Starting phenix.real_space_refine on Mon Sep 14 22:33:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8abm_15326/09_2026/8abm_15326.cif Found real_map, /net/cci-nas-00/data/ceres_data/8abm_15326/09_2026/8abm_15326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8abm_15326/09_2026/8abm_15326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8abm_15326/09_2026/8abm_15326.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8abm_15326/09_2026/8abm_15326.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8abm_15326/09_2026/8abm_15326.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8abm_15326/09_2026/8abm_15326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8abm_15326/09_2026/8abm_15326.map" } resolution = 2.8 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 130 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 287 Unusual residues: {'CDL': 2, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 138 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 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: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 337 Unusual residues: {'CDL': 3, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 188 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "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 30.322 49.694 34.768 1.00105.62 S ATOM 4207 SG CYS P 187 32.789 46.843 33.790 1.00114.09 S Time building chain proxies: 6.12, per 1000 atoms: 0.19 Number of scatterers: 32540 At special positions: 0 Unit cell: (119.691, 129.735, 164.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 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=2.05 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.07 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 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 187 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " 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: 198 helices and 21 sheets defined 61.7% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 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: 3.771A 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 150 Processing helix chain 'C' and resid 151 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: 6.802A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.763A 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: 3.746A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.790A 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: 4.098A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 383 Processing helix chain 'P' and resid 58 through 89 removed outlier: 3.657A 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: 4.224A 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: 3.597A 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: 3.513A 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: 3.997A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 5.045A pdb=" N ASN A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.519A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.963A 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: 3.673A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.574A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.621A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 69 through 80 Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.610A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.871A 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: 3.606A 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: 3.522A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.807A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.859A 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: 3.705A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.592A 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: 3.939A pdb=" N LEU D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.884A 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 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 56 removed outlier: 4.309A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 81 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: 3.527A 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: 3.535A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.831A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.643A 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: 3.778A 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: 6.807A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.753A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.792A 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: 4.100A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 383 Processing helix chain 'E' and resid 58 through 89 removed outlier: 3.643A 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 94 through 98 Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 4.185A 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: 3.595A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 71 through 80 Processing helix chain 'L' and resid 88 through 100 Processing helix chain 'L' and resid 122 through 136 Processing helix chain 'L' and resid 140 through 155 removed outlier: 3.996A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 removed outlier: 5.050A pdb=" N ASN L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 156 through 160' Processing helix chain 'L' and resid 161 through 175 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 removed outlier: 3.519A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 3.965A 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: 3.675A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.650A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU L 394 " --> pdb=" O LYS L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 414 Processing helix chain 'L' and resid 419 through 429 Processing helix chain 'L' and resid 431 through 443 Processing helix chain 'L' and resid 461 through 468 removed outlier: 3.624A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 48 Processing helix chain 'M' and resid 52 through 60 Processing helix chain 'M' and resid 69 through 80 Processing helix chain 'M' and resid 103 through 118 removed outlier: 3.603A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.882A 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: 3.599A 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: 3.529A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.817A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.852A pdb=" N VAL M 283 " --> pdb=" O GLN M 280 " (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: 3.829A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.602A 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: 3.940A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.901A 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 320 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 56 removed outlier: 4.305A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 81 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: 3.517A 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: 