Starting phenix.real_space_refine on Mon Jul 6 07:16:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8abg_15320/07_2026/8abg_15320.cif Found real_map, /net/cci-nas-00/data/ceres_data/8abg_15320/07_2026/8abg_15320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8abg_15320/07_2026/8abg_15320.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8abg_15320/07_2026/8abg_15320.cif" model { file = "/net/cci-nas-00/data/ceres_data/8abg_15320/07_2026/8abg_15320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8abg_15320/07_2026/8abg_15320.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8abg_15320/07_2026/8abg_15320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8abg_15320/07_2026/8abg_15320.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 125 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 34 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "U" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'XP4': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 32.796 46.948 25.681 1.00122.05 S ATOM 4207 SG CYS P 187 35.255 45.737 22.963 1.00124.92 S Time building chain proxies: 6.76, per 1000 atoms: 0.21 Number of scatterers: 32540 At special positions: 0 Unit cell: (118.854, 129.735, 167.4, 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=2.03 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.07 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.3 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: 196 helices and 21 sheets defined 61.4% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 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: 3.777A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 removed outlier: 3.565A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 149 Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 172 through 202 Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 221 through 247 removed outlier: 6.886A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.875A 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: 3.814A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.831A 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: 4.135A 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: 3.639A 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 101 removed outlier: 3.618A pdb=" N ALA P 101 " --> pdb=" O VAL P 97 " (cutoff:3.500A) 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 removed outlier: 3.554A pdb=" N GLY G 36 " --> pdb=" O VAL G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 63 through 83 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 102 through 120 Processing helix chain 'F' and resid 77 through 89 removed outlier: 4.284A 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: 3.594A 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: 3.541A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 122 through 136 Processing helix chain 'A' and resid 140 through 155 removed outlier: 4.009A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.568A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.510A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 4.031A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.625A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.519A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.293A 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: 3.633A 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: 3.578A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.831A 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: 3.561A pdb=" N THR B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.829A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.752A 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: 3.688A 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 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 81 removed outlier: 4.355A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.510A 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: 3.527A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.786A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.671A 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: 3.764A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.571A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 149 Processing helix chain 'N' and resid 150 through 154 Processing helix chain 'N' and resid 157 through 167 Processing helix chain 'N' and resid 172 through 202 Proline residue: N 187 - end of helix Processing helix chain 'N' and resid 221 through 247 removed outlier: 6.874A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.882A 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: 3.799A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.828A 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: 4.132A 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: 3.646A 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 removed outlier: 3.546A pdb=" N GLY R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 41 Processing helix chain 'R' and resid 43 through 