Q 88 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8097 (mp0) REVERT: Q 96 HIS cc_start: 0.8871 (t-170) cc_final: 0.8658 (t70) REVERT: Q 100 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8169 (mt-10) REVERT: Q 103 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8513 (pp20) REVERT: Q 107 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9135 (mttp) REVERT: Q 131 GLN cc_start: 0.9154 (tp40) cc_final: 0.8474 (mp10) REVERT: M 339 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8866 (ttp-110) REVERT: T 30 ASP cc_start: 0.9269 (t70) cc_final: 0.8951 (t0) REVERT: U 13 SER cc_start: 0.9274 (t) cc_final: 0.8999 (t) REVERT: U 55 ARG cc_start: 0.8925 (ttm-80) cc_final: 0.8582 (ttm-80) REVERT: U 59 ASP cc_start: 0.8680 (m-30) cc_final: 0.8454 (m-30) REVERT: U 80 ASN cc_start: 0.9131 (t0) cc_final: 0.8231 (p0) outliers start: 29 outliers final: 21 residues processed: 333 average time/residue: 0.2172 time to fit residues: 116.9425 Evaluate side-chains 323 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 298 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain Q residue 124 VAL Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 339 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 13 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 chunk 162 optimal weight: 0.2980 chunk 1 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 45 ASN ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.067707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.053723 restraints weight = 80839.141| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.05 r_work: 0.2611 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9230 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.456 33382 Z= 0.126 Angle : 0.523 15.852 45365 Z= 0.249 Chirality : 0.040 0.142 4962 Planarity : 0.004 0.053 5700 Dihedral : 8.907 88.322 4818 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.81 % Allowed : 13.68 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.42 (0.14), residues: 3955 helix: 2.36 (0.11), residues: 2148 sheet: 0.82 (0.27), residues: 371 loop : 0.76 (0.18), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 144 TYR 0.034 0.001 TYR G 31 PHE 0.015 0.001 PHE P 64 TRP 0.013 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (33367) covalent geometry : angle 0.51490 / 0.25 (45352) SS BOND : bond 0.00275 / 0.17 ( 5) SS BOND : angle 0.74217 / 0.38 ( 10) hydrogen bonds : bond 0.03597 / 2.38 ( 1886) hydrogen bonds : angle 4.13797 / 2.94 ( 5331) metal coordination : bond 0.00454 / 0.24 ( 4) metal coordination : angle 10.93441 / 5.73 ( 3) Misc. bond : bond 0.29450 / 15.48 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 1.364 Fit side-chains REVERT: C 229 ASP cc_start: 0.8385 (m-30) cc_final: 0.8094 (m-30) REVERT: P 130 ARG cc_start: 0.6413 (mtp-110) cc_final: 0.5874 (mmt90) REVERT: P 222 LEU cc_start: 0.8832 (pp) cc_final: 0.8532 (tt) REVERT: G 120 ASP cc_start: 0.9048 (m-30) cc_final: 0.8679 (m-30) REVERT: F 110 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8189 (pt0) REVERT: F 114 TYR cc_start: 0.8914 (t80) cc_final: 0.8648 (t80) REVERT: F 144 ARG cc_start: 0.8758 (mtp-110) cc_final: 0.8497 (mtm-85) REVERT: A 63 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8859 (ttt180) REVERT: I 30 ASP cc_start: 0.9287 (t70) cc_final: 0.9004 (t0) REVERT: J 51 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8849 (tm-30) REVERT: N 159 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8531 (mm-30) REVERT: E 55 ASP cc_start: 0.8484 (m-30) cc_final: 0.8269 (p0) REVERT: R 85 LYS cc_start: 0.9244 (mttm) cc_final: 0.9005 (mtmm) REVERT: Q 84 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8549 (mt-10) REVERT: Q 88 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8098 (mp0) REVERT: Q 96 HIS cc_start: 0.8864 (t-170) cc_final: 0.8428 (t70) REVERT: Q 100 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8220 (mm-30) REVERT: Q 103 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8497 (pp20) REVERT: Q 107 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9083 (mttp) REVERT: Q 112 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7137 (pp20) REVERT: Q 113 ASP cc_start: 0.8235 (t0) cc_final: 0.8028 (t0) REVERT: Q 131 GLN cc_start: 0.9145 (tp40) cc_final: 0.8430 (mp10) REVERT: M 339 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8882 (ttp-110) REVERT: O 248 MET cc_start: 0.8762 (tpp) cc_final: 0.8004 (tpp) REVERT: T 30 ASP cc_start: 0.9283 (t70) cc_final: 0.8971 (t0) REVERT: U 13 SER cc_start: 0.9283 (t) cc_final: 0.9021 (t) REVERT: U 55 ARG cc_start: 0.8923 (ttm-80) cc_final: 0.8571 (ttm-80) REVERT: U 59 ASP cc_start: 0.8615 (m-30) cc_final: 0.8396 (m-30) REVERT: U 80 ASN cc_start: 0.9145 (t0) cc_final: 0.8182 (p0) outliers start: 27 outliers final: 18 residues processed: 320 average time/residue: 0.2056 time to fit residues: 107.8037 Evaluate side-chains 316 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 294 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 339 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 179 optimal weight: 0.9990 chunk 354 optimal weight: 5.9990 chunk 387 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 370 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 377 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 93 HIS ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.067750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.053701 restraints weight = 80716.500| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.05 r_work: 0.2615 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9228 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.417 33382 Z= 0.121 Angle : 0.516 15.804 45365 Z= 0.245 Chirality : 0.040 0.140 4962 Planarity : 0.004 0.053 5700 Dihedral : 8.794 86.857 4818 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.78 % Allowed : 13.98 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.44 (0.14), residues: 3955 helix: 2.38 (0.11), residues: 2150 sheet: 0.80 (0.27), residues: 371 loop : 0.79 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 144 TYR 0.033 0.001 TYR G 31 PHE 0.013 0.001 PHE A 334 TRP 0.012 0.001 TRP C 142 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (33367) covalent geometry : angle 0.50834 / 0.25 (45352) SS BOND : bond 0.00247 / 0.16 ( 5) SS BOND : angle 0.69680 / 0.36 ( 10) hydrogen bonds : bond 0.03557 / 2.35 ( 1886) hydrogen bonds : angle 4.11752 / 2.93 ( 5331) metal coordination : bond 0.00402 / 0.21 ( 4) metal coordination : angle 11.16276 / 5.88 ( 3) Misc. bond : bond 0.28877 / 15.40 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7591.84 seconds wall clock time: 131 minutes 13.07 seconds (7873.07 seconds total)