3.563A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.833A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.642A 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 removed outlier: 3.509A pdb=" N VAL P 103 " --> pdb=" O ILE P 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.894A 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: 3.606A 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: 6.525A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU A 44 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308 removed outlier: 3.950A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.833A 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: 6.568A pdb=" N LYS B 24 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY B 195 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.733A 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: 6.630A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.620A 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: 6.525A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU L 44 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 307 through 308 removed outlier: 3.916A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 16 through 20 removed outlier: 6.564A pdb=" N LYS M 24 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY M 195 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA M 26 " --> pdb=" O GLY M 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.637A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.611A 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 1881 hydrogen bonds defined for protein. 5304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.89 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 13593 1.41 - 1.61: 19565 1.61 - 1.82: 173 1.82 - 2.03: 18 2.03 - 2.24: 18 Bond restraints: 33367 Sorted by residual: bond pdb=" C32 CDL A3001 " pdb=" C33 CDL A3001 " ideal model delta sigma weight residual 1.517 1.653 -0.136 1.70e-02 3.46e+03 6.38e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.607 -0.149 1.90e-02 2.77e+03 6.15e+01 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.603 -0.145 1.90e-02 2.77e+03 5.86e+01 bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.465 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C18 XP4 A3003 " pdb=" O7 XP4 A3003 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.14e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 42695 3.31 - 6.61: 2313 6.61 - 9.92: 276 9.92 - 13.23: 56 13.23 - 16.54: 12 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 93.81 10.52 1.14e+00 7.69e-01 8.52e+01 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 98.08 13.19 1.47e+00 4.63e-01 8.05e+01 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.64 10.69 1.20e+00 6.94e-01 7.94e+01 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 95.46 16.54 2.20e+00 2.07e-01 5.65e+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 84.20 -8.54 1.14e+00 7.69e-01 5.61e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.30: 18524 32.30 - 64.59: 901 64.59 - 96.89: 88 96.89 - 129.18: 1 129.18 - 161.48: 1 Dihedral angle restraints: 19515 sinusoidal: 7896 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -106.21 -16.39 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " pdb=" CAB HEC O 401 " pdb=" CBB HEC O 401 " ideal model delta sinusoidal sigma weight residual 60.00 -1.09 61.09 2 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " pdb=" CBB HEC D 401 " ideal model delta sinusoidal sigma weight residual 60.00 -0.83 60.83 2 1.00e+01 1.00e-02 3.66e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 4551 0.198 - 0.396: 389 0.396 - 0.594: 16 0.594 - 0.792: 2 0.792 - 0.990: 4 Chirality restraints: 4962 Sorted by residual: 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 -1.58 -0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" CB4 CDL C 507 " pdb=" CB3 CDL C 507 " pdb=" CB6 CDL C 507 " pdb=" OB6 CDL C 507 " both_signs ideal model delta sigma weight residual False -2.57 -1.59 -0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CB4 CDL N 508 " pdb=" CB3 CDL N 508 " pdb=" CB6 CDL N 508 " pdb=" OB6 CDL N 508 " both_signs ideal model delta sigma weight residual False -2.57 -1.71 -0.86 2.00e-01 2.50e+01 1.87e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEC D 401 " -0.012 2.00e-02 2.50e+03 3.33e-02 2.49e+01 pdb=" C2A HEC D 401 " -0.040 2.00e-02 2.50e+03 pdb=" C3A HEC D 401 " -0.024 2.00e-02 2.50e+03 pdb=" C4A HEC D 401 " -0.039 2.00e-02 2.50e+03 pdb=" CAA HEC D 401 " 0.053 2.00e-02 2.50e+03 pdb=" CHA HEC D 401 " 0.010 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " 0.056 2.00e-02 2.50e+03 pdb=" CMA HEC D 401 " -0.005 2.00e-02 2.50e+03 pdb=" NA HEC D 401 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM C 502 " 0.039 2.00e-02 2.50e+03 3.00e-02 2.02e+01 pdb=" C1B HEM C 502 " 0.025 2.00e-02 2.50e+03 pdb=" C2B HEM C 502 " 0.024 2.00e-02 2.50e+03 pdb=" C3B HEM C 502 " 0.012 2.00e-02 2.50e+03 pdb=" C4B HEM C 502 " 0.016 2.00e-02 2.50e+03 pdb=" CAB HEM C 502 " -0.014 2.00e-02 2.50e+03 pdb=" CHB HEM C 502 " -0.054 2.00e-02 2.50e+03 pdb=" CHC HEM C 502 " -0.042 2.00e-02 2.50e+03 pdb=" CMB HEM C 502 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 401 " 0.023 2.00e-02 2.50e+03 2.76e-02 1.71e+01 pdb=" C2C HEC D 401 " 0.018 2.00e-02 2.50e+03 pdb=" C3C HEC D 401 " -0.012 2.00e-02 2.50e+03 pdb=" C4C HEC D 401 " 0.009 2.00e-02 2.50e+03 pdb=" CAC HEC D 401 " -0.039 2.00e-02 2.50e+03 pdb=" CHC HEC D 401 " -0.055 2.00e-02 2.50e+03 pdb=" CHD HEC D 401 " 0.009 2.00e-02 2.50e+03 pdb=" CMC HEC D 401 " 0.030 2.00e-02 2.50e+03 pdb=" NC HEC D 401 " 0.017 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 229 2.62 - 3.19: 28447 3.19 - 3.76: 53227 3.76 - 4.33: 78638 4.33 - 4.90: 121609 Nonbonded interactions: 282150 Sorted by model distance: nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.055 3.080 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.057 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.069 3.120 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.164 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEM C 502 " model vdw 2.226 3.080 ... (remaining 282145 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' } 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.740 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9486 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 0.206 33382 Z= 0.651 Angle : 1.759 16.537 45365 Z= 1.095 Chirality : 0.116 0.990 4962 Planarity : 0.007 0.042 5700 Dihedral : 17.783 161.478 12014 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.55 % Favored : 97.40 % Rotamer: Outliers : 3.85 % Allowed : 7.67 % Favored : 88.48 % Cbeta Deviations : 1.47 % 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: -1.57 (0.12), residues: 3955 helix: -1.19 (0.09), residues: 2104 sheet: -0.19 (0.25), residues: 363 loop : -0.75 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG C 283 TYR 0.044 0.007 TYR B 166 PHE 0.048 0.006 PHE B 107 TRP 0.046 0.007 TRP A 474 HIS 0.028 0.004 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.01081 / 0.65 (33367) covalent geometry : angle 1.75623 / 1.09 (45352) SS BOND : bond 0.02774 / 1.64 ( 5) SS BOND : angle 2.87388 / 1.49 ( 