48 Processing helix chain 'R' and resid 52 through 61 Processing helix chain 'R' and resid 63 through 83 Processing helix chain 'R' and resid 88 through 92 Processing helix chain 'R' and resid 94 through 98 Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 4.285A pdb=" N ALA Q 81 " --> pdb=" O ASP Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 111 Processing helix chain 'Q' and resid 123 through 137 Processing helix chain 'Q' and resid 138 through 145 removed outlier: 3.602A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 71 through 78 removed outlier: 3.515A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 100 Processing helix chain 'L' and resid 122 through 136 Processing helix chain 'L' and resid 140 through 155 removed outlier: 4.006A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 160 removed outlier: 3.570A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 157 through 160' Processing helix chain 'L' and resid 161 through 175 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 removed outlier: 3.501A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 4.029A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 328 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.624A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.704A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.329A 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: 3.628A 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: 3.576A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.836A 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: 3.562A pdb=" N THR M 147 " --> pdb=" O ASP M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 163 Processing helix chain 'M' and resid 174 through 186 Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'M' and resid 199 through 211 Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.837A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.774A 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: 3.866A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.582A 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: 3.976A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.982A 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 219 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 320 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.358A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 85 through 93 Processing helix chain 'T' and resid 5 through 12 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 49 through 54 removed outlier: 3.506A 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: 3.606A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.572A 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: 3.787A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.674A pdb=" N ASN U 80 " --> pdb=" O ALA U 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'P' and resid 103 through 106 Processing sheet with id=AA3, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.886A 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: 3.508A pdb=" N SER P 192 " --> pdb=" O CYS P 187 " (cutoff:3.500A) removed outlier: 3.648A 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: 6.516A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.279A 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: 3.941A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.801A 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: 4.190A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.580A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.612A 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: 6.509A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.274A 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: 3.928A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 16 through 20 removed outlier: 4.183A pdb=" N LYS M 24 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.597A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.587A 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 1885 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: 5.46 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 13575 1.40 - 1.61: 19589 1.61 - 1.82: 163 1.82 - 2.03: 20 2.03 - 2.24: 20 Bond restraints: 33367 Sorted by residual: bond pdb=" C18 XP4 U 101 " pdb=" O7 XP4 U 101 " ideal model delta sigma weight residual 1.328 1.463 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C18 XP4 A3003 " pdb=" O7 XP4 A3003 " ideal model delta sigma weight residual 1.328 1.455 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.458 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " ideal model delta sigma weight residual 1.334 1.457 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.456 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 43458 3.59 - 7.18: 1668 7.18 - 10.78: 181 10.78 - 14.37: 35 14.37 - 17.96: 10 Bond angle restraints: 45352 Sorted by residual: angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 94.73 16.54 1.47e+00 4.63e-01 1.27e+02 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.79 12.54 1.14e+00 7.69e-01 1.21e+02 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 95.29 15.98 1.47e+00 4.63e-01 1.18e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.88 12.45 1.20e+00 6.94e-01 1.08e+02 angle pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " pdb="FE2 FES P 301 " ideal model delta sigma weight residual 75.66 86.29 -10.63 1.14e+00 7.69e-01 8.70e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.83: 18459 30.83 - 61.67: 947 61.67 - 92.50: 107 92.50 - 123.34: 0 123.34 - 154.17: 2 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 -103.50 -19.10 0 2.50e+00 1.60e-01 5.84e+01 dihedral pdb=" C GLU D 283 " pdb=" N GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta harmonic sigma weight residual -122.60 -103.75 -18.85 0 2.50e+00 1.60e-01 5.69e+01 dihedral pdb=" C GLN B 215 " pdb=" N GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta harmonic sigma weight residual -122.60 -104.41 -18.19 0 2.50e+00 1.60e-01 5.30e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 4348 0.163 - 0.327: 563 0.327 - 0.490: 47 0.490 - 0.653: 0 0.653 - 0.817: 4 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB4 CDL N 505 " pdb=" CB3 CDL N 505 " pdb=" CB6 CDL N 505 " pdb=" OB6 CDL N 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.76 -0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.77 -0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CB4 CDL H 702 " pdb=" CB3 CDL H 702 " pdb=" CB6 CDL H 702 " pdb=" OB6 CDL H 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.79 -0.78 2.00e-01 2.50e+01 1.53e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS L 78 " 0.024 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C HIS L 78 " -0.087 2.00e-02 2.50e+03 pdb=" O HIS L 78 " 0.033 2.00e-02 2.50e+03 pdb=" N LEU L 79 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM C 502 " 0.004 2.00e-02 2.50e+03 2.80e-02 1.77e+01 pdb=" C2C HEM C 502 " -0.023 2.00e-02 2.50e+03 pdb=" C3C HEM C 502 " -0.006 2.00e-02 2.50e+03 pdb=" C4C HEM C 502 " -0.035 2.00e-02 2.50e+03 pdb=" CAC HEM C 502 " 0.034 2.00e-02 2.50e+03 pdb=" CHC HEM C 502 " 0.047 2.00e-02 2.50e+03 pdb=" CHD HEM C 502 " 0.026 2.00e-02 2.50e+03 pdb=" CMC HEM C 502 " -0.016 2.00e-02 2.50e+03 pdb=" NC HEM C 502 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 76 " 0.294 9.50e-02 1.11e+02 1.34e-01 1.77e+01 pdb=" NE ARG R 76 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG R 76 " 0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG R 76 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG R 76 " -0.005 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 251 2.63 - 3.20: 28563 3.20 - 3.76: 53641 3.76 - 4.33: 78656 4.33 - 4.90: 121891 Nonbonded interactions: 283002 Sorted by model distance: nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.059 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.060 3.120 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.071 3.080 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.142 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEM C 502 " model vdw 2.256 3.080 ... (remaining 282997 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' and resid 26 through 3002) selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'N' } 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' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = (chain 'U' and resid 8 through 82) } 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: 4.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.820 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9497 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 0.701 33385 Z= 0.809 Angle : 1.689 17.962 45365 Z= 1.045 Chirality : 0.111 0.817 4962 Planarity : 0.008 0.141 5700 Dihedral : 17.454 154.171 12014 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.25 % Allowed : 6.83 % Favored : 89.92 % Cbeta Deviations : 1.20 % 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: -1.11 (0.12), residues: 3955 helix: -0.75 (0.10), residues: 2134 sheet: 0.10 (0.25), residues: 351 loop : -0.65 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.003 ARG R 76 TYR 0.051 0.008 TYR D 177 PHE 0.065 0.007 PHE B 107 TRP 0.043 0.008 TRP D 280 HIS 0.019 0.004 HIS Q 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01006 / 0.61 (33367) covalent geometry : angle 1.68640 / 1.05 (45352) SS BOND : bond 0.02655 / 1.54 ( 5) SS BOND : angle 2.15714 / 1.15 ( 10) hydrogen bonds : bond 0.18378 / 12.30 ( 1885) hydrogen bonds : angle 6.83227 / 4.99 ( 5304) metal coordination : bond 0.06675 / 3.26 ( 4) metal coordination : angle 11.37479 / 5.95 ( 3) Misc. bond : bond 0.33309 / 16.32 ( 9) *********************** 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 571 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 463 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 288 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8828 (tttt) REVERT: P 143 VAL cc_start: 0.7233 (OUTLIER) cc_final: 0.6883 (m) REVERT: P 146 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7506 (mp) REVERT: F 99 ASP cc_start: 