10) hydrogen bonds : bond 0.18921 / 12.64 ( 1881) hydrogen bonds : angle 6.99454 / 5.07 ( 5304) metal coordination : bond 0.08981 / 4.39 ( 4) metal coordination : angle 12.40312 / 6.70 ( 3) Misc. bond : bond 0.13582 / 6.98 ( 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 475 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 347 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: P 115 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7729 (p0) REVERT: P 176 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8836 (pp) REVERT: P 182 PHE cc_start: 0.8122 (m-80) cc_final: 0.7679 (m-80) REVERT: P 221 THR cc_start: 0.8633 (p) cc_final: 0.8269 (p) REVERT: F 99 ASP cc_start: 0.9325 (m-30) cc_final: 0.9041 (m-30) REVERT: F 122 ASP cc_start: 0.8641 (p0) cc_final: 0.8430 (p0) REVERT: F 137 ASN cc_start: 0.9266 (m-40) cc_final: 0.9020 (m-40) REVERT: A 87 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7828 (mtp85) REVERT: B 170 TYR cc_start: 0.8658 (p90) cc_final: 0.8193 (p90) REVERT: D 248 MET cc_start: 0.9335 (ttp) cc_final: 0.8562 (ttp) REVERT: H 78 GLU cc_start: 0.9392 (tt0) cc_final: 0.9110 (tm-30) REVERT: J 55 ARG cc_start: 0.8884 (ttm-80) cc_final: 0.8650 (ttm110) REVERT: J 74 GLU cc_start: 0.9006 (mp0) cc_final: 0.8502 (pp20) REVERT: N 288 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7948 (ttpm) REVERT: Q 84 GLU cc_start: 0.9147 (tt0) cc_final: 0.8687 (tp30) REVERT: Q 88 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8667 (mm-30) REVERT: Q 96 HIS cc_start: 0.8887 (m-70) cc_final: 0.8313 (m-70) REVERT: Q 100 GLU cc_start: 0.9485 (OUTLIER) cc_final: 0.8927 (mp0) REVERT: Q 114 TYR cc_start: 0.8716 (t80) cc_final: 0.8452 (t80) REVERT: L 97 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.9085 (mm-30) REVERT: M 19 GLU cc_start: 0.9404 (OUTLIER) cc_final: 0.9116 (mm-30) REVERT: M 331 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8964 (pm20) REVERT: M 343 LYS cc_start: 0.9645 (OUTLIER) cc_final: 0.9017 (mttt) REVERT: S 78 GLU cc_start: 0.9402 (tt0) cc_final: 0.9095 (mt-10) REVERT: T 31 MET cc_start: 0.9387 (mmp) cc_final: 0.9106 (mmm) REVERT: U 13 SER cc_start: 0.9241 (t) cc_final: 0.8996 (p) REVERT: U 55 ARG cc_start: 0.9017 (ttm-80) cc_final: 0.8815 (ttm-80) outliers start: 128 outliers final: 21 residues processed: 444 average time/residue: 0.7489 time to fit residues: 387.3671 Evaluate side-chains 292 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 262 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 132 VAL 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 90 ASN Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 331 GLU Chi-restraints excluded: chain M residue 343 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 22 GLN C 173 ASN C 202 HIS C 332 ASN G 54 ASN F 109 GLN F 132 HIS A 135 GLN A 222 HIS A 332 ASN A 371 ASN B 87 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 215 GLN B 377 ASN D 193 GLN N 14 ASN N 202 HIS N 332 ASN E 90 ASN Q 109 GLN Q 132 HIS L 135 GLN L 332 ASN L 371 ASN M 87 HIS M 92 HIS M 215 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.062098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.045721 restraints weight = 82469.256| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 2.22 r_work: 0.2509 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2375 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9314 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.466 33382 Z= 0.157 Angle : 0.638 16.923 45365 Z= 0.314 Chirality : 0.042 0.192 4962 Planarity : 0.004 0.044 5700 Dihedral : 12.110 133.102 4877 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.65 % Allowed : 11.34 % Favored : 87.01 % 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: 0.81 (0.13), residues: 3955 helix: 1.01 (0.11), residues: 2157 sheet: 0.45 (0.26), residues: 368 loop : 0.01 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 144 TYR 0.020 0.002 TYR O 237 PHE 0.019 0.002 PHE L 334 TRP 0.026 0.001 TRP C 156 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (33367) covalent geometry : angle 0.63424 / 0.31 (45352) SS BOND : bond 0.00188 / 0.11 ( 5) SS BOND : angle 0.72506 / 0.39 ( 10) hydrogen bonds : bond 0.05183 / 3.45 ( 1881) hydrogen bonds : angle 4.72592 / 3.41 ( 5304) metal coordination : bond 0.02156 / 1.08 ( 4) metal coordination : angle 8.60819 / 4.56 ( 3) Misc. bond : bond 0.32958 / 16.31 ( 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 336 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 281 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 287 ASP cc_start: 0.8151 (t0) cc_final: 0.7902 (t0) REVERT: G 120 ASP cc_start: 0.8905 (m-30) cc_final: 0.8703 (m-30) REVERT: F 95 LYS cc_start: 0.9132 (tppt) cc_final: 0.8669 (tppp) REVERT: F 99 ASP cc_start: 0.9132 (m-30) cc_final: 0.8882 (m-30) REVERT: F 107 LYS cc_start: 0.9383 (ttmm) cc_final: 0.9182 (mtpp) REVERT: F 114 TYR cc_start: 0.8564 (t80) cc_final: 0.8274 (t80) REVERT: F 115 ASP cc_start: 0.8857 (p0) cc_final: 0.8607 (p0) REVERT: F 122 ASP cc_start: 0.8507 (p0) cc_final: 0.8064 (p0) REVERT: F 126 GLU cc_start: 0.9189 (mp0) cc_final: 0.8944 (mp0) REVERT: F 137 ASN cc_start: 0.8837 (m-40) cc_final: 0.8568 (m-40) REVERT: A 87 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7666 (mtp85) REVERT: B 170 TYR cc_start: 0.8592 (p90) cc_final: 0.7855 (p90) REVERT: H 51 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.6486 (ptm160) REVERT: H 57 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8627 (tp) REVERT: H 78 GLU cc_start: 0.9121 (tt0) cc_final: 0.8706 (tm-30) REVERT: I 34 GLU cc_start: 0.8660 (tt0) cc_final: 0.8323 (pt0) REVERT: J 15 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8497 (mtmm) REVERT: N 288 LYS cc_start: 0.8024 (tttp) cc_final: 0.7815 (ttpm) REVERT: R 19 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8617 (tm) REVERT: R 97 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8696 (mt-10) REVERT: R 115 GLU cc_start: 0.8879 (tt0) cc_final: 0.8673 (tt0) REVERT: R 116 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8516 (ttmt) REVERT: Q 84 GLU cc_start: 0.8888 (tt0) cc_final: 0.8534 (tp30) REVERT: Q 95 LYS cc_start: 0.9278 (tppt) cc_final: 0.8968 (tptm) REVERT: Q 99 ASP cc_start: 0.9142 (m-30) cc_final: 0.8903 (p0) REVERT: Q 100 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8598 (mt-10) REVERT: Q 114 TYR cc_start: 0.8607 (t80) cc_final: 0.8355 (t80) REVERT: Q 122 ASP cc_start: 0.8698 (p0) cc_final: 0.8006 (p0) REVERT: Q 126 GLU cc_start: 0.9306 (mp0) cc_final: 0.9082 (mp0) REVERT: M 19 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8904 (mm-30) REVERT: M 292 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8591 (p) REVERT: O 248 MET cc_start: 0.9241 (ttp) cc_final: 0.8738 (ttm) REVERT: S 51 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.6702 (ptm160) REVERT: S 57 LEU cc_start: 0.9083 (mm) cc_final: 0.8802 (tp) REVERT: S 78 GLU cc_start: 0.9227 (tt0) cc_final: 0.8847 (mt-10) REVERT: U 13 SER cc_start: 0.9046 (t) cc_final: 0.8612 (p) REVERT: U 55 ARG cc_start: 0.8893 (ttm-80) cc_final: 0.8521 (ttm-80) outliers start: 55 outliers final: 9 residues processed: 320 average time/residue: 0.7857 time to fit residues: 293.8874 Evaluate side-chains 273 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 275 optimal weight: 0.9980 chunk 317 optimal weight: 0.5980 chunk 252 optimal weight: 0.8980 chunk 255 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 377 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 292 optimal weight: 6.9990 chunk 384 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 85 GLN P 115 ASN P 157 GLN F 109 GLN A 317 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN B 377 ASN D 193 GLN Q 109 GLN L 317 GLN M 316 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.061952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.045775 restraints weight = 83201.494| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.21 r_work: 0.2521 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2389 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9326 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.377 33382 Z= 0.150 Angle : 0.566 15.353 45365 Z= 0.276 Chirality : 0.041 0.169 4962 Planarity : 0.004 0.052 5700 Dihedral : 10.927 102.556 4833 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.47 % Allowed : 12.09 % Favored : 86.44 % 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: 1.60 (0.14), residues: 3955 helix: 1.66 (0.11), residues: 2154 sheet: 0.73 (0.27), residues: 367 loop : 0.38 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 62 TYR 0.017 0.001 TYR N 225 PHE 0.018 0.001 PHE L 334 TRP 0.018 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (33367) covalent geometry : angle 0.56070 / 0.28 (45352) SS BOND : bond 0.00252 / 0.15 ( 5) SS BOND : angle 0.98181 / 0.48 ( 10) hydrogen bonds : bond 0.04496 / 2.98 ( 1881) hydrogen bonds : angle 4.40476 / 3.17 ( 5304) metal coordination : bond 0.01819 / 0.91 ( 4) metal coordination : angle 9.27311 / 5.03 ( 3) Misc. bond : bond 0.27549 / 13.38 ( 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 320 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 ASP cc_start: 0.8210 (t0) cc_final: 0.7957 (t0) REVERT: G 123 GLU cc_start: 0.9012 (tt0) cc_final: 0.8774 (tt0) REVERT: F 99 ASP cc_start: 0.9159 (m-30) cc_final: 0.8830 (m-30) REVERT: F 107 LYS cc_start: 0.9341 (ttmm) cc_final: 0.8262 (mtpp) REVERT: F 122 ASP cc_start: 0.8600 (p0) cc_final: 0.8132 (p0) REVERT: F 137 ASN cc_start: 0.8830 (m-40) cc_final: 0.8466 (m-40) REVERT: A 461 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8110 (p0) REVERT: B 170 TYR cc_start: 0.8576 (p90) cc_final: 0.7830 (p90) REVERT: H 22 LYS cc_start: 0.9495 (ttpp) cc_final: 0.9292 (tttt) REVERT: H 51 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.6637 (ptm160) REVERT: H 57 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8684 (tp) REVERT: H 78 GLU cc_start: 0.9097 (tt0) cc_final: 0.8750 (tm-30) REVERT: I 34 GLU cc_start: 0.8666 (tt0) cc_final: 0.8288 (pt0) REVERT: J 74 GLU cc_start: 0.7493 (pp20) cc_final: 0.7249 (pp20) REVERT: N 287 ASP cc_start: 0.8171 (t70) cc_final: 0.7843 (t0) REVERT: R 97 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8724 (mt-10) REVERT: Q 84 GLU cc_start: 0.8899 (tt0) cc_final: 0.8545 (tp30) REVERT: Q 99 ASP cc_start: 0.9188 (m-30) cc_final: 0.8946 (p0) REVERT: Q 114 TYR cc_start: 0.8615 (t80) cc_final: 0.8405 (t80) REVERT: Q 122 ASP cc_start: 0.8736 (p0) cc_final: 0.8418 (p0) REVERT: S 51 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.7281 (ptm160) REVERT: S 57 LEU cc_start: 0.9078 (mm) cc_final: 0.8827 (tp) REVERT: S 78 GLU cc_start: 0.9222 (tt0) cc_final: 0.8878 (mt-10) REVERT: U 13 SER cc_start: 0.9056 (t) cc_final: 0.8595 (p) outliers start: 49 outliers final: 12 residues processed: 302 average time/residue: 0.7700 time to fit residues: 271.7810 Evaluate side-chains 269 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 71 THR 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: 6.9990 chunk 166 optimal weight: 30.0000 chunk 295 optimal weight: 0.9980 chunk 224 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.489 > 50:) chunk 68 optimal weight: 8.9990 chunk 289 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 220 optimal weight: 0.9980 chunk 384 optimal weight: 9.9990 chunk 337 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 92 HIS F 109 GLN A 74 HIS ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN D 193 GLN R 84 HIS Q 83 HIS Q 109 GLN O 90 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.061326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.044890 restraints weight = 83123.565| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 2.23 r_work: 0.2494 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2362 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9336 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.401 33382 Z= 0.187 Angle : 0.577 16.537 45365 Z= 0.276 Chirality : 0.042 0.154 4962 Planarity : 0.004 0.055 5700 Dihedral : 10.387 90.304 4819 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.41 % Allowed : 12.69 % Favored : 85.89 % 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: 1.83 (0.14), residues: 3955 helix: 1.82 (0.11), residues: 2152 sheet: 0.83 (0.27), residues: 369 loop : 0.53 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 55 TYR 0.019 0.001 TYR N 225 PHE 0.017 0.001 PHE L 334 TRP 0.020 0.001 TRP C 142 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (33367) covalent geometry : angle 0.57150 / 0.28 (45352) SS BOND : bond 0.00258 / 0.15 ( 5) SS BOND : angle 0.78106 / 0.38 ( 10) hydrogen bonds : bond 0.04454 / 2.95 ( 1881) hydrogen bonds : angle 4.31934 / 3.11 ( 5304) metal coordination : bond 0.01473 / 0.74 ( 4) metal coordination : angle 9.97500 / 5.36 ( 3) Misc. bond : bond 0.29271 / 14.37 ( 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 309 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 ASP cc_start: 0.8256 (t0) cc_final: 0.8006 (t0) REVERT: G 16 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8464 (ptmt) REVERT: G 123 GLU cc_start: 0.8977 (tt0) cc_final: 0.8770 (tt0) REVERT: F 99 ASP cc_start: 0.9152 (m-30) cc_final: 0.8886 (m-30) REVERT: F 107 LYS cc_start: 0.9035 (ttmm) cc_final: 0.8742 (mmmm) REVERT: F 122 ASP cc_start: 0.8499 (p0) cc_final: 0.7975 (p0) REVERT: F 126 GLU cc_start: 0.9193 (mp0) cc_final: 0.8632 (mp0) REVERT: F 137 ASN cc_start: 0.8803 (m-40) cc_final: 0.8482 (m-40) REVERT: A 240 GLN cc_start: 0.8782 (pm20) cc_final: 0.8371 (pm20) REVERT: A 461 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8101 (p0) REVERT: B 170 TYR cc_start: 0.8480 (p90) cc_final: 0.7763 (p90) REVERT: D 185 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8650 (tt0) REVERT: H 51 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.5892 (ptm-80) REVERT: H 57 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8678 (tp) REVERT: H 78 GLU cc_start: 0.9094 (tt0) cc_final: 0.8725 (tm-30) REVERT: I 34 GLU cc_start: 0.8703 (tt0) cc_final: 0.8302 (pt0) REVERT: J 74 GLU cc_start: 0.7534 (pp20) cc_final: 0.7319 (pp20) REVERT: N 287 ASP cc_start: 0.8142 (t70) cc_final: 0.7823 (t0) REVERT: R 97 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8720 (mt-10) REVERT: Q 84 GLU cc_start: 0.8914 (tt0) cc_final: 0.8538 (tp30) REVERT: Q 99 ASP cc_start: 0.9167 (m-30) cc_final: 