0.8912 (m-30) cc_final: 0.8708 (m-30) REVERT: F 107 LYS cc_start: 0.9206 (tttt) cc_final: 0.8744 (tppp) REVERT: A 390 LYS cc_start: 0.9044 (tptt) cc_final: 0.8749 (mttt) REVERT: B 205 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8588 (tm130) REVERT: B 354 ASN cc_start: 0.8415 (t0) cc_final: 0.8168 (t0) REVERT: I 30 ASP cc_start: 0.9074 (t70) cc_final: 0.8724 (t70) REVERT: E 55 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7914 (p0) REVERT: R 9 LYS cc_start: 0.9039 (mttp) cc_final: 0.8751 (ttpt) REVERT: L 153 ARG cc_start: 0.8356 (ttp-110) cc_final: 0.7888 (ttt-90) REVERT: L 159 ASN cc_start: 0.7323 (p0) cc_final: 0.7115 (p0) REVERT: L 390 LYS cc_start: 0.9030 (tptt) cc_final: 0.8704 (mttt) REVERT: L 422 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8562 (mt-10) REVERT: M 16 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8626 (p) REVERT: M 236 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8226 (mtp85) REVERT: U 10 LYS cc_start: 0.9038 (tttm) cc_final: 0.8714 (tmmt) outliers start: 108 outliers final: 12 residues processed: 533 average time/residue: 0.8093 time to fit residues: 496.2735 Evaluate side-chains 346 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 328 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 272 SER 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: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 P 90 ASN G 84 HIS A 222 HIS A 332 ASN A 371 ASN A 379 ASN B 87 HIS B 197 ASN B 316 GLN N 14 ASN N 22 GLN N 202 HIS N 332 ASN E 90 ASN R 84 HIS Q 137 ASN L 332 ASN L 371 ASN M 87 HIS M 197 ASN M 354 ASN M 377 ASN O 93 HIS T 49 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.076447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.057757 restraints weight = 56115.509| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 1.66 r_work: 0.2607 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9370 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.398 33385 Z= 0.129 Angle : 0.600 13.937 45365 Z= 0.299 Chirality : 0.041 0.162 4962 Planarity : 0.004 0.038 5700 Dihedral : 11.733 125.348 4857 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.50 % Allowed : 10.47 % Favored : 88.03 % 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: 1.09 (0.13), residues: 3955 helix: 1.23 (0.11), residues: 2152 sheet: 0.52 (0.26), residues: 366 loop : 0.17 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 76 TYR 0.019 0.001 TYR O 237 PHE 0.021 0.002 PHE L 334 TRP 0.026 0.002 TRP N 156 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (33367) covalent geometry : angle 0.60006 / 0.30 (45352) SS BOND : bond 0.00311 / 0.18 ( 5) SS BOND : angle 0.73559 / 0.37 ( 10) hydrogen bonds : bond 0.04870 / 3.26 ( 1885) hydrogen bonds : angle 4.61688 / 3.33 ( 5304) metal coordination : bond 0.01775 / 0.90 ( 4) metal coordination : angle 1.63848 / 0.90 ( 3) Misc. bond : bond 0.21638 / 11.96 ( 9) *********************** 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 409 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 359 time to evaluate : 1.121 Fit side-chains REVERT: C 69 MET cc_start: 0.9540 (mmm) cc_final: 0.9287 (mmm) REVERT: C 288 LYS cc_start: 0.8538 (tttp) cc_final: 0.8336 (tttt) REVERT: P 199 ARG cc_start: 0.7999 (ptp-170) cc_final: 0.7667 (ptp90) REVERT: G 97 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8787 (mt-10) REVERT: F 99 ASP cc_start: 0.8854 (m-30) cc_final: 0.8593 (m-30) REVERT: F 107 LYS cc_start: 0.9124 (tttt) cc_final: 0.8755 (tppp) REVERT: F 110 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7599 (pt0) REVERT: A 390 LYS cc_start: 0.9048 (tptt) cc_final: 0.8788 (mttt) REVERT: A 397 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8445 (mt) REVERT: B 205 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8186 (tm130) REVERT: B 354 ASN cc_start: 0.8341 (t0) cc_final: 0.8139 (t0) REVERT: B 388 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: I 30 ASP cc_start: 0.8977 (t70) cc_final: 0.8565 (t70) REVERT: J 73 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8210 (ptt180) REVERT: R 9 LYS cc_start: 0.8769 (mttp) cc_final: 0.8547 (tttm) REVERT: Q 84 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8061 (mm-30) REVERT: Q 115 ASP cc_start: 0.8932 (m-30) cc_final: 0.8533 (t0) REVERT: L 51 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8895 (p) REVERT: L 153 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.7939 (ttt-90) REVERT: L 422 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8329 (mt-10) REVERT: M 83 LYS cc_start: 0.9252 (mmtm) cc_final: 0.9010 (mmtp) REVERT: M 101 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9123 (tttt) REVERT: M 353 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.6874 (mt-10) REVERT: M 364 MET cc_start: 0.9152 (tpp) cc_final: 0.8938 (tpt) REVERT: O 248 MET cc_start: 0.9289 (ttp) cc_final: 0.9059 (ttp) REVERT: S 76 LYS cc_start: 0.9187 (tptp) cc_final: 0.8985 (tppt) REVERT: U 10 LYS cc_start: 0.8963 (tttm) cc_final: 0.8697 (tmmt) outliers start: 50 outliers final: 8 residues processed: 388 average time/residue: 