0.8908 (p0) REVERT: Q 114 TYR cc_start: 0.8563 (t80) cc_final: 0.8238 (t80) REVERT: Q 122 ASP cc_start: 0.8698 (p0) cc_final: 0.8467 (p0) REVERT: Q 141 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9142 (mtpp) REVERT: M 292 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8665 (p) REVERT: S 57 LEU cc_start: 0.9086 (mm) cc_final: 0.8812 (tp) REVERT: U 13 SER cc_start: 0.9112 (t) cc_final: 0.8666 (p) outliers start: 47 outliers final: 17 residues processed: 296 average time/residue: 0.7736 time to fit residues: 268.6631 Evaluate side-chains 275 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 141 LYS Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 99 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 287 optimal weight: 9.9990 chunk 275 optimal weight: 9.9990 chunk 294 optimal weight: 7.9990 chunk 369 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 HIS F 109 GLN B 121 GLN B 377 ASN D 193 GLN Q 109 GLN M 121 GLN O 90 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.062074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.045720 restraints weight = 82915.977| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 2.24 r_work: 0.2515 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9323 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.380 33382 Z= 0.140 Angle : 0.539 14.842 45365 Z= 0.259 Chirality : 0.040 0.145 4962 Planarity : 0.004 0.055 5700 Dihedral : 9.945 89.896 4819 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.44 % Allowed : 13.05 % 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: 2.01 (0.14), residues: 3955 helix: 1.95 (0.11), residues: 2158 sheet: 0.91 (0.27), residues: 369 loop : 0.62 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 55 TYR 0.017 0.001 TYR N 225 PHE 0.016 0.001 PHE L 334 TRP 0.017 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (33367) covalent geometry : angle 0.53330 / 0.26 (45352) SS BOND : bond 0.00205 / 0.12 ( 5) SS BOND : angle 0.57435 / 0.30 ( 10) hydrogen bonds : bond 0.04121 / 2.73 ( 1881) hydrogen bonds : angle 4.21887 / 3.04 ( 5304) metal coordination : bond 0.01043 / 0.51 ( 4) metal coordination : angle 9.59061 / 5.06 ( 3) Misc. bond : bond 0.26404 / 12.83 ( 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 318 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 ASP cc_start: 0.8263 (t0) cc_final: 0.8018 (t0) REVERT: C 374 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8093 (mm-30) REVERT: G 16 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8505 (ptmt) REVERT: F 95 LYS cc_start: 0.9126 (tppt) cc_final: 0.8767 (tppp) REVERT: F 99 ASP cc_start: 0.9158 (m-30) cc_final: 0.8951 (m-30) REVERT: F 107 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8785 (mmmm) REVERT: F 122 ASP cc_start: 0.8453 (p0) cc_final: 0.7992 (p0) REVERT: F 137 ASN cc_start: 0.8750 (m-40) cc_final: 0.8398 (m-40) REVERT: A 240 GLN cc_start: 0.8792 (pm20) cc_final: 0.8397 (pm20) REVERT: B 31 GLN cc_start: 0.8935 (mt0) cc_final: 0.8568 (mm110) REVERT: B 170 TYR cc_start: 0.8440 (p90) cc_final: 0.7712 (p90) REVERT: H 22 LYS cc_start: 0.9489 (ttpp) cc_final: 0.9280 (tttt) REVERT: H 51 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.6588 (ptm160) REVERT: H 57 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8696 (tt) REVERT: H 78 GLU cc_start: 0.9092 (tt0) cc_final: 0.8726 (tm-30) REVERT: I 34 GLU cc_start: 0.8732 (tt0) cc_final: 0.8352 (pt0) REVERT: J 74 GLU cc_start: 0.7605 (pp20) cc_final: 0.7400 (pp20) REVERT: N 287 ASP cc_start: 0.8129 (t70) cc_final: 0.7811 (t0) REVERT: R 97 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8696 (mt-10) REVERT: Q 84 GLU cc_start: 0.8924 (tt0) cc_final: 0.8517 (tp30) REVERT: Q 88 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8492 (mm-30) REVERT: Q 95 LYS cc_start: 0.9370 (ttmm) cc_final: 0.8660 (ttpt) REVERT: Q 114 TYR cc_start: 0.8454 (t80) cc_final: 0.8156 (t80) REVERT: Q 141 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9135 (mtpp) REVERT: M 292 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8700 (p) REVERT: S 51 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.6856 (ptm-80) REVERT: S 57 LEU cc_start: 0.9085 (mm) cc_final: 0.8838 (tp) REVERT: U 13 SER cc_start: 0.9040 (t) cc_final: 0.8570 (p) REVERT: U 55 ARG cc_start: 0.8945 (ttm-80) cc_final: 0.8706 (ttm-80) outliers start: 48 outliers final: 20 residues processed: 307 average time/residue: 0.7760 time to fit residues: 279.4653 Evaluate side-chains 285 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 141 LYS Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 297 optimal weight: 0.9980 chunk 266 optimal weight: 10.0000 chunk 352 optimal weight: 0.0170 chunk 153 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 overall best weight: 1.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 GLN F 109 GLN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN D 193 GLN Q 109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.062263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.045935 restraints weight = 82912.030| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.24 r_work: 0.2523 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9316 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.371 33382 Z= 0.131 Angle : 0.531 14.681 45365 Z= 0.254 Chirality : 0.040 0.139 4962 Planarity : 0.004 0.054 5700 Dihedral : 9.601 88.775 4819 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.47 % Allowed : 13.11 % Favored : 85.41 % 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: 2.13 (0.14), residues: 3955 helix: 2.04 (0.11), residues: 2164 sheet: 0.97 (0.27), residues: 369 loop : 0.70 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 144 TYR 0.021 0.001 TYR F 114 PHE 0.018 0.001 PHE L 334 TRP 0.016 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (33367) covalent geometry : angle 0.52608 / 0.25 (45352) SS BOND : bond 0.00201 / 0.11 ( 5) SS BOND : angle 0.62067 / 0.31 ( 10) hydrogen bonds : bond 0.03987 / 2.63 ( 1881) hydrogen bonds : angle 4.15927 / 3.00 ( 5304) metal coordination : bond 0.01112 / 0.54 ( 4) metal coordination : angle 9.12802 / 4.80 ( 3) Misc. bond : bond 0.25522 / 12.37 ( 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 320 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 ASP cc_start: 0.8299 (t0) cc_final: 0.8038 (t0) REVERT: C 374 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8095 (mm-30) REVERT: G 16 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8511 (ptmt) REVERT: G 50 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8509 (pt0) REVERT: G 97 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8616 (mp0) REVERT: F 95 LYS cc_start: 0.9155 (tppt) cc_final: 0.8776 (tppp) REVERT: F 99 ASP cc_start: 0.9165 (m-30) cc_final: 0.8946 (m-30) REVERT: F 107 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8824 (mmmm) REVERT: F 122 ASP cc_start: 0.8414 (p0) cc_final: 0.7877 (p0) REVERT: F 126 GLU cc_start: 0.9207 (mp0) cc_final: 0.8687 (mp0) REVERT: F 137 ASN cc_start: 0.8730 (m-40) cc_final: 0.8390 (m-40) REVERT: A 240 GLN cc_start: 0.8806 (pm20) cc_final: 0.8416 (pm20) REVERT: B 31 GLN cc_start: 0.8943 (mt0) cc_final: 0.8577 (mm110) REVERT: B 170 TYR cc_start: 0.8431 (p90) cc_final: 0.7688 (p90) REVERT: H 22 LYS cc_start: 0.9483 (ttpp) cc_final: 0.9277 (tttt) REVERT: H 51 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.6665 (ptm160) REVERT: H 57 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8673 (tt) REVERT: H 78 GLU cc_start: 0.9072 (tt0) cc_final: 0.8737 (tm-30) REVERT: I 34 GLU cc_start: 0.8743 (tt0) cc_final: 0.8364 (pt0) REVERT: N 287 ASP cc_start: 0.8130 (t70) cc_final: 0.7815 (t0) REVERT: R 97 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8723 (mt-10) REVERT: Q 84 GLU cc_start: 0.8918 (tt0) cc_final: 0.8552 (tp30) REVERT: Q 88 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8495 (mm-30) REVERT: Q 95 LYS cc_start: 0.9339 (ttmm) cc_final: 0.8704 (ttpt) REVERT: Q 99 ASP cc_start: 0.9138 (m-30) cc_final: 0.8907 (p0) REVERT: Q 114 TYR cc_start: 0.8409 (t80) cc_final: 0.8144 (t80) REVERT: Q 141 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9169 (mtpp) REVERT: L 212 MET cc_start: 0.9343 (mtm) cc_final: 0.9068 (mtp) REVERT: M 292 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8713 (p) REVERT: O 248 MET cc_start: 0.9299 (ttp) cc_final: 0.8581 (ttm) REVERT: S 51 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.6997 (ptm-80) REVERT: S 57 LEU cc_start: 0.9092 (mm) cc_final: 0.8835 (tp) REVERT: U 13 SER cc_start: 0.9022 (t) cc_final: 0.8486 (p) REVERT: U 69 GLU cc_start: 0.7938 (pp20) cc_final: 0.7720 (pp20) outliers start: 49 outliers final: 18 residues processed: 307 average time/residue: 0.7470 time to fit residues: 269.4136 Evaluate side-chains 285 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 141 LYS Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 132 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 304 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 109 GLN B 215 GLN B 377 ASN D 193 GLN N 177 GLN Q 109 GLN O 90 HIS U 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.062384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.046168 restraints weight = 82956.642| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.26 r_work: 0.2532 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2401 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9306 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.354 33382 Z= 0.120 Angle : 0.524 14.037 45365 Z= 0.251 Chirality : 0.040 0.140 4962 Planarity : 0.004 0.052 5700 Dihedral : 9.320 87.792 4819 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.17 % Allowed : 13.53 % Favored : 85.29 % 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: 2.23 (0.14), residues: 3955 helix: 2.11 (0.11), residues: 2160 sheet: 1.03 (0.27), residues: 369 loop : 0.74 (0.18), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG U 55 TYR 0.015 0.001 TYR N 225 PHE 0.016 0.001 PHE L 334 TRP 0.014 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (33367) covalent geometry : angle 0.51854 / 0.25 (45352) SS BOND : bond 0.00209 / 0.11 ( 5) SS BOND : angle 0.65124 / 0.33 ( 10) hydrogen bonds : bond 0.03850 / 2.53 ( 1881) hydrogen bonds : angle 4.10983 / 2.96 ( 5304) metal coordination : bond 0.01159 / 0.56 ( 4) metal coordination : angle 8.83114 / 4.66 ( 3) Misc. bond : bond 0.24174 / 11.70 ( 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 308 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 ASP cc_start: 0.8304 (t0) cc_final: 0.8099 (t0) REVERT: C 374 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8032 (mm-30) REVERT: G 16 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8519 (ptmt) REVERT: G 94 LYS cc_start: 0.8954 (mttp) cc_final: 0.8728 (mttp) REVERT: G 97 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8708 (mp0) REVERT: F 95 LYS cc_start: 0.9162 (tppt) cc_final: 0.8782 (tppp) REVERT: F 99 ASP cc_start: 0.9170 (m-30) cc_final: 0.8948 (m-30) REVERT: F 107 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8823 (mmmm) REVERT: F 122 ASP cc_start: 0.8385 (p0) cc_final: 0.7889 (p0) REVERT: F 126 GLU cc_start: 0.9134 (mp0) cc_final: 0.8567 (mp0) REVERT: F 137 ASN cc_start: 0.8701 (m-40) cc_final: 0.8363 (m-40) REVERT: A 240 GLN cc_start: 0.8827 (pm20) cc_final: 0.8446 (pm20) REVERT: B 31 GLN cc_start: 0.8942 (mt0) cc_final: 0.8575 (mm110) REVERT: B 170 TYR cc_start: 0.8443 (p90) cc_final: 0.7701 (p90) REVERT: H 51 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.6612 (ptm160) REVERT: H 57 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8676 (tt) REVERT: H 78 GLU cc_start: 0.9073 (tt0) cc_final: 0.8736 (tm-30) REVERT: I 30 ASP cc_start: 0.9025 (t70) cc_final: 0.8691 (t70) REVERT: I 34 GLU cc_start: 0.8747 (tt0) cc_final: 0.8373 (pt0) REVERT: N 217 ASP cc_start: 0.8428 (t0) cc_final: 0.8196 (t0) REVERT: N 287 ASP cc_start: 0.8114 (t70) cc_final: 0.7809 (t0) REVERT: R 97 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8739 (mt-10) REVERT: R 123 GLU cc_start: 0.8901 (tt0) cc_final: 0.8181 (pp20) REVERT: Q 84 GLU cc_start: 0.8896 (tt0) cc_final: 0.8541 (tp30) REVERT: Q 88 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8621 (mm-30) REVERT: Q 95 LYS cc_start: 0.9317 (ttmm) cc_final: 0.8660 (ttpt) REVERT: Q 99 ASP cc_start: 0.9132 (m-30) cc_final: 0.8889 (p0) REVERT: Q 114 TYR cc_start: 0.8338 (t80) cc_final: 0.8075 (t80) REVERT: Q 141 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9163 (mtpp) REVERT: L 212 MET cc_start: 0.9338 (mtm) cc_final: 0.9058 (mtp) REVERT: M 119 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8147 (mtpp) REVERT: M 292 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8716 (p) REVERT: M 364 MET cc_start: 0.9013 (mmm) cc_final: 0.8811 (mmm) REVERT: S 51 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.7004 (ptm-80) REVERT: S 57 LEU cc_start: 0.9099 (mm) cc_final: 0.8851 (tp) REVERT: S 78 GLU cc_start: 0.9224 (tt0) cc_final: 0.8875 (mt-10) REVERT: U 13 SER cc_start: 0.9047 (t) cc_final: 0.8521 (p) outliers start: 39 outliers final: 19 residues processed: 298 average time/residue: 0.7102 time to fit residues: 248.9597 Evaluate side-chains 286 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 141 LYS Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 344 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 389 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 307 optimal weight: 0.9980 chunk 341 optimal weight: 6.9990 chunk 286 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 294 optimal weight: 7.