0.8406 time to fit residues: 375.2735 Evaluate side-chains 327 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 312 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 353 GLU Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 275 optimal weight: 8.9990 chunk 317 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 377 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 292 optimal weight: 0.9990 chunk 384 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN A 177 ASN D 90 HIS D 166 ASN Q 109 GLN L 332 ASN M 316 GLN M 377 ASN M 408 HIS T 39 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.073572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.054471 restraints weight = 56312.102| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 1.66 r_work: 0.2539 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9420 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.363 33385 Z= 0.227 Angle : 0.634 15.319 45365 Z= 0.311 Chirality : 0.044 0.165 4962 Planarity : 0.004 0.045 5700 Dihedral : 11.147 93.145 4822 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.71 % Allowed : 10.56 % Favored : 87.73 % 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: 1.57 (0.13), residues: 3955 helix: 1.63 (0.11), residues: 2155 sheet: 0.59 (0.26), residues: 369 loop : 0.41 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 236 TYR 0.019 0.002 TYR N 225 PHE 0.024 0.002 PHE L 334 TRP 0.017 0.002 TRP N 142 HIS 0.011 0.001 HIS N 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (33367) covalent geometry : angle 0.63407 / 0.31 (45352) SS BOND : bond 0.00336 / 0.20 ( 5) SS BOND : angle 0.60363 / 0.32 ( 10) hydrogen bonds : bond 0.05473 / 3.66 ( 1885) hydrogen bonds : angle 4.48017 / 3.23 ( 5304) metal coordination : bond 0.01960 / 0.99 ( 4) metal coordination : angle 0.86248 / 0.45 ( 3) Misc. bond : bond 0.22471 / 12.87 ( 9) *********************** 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 379 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 322 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: P 199 ARG cc_start: 0.8139 (ptp-170) cc_final: 0.7909 (ptp-170) REVERT: G 66 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8709 (mm-30) REVERT: F 99 ASP cc_start: 0.8813 (m-30) cc_final: 0.8546 (m-30) REVERT: F 107 LYS cc_start: 0.9143 (tttt) cc_final: 0.8857 (tppp) REVERT: F 110 GLU cc_start: 0.8269 (pt0) cc_final: 0.8060 (pp20) REVERT: A 153 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8307 (ttt90) REVERT: A 390 LYS cc_start: 0.9031 (tptt) cc_final: 0.8766 (mttt) REVERT: A 397 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8367 (mt) REVERT: B 354 ASN cc_start: 0.8307 (t0) cc_final: 0.8087 (t0) REVERT: B 388 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: I 30 ASP cc_start: 0.9000 (t70) cc_final: 0.8593 (t70) REVERT: J 10 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8739 (tptt) REVERT: J 73 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8074 (ptt180) REVERT: N 283 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8347 (mtp180) REVERT: R 9 LYS cc_start: 0.8782 (mttp) cc_final: 0.8575 (tttm) REVERT: R 19 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8098 (tp) REVERT: Q 84 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8027 (mm-30) REVERT: Q 115 ASP cc_start: 0.8964 (m-30) cc_final: 0.8594 (t0) REVERT: L 29 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8675 (tptp) REVERT: L 153 ARG cc_start: 0.8406 (ttp-110) cc_final: 0.7942 (ttt-90) REVERT: L 422 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8422 (mt-10) REVERT: M 31 GLN cc_start: 0.8800 (mt0) cc_final: 0.8477 (mt0) REVERT: M 83 LYS cc_start: 0.9306 (mmtm) cc_final: 0.9083 (mmtp) REVERT: M 101 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9170 (tttt) REVERT: M 364 MET cc_start: 0.9099 (tpp) cc_final: 0.8726 (tpt) REVERT: O 146 ASP cc_start: 0.8972 (m-30) cc_final: 0.8725 (m-30) REVERT: S 75 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8565 (mt-10) REVERT: S 76 LYS cc_start: 0.9197 (tptp) cc_final: 0.8993 (tppt) REVERT: U 11 LYS cc_start: 0.9009 (ptmm) cc_final: 0.8738 (ptpp) outliers start: 57 outliers final: 16 residues processed: 359 average time/residue: 0.8393 time to fit residues: 349.0443 Evaluate side-chains 331 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain U residue 55 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 364 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 166 optimal weight: 0.0870 chunk 295 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 289 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 384 optimal weight: 6.9990 chunk 337 optimal weight: 2.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS P 115 ASN Q 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.075426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.056514 restraints weight = 55961.964| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 1.65 r_work: 0.2587 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9391 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.362 33385 Z= 0.137 