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 97 HIS F 109 GLN A 240 GLN B 377 ASN D 90 HIS D 193 GLN Q 109 GLN U 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.061497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.045270 restraints weight = 83106.976| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 2.22 r_work: 0.2508 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2378 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9327 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.384 33382 Z= 0.165 Angle : 0.555 15.651 45365 Z= 0.265 Chirality : 0.041 0.141 4962 Planarity : 0.004 0.052 5700 Dihedral : 9.298 88.530 4819 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.20 % Allowed : 13.89 % Favored : 84.90 % 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: 2.21 (0.14), residues: 3955 helix: 2.10 (0.11), residues: 2162 sheet: 1.01 (0.27), residues: 369 loop : 0.75 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 55 TYR 0.021 0.001 TYR F 114 PHE 0.018 0.001 PHE L 334 TRP 0.018 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (33367) covalent geometry : angle 0.55139 / 0.26 (45352) SS BOND : bond 0.00215 / 0.12 ( 5) SS BOND : angle 0.67764 / 0.34 ( 10) hydrogen bonds : bond 0.04112 / 2.71 ( 1881) hydrogen bonds : angle 4.13948 / 2.98 ( 5304) metal coordination : bond 0.01086 / 0.53 ( 4) metal coordination : angle 8.22977 / 4.32 ( 3) Misc. bond : bond 0.26699 / 13.04 ( 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 300 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 ASP cc_start: 0.8297 (t0) cc_final: 0.8083 (t0) REVERT: C 374 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8110 (mm-30) REVERT: G 16 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8547 (ptmt) REVERT: G 50 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: G 94 LYS cc_start: 0.8887 (mttp) cc_final: 0.8675 (mttp) REVERT: G 97 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8668 (mp0) REVERT: G 123 GLU cc_start: 0.9060 (tt0) cc_final: 0.8833 (pt0) REVERT: F 95 LYS cc_start: 0.9176 (tppt) cc_final: 0.8777 (tppp) REVERT: F 99 ASP cc_start: 0.9184 (m-30) cc_final: 0.8950 (m-30) REVERT: F 107 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8801 (mmmm) REVERT: F 122 ASP cc_start: 0.8366 (p0) cc_final: 0.7868 (p0) REVERT: F 137 ASN cc_start: 0.8717 (m-40) cc_final: 0.8426 (m-40) REVERT: F 144 ARG cc_start: 0.9135 (ttm-80) cc_final: 0.8918 (ttp80) REVERT: A 240 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8488 (pm20) REVERT: B 31 GLN cc_start: 0.8966 (mt0) cc_final: 0.8592 (mm110) REVERT: B 170 TYR cc_start: 0.8420 (p90) cc_final: 0.7675 (p90) REVERT: H 51 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.5909 (ptm-80) REVERT: H 57 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8680 (tt) REVERT: H 78 GLU cc_start: 0.9081 (tt0) cc_final: 0.8704 (tm-30) REVERT: I 34 GLU cc_start: 0.8759 (tt0) cc_final: 0.8369 (pt0) REVERT: N 217 ASP cc_start: 0.8471 (t0) cc_final: 0.8229 (t0) REVERT: N 287 ASP cc_start: 0.8158 (t70) cc_final: 0.7852 (t0) REVERT: R 97 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8751 (mt-10) REVERT: Q 84 GLU cc_start: 0.8929 (tt0) cc_final: 0.8573 (tp30) REVERT: Q 88 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8624 (mm-30) REVERT: Q 95 LYS cc_start: 0.9329 (ttmm) cc_final: 0.8665 (ttpt) REVERT: Q 99 ASP cc_start: 0.9160 (m-30) cc_final: 0.8897 (p0) REVERT: Q 114 TYR cc_start: 0.8335 (t80) cc_final: 0.8050 (t80) REVERT: Q 141 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9171 (mtpp) REVERT: M 119 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8175 (mtpp) REVERT: M 292 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8692 (p) REVERT: M 364 MET cc_start: 0.9011 (mmm) cc_final: 0.8742 (mmm) REVERT: S 51 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.7982 (ptm-80) REVERT: S 57 LEU cc_start: 0.9094 (mm) cc_final: 0.8835 (tp) REVERT: U 13 SER cc_start: 0.9052 (t) cc_final: 0.8544 (p) outliers start: 40 outliers final: 20 residues processed: 286 average time/residue: 0.7570 time to fit residues: 253.5502 Evaluate side-chains 286 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 141 LYS Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 71 THR 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: 10.0000 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 50 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 362 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 294 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 250 optimal weight: 0.9980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 85 GLN F 109 GLN A 240 GLN B 377 ASN D 90 HIS D 193 GLN Q 109 GLN U 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.061399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.045170 restraints weight = 82792.538| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 2.22 r_work: 0.2503 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2372 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9330 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.383 33382 Z= 0.169 Angle : 0.558 15.520 45365 Z= 0.267 Chirality : 0.041 0.139 4962 Planarity : 0.004 0.051 5700 Dihedral : 9.273 88.453 4819 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.11 % Allowed : 13.95 % Favored : 84.93 % 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: 2.21 (0.14), residues: 3955 helix: 2.10 (0.11), residues: 2162 sheet: 0.99 (0.27), residues: 369 loop : 0.75 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 55 TYR 0.018 0.001 TYR N 225 PHE 0.019 0.001 PHE L 334 TRP 0.018 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (33367) covalent geometry : angle 0.55426 / 0.27 (45352) SS BOND : bond 0.00180 / 0.11 ( 5) SS BOND : angle 0.59985 / 0.32 ( 10) hydrogen bonds : bond 0.04120 / 2.72 ( 1881) hydrogen bonds : angle 4.14353 / 2.98 ( 5304) metal coordination : bond 0.01060 / 0.52 ( 4) metal coordination : angle 7.98893 / 4.16 ( 3) Misc. bond : bond 0.26629 / 12.98 ( 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 298 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 374 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8106 (mm-30) REVERT: G 16 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8541 (ptmt) REVERT: G 50 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8496 (pt0) REVERT: G 94 LYS cc_start: 0.8920 (mttp) cc_final: 0.8689 (mttp) REVERT: G 97 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8685 (mp0) REVERT: G 123 GLU cc_start: 0.9062 (tt0) cc_final: 0.8814 (pt0) REVERT: F 95 LYS cc_start: 0.9190 (tppt) cc_final: 0.8765 (tppp) REVERT: F 99 ASP cc_start: 0.9192 (m-30) cc_final: 0.8957 (m-30) REVERT: F 107 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8787 (mmmm) REVERT: F 122 ASP cc_start: 0.8301 (p0) cc_final: 0.7864 (p0) REVERT: F 137 ASN cc_start: 0.8731 (m-40) cc_final: 0.8430 (m-40) REVERT: F 144 ARG cc_start: 0.9137 (ttm-80) cc_final: 0.8907 (ttp80) REVERT: A 240 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8477 (pm20) REVERT: B 31 GLN cc_start: 0.8957 (mt0) cc_final: 0.8580 (mm110) REVERT: B 170 TYR cc_start: 0.8421 (p90) cc_final: 0.7695 (p90) REVERT: H 51 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.5929 (ptm-80) REVERT: H 57 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8685 (tt) REVERT: H 78 GLU cc_start: 0.9074 (tt0) cc_final: 0.8704 (tm-30) REVERT: I 34 GLU cc_start: 0.8762 (tt0) cc_final: 0.8422 (pt0) REVERT: N 217 ASP cc_start: 0.8490 (t0) cc_final: 0.8277 (t0) REVERT: N 287 ASP cc_start: 0.8168 (t70) cc_final: 0.7859 (t0) REVERT: R 51 GLU cc_start: 0.9029 (mp0) cc_final: 0.8736 (mp0) REVERT: R 97 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8762 (mt-10) REVERT: Q 84 GLU cc_start: 0.8881 (tt0) cc_final: 0.8545 (tp30) REVERT: Q 88 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8677 (mm-30) REVERT: Q 95 LYS cc_start: 0.9339 (ttmm) cc_final: 0.8666 (ttpt) REVERT: Q 99 ASP cc_start: 0.9170 (m-30) cc_final: 0.8900 (p0) REVERT: Q 114 TYR cc_start: 0.8320 (t80) cc_final: 0.8039 (t80) REVERT: Q 141 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9171 (mtpp) REVERT: L 212 MET cc_start: 0.9342 (mtm) cc_final: 0.9071 (mtp) REVERT: M 119 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8177 (mtpp) REVERT: M 292 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8674 (p) REVERT: M 364 MET cc_start: 0.9025 (mmm) cc_final: 0.8760 (mmm) REVERT: S 51 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8521 (ptm-80) REVERT: S 57 LEU cc_start: 0.9104 (mm) cc_final: 0.8830 (tp) REVERT: U 13 SER cc_start: 0.9068 (t) cc_final: 0.8553 (p) outliers start: 37 outliers final: 20 residues processed: 286 average time/residue: 0.7823 time to fit residues: 261.9872 Evaluate side-chains 288 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 141 LYS Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 13 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 chunk 162 optimal weight: 0.0000 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 265 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 109 GLN A 240 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN D 90 HIS D 193 GLN J 70 HIS Q 109 GLN U 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.046367 restraints weight = 83060.652| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.23 r_work: 0.2535 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9308 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.354 33382 Z= 0.112 Angle : 0.528 13.627 45365 Z= 0.255 Chirality : 0.040 0.137 4962 Planarity : 0.004 0.051 5700 Dihedral : 9.098 86.781 4819 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.84 % Allowed : 14.26 % Favored : 84.90 % 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: 2.29 (0.14), residues: 3955 helix: 2.17 (0.11), residues: 2160 sheet: 1.02 (0.27), residues: 369 loop : 0.78 (0.18), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 55 TYR 0.015 0.001 TYR M 170 PHE 0.017 0.001 PHE L 334 TRP 0.014 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (33367) covalent geometry : angle 0.52427 / 0.25 (45352) SS BOND : bond 0.00193 / 0.12 ( 5) SS BOND : angle 0.58591 / 0.31 ( 10) hydrogen bonds : bond 0.03807 / 2.51 ( 1881) hydrogen bonds : angle 4.08166 / 2.94 ( 5304) metal coordination : bond 0.01239 / 0.60 ( 4) metal coordination : angle 8.12827 / 4.26 ( 3) Misc. bond : bond 0.24012 / 11.62 ( 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 298 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 374 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8102 (mm-30) REVERT: G 16 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8567 (ptmt) REVERT: G 50 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: G 94 LYS cc_start: 0.8904 (mttp) cc_final: 0.8699 (mttp) REVERT: G 97 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8734 (mp0) REVERT: G 123 GLU cc_start: 0.9070 (tt0) cc_final: 0.8821 (pt0) REVERT: F 95 LYS cc_start: 0.9185 (tppt) cc_final: 0.8791 (tppp) REVERT: F 99 ASP cc_start: 0.9178 (m-30) cc_final: 0.8948 (m-30) REVERT: F 107 LYS cc_start: 0.9107 (ttmm) cc_final: 0.8789 (mmmm) REVERT: F 122 ASP cc_start: 0.8302 (p0) cc_final: 0.7808 (p0) REVERT: F 137 ASN cc_start: 0.8690 (m-40) cc_final: 0.8392 (m-40) REVERT: F 144 ARG cc_start: 0.9139 (ttm-80) cc_final: 0.8934 (ttp80) REVERT: A 240 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8457 (pm20) REVERT: B 31 GLN cc_start: 0.8931 (mt0) cc_final: 0.8564 (mm110) REVERT: B 170 TYR cc_start: 0.8440 (p90) cc_final: 0.7695 (p90) REVERT: H 51 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.6610 (ptm160) REVERT: H 57 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8684 (tt) REVERT: H 78 GLU cc_start: 0.9073 (tt0) cc_final: 0.8732 (tm-30) REVERT: I 30 ASP cc_start: 0.9020 (t70) cc_final: 0.8709 (t70) REVERT: I 34 GLU cc_start: 0.8748 (tt0) cc_final: 0.8350 (pt0) REVERT: N 217 ASP cc_start: 0.8452 (t0) cc_final: 0.8237 (t0) REVERT: N 287 ASP cc_start: 0.8158 (t70) cc_final: 0.7849 (t0) REVERT: R 85 LYS cc_start: 0.9155 (mttp) cc_final: 0.8950 (mtpp) REVERT: R 97 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8768 (mt-10) REVERT: R 123 GLU cc_start: 0.8884 (tt0) cc_final: 0.8194 (pp20) REVERT: Q 84 GLU cc_start: 0.8889 (tt0) cc_final: 0.8543 (tp30) REVERT: Q 88 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8638 (mm-30) REVERT: Q 95 LYS cc_start: 0.9338 (ttmm) cc_final: 0.8661 (ttpt) REVERT: Q 99 ASP cc_start: 0.9176 (m-30) cc_final: 0.8888 (p0) REVERT: Q 114 TYR cc_start: 0.8319 (t80) cc_final: 0.8037 (t80) REVERT: L 212 MET cc_start: 0.9321 (mtm) cc_final: 0.9088 (mtp) REVERT: M 119 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8298 (ptmt) REVERT: M 292 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8714 (p) REVERT: M 364 MET cc_start: 0.9021 (mmm) cc_final: 0.8772 (mmm) REVERT: S 51 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.7045 (ptm-80) REVERT: S 57 LEU cc_start: 0.9109 (mm) cc_final: 0.8861 (tp) REVERT: S 78 GLU cc_start: 0.9236 (tt0) cc_final: 0.8886 (mt-10) REVERT: U 13 SER cc_start: 0.9075 (t) cc_final: 0.8548 (p) outliers start: 28 outliers final: 20 residues processed: 291 average time/residue: 0.7623 time to fit residues: 259.9836 Evaluate side-chains 288 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 261 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 179 optimal weight: 4.9990 chunk 354 optimal weight: 0.9980 chunk 387 optimal weight: 0.9990 chunk 198 optimal weight: 6.9990 chunk 370 optimal weight: 6.9990 chunk 229 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 377 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 234 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 109 GLN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN D 193 GLN J 70 HIS Q 109 GLN U 58 GLN ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.062704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.046509 restraints weight = 82853.339| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 2.26 r_work: 0.2545 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9299 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.340 33382 Z= 0.109 Angle : 0.531 13.505 45365 Z= 0.257 Chirality : 0.039 0.166 4962 Planarity : 0.004 0.051 5700 Dihedral : 8.983 86.702 4819 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.84 % Allowed : 14.26 % Favored : 84.90 % 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: 2.33 (0.14), residues: 3955 helix: 2.21 (0.11), residues: 2162 sheet: 1.05 (0.27), residues: 369 loop : 0.78 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 55 TYR 0.014 0.001 TYR M 170 PHE 0.017 0.001 PHE L 334 TRP 0.014 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (33367) covalent geometry : angle 0.52735 / 0.26 (45352) SS BOND : bond 0.00306 / 0.17 ( 5) SS BOND : angle 0.64831 / 0.33 ( 10) hydrogen bonds : bond 0.03725 / 2.45 ( 1881) hydrogen bonds : angle 4.04693 / 2.92 ( 5304) metal coordination : bond 0.01262 / 0.61 ( 4) metal coordination : angle 8.12428 / 4.28 ( 3) Misc. bond : bond 0.23354 / 11.31 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10534.33 seconds wall clock time: 180 minutes 35.64 seconds (10835.64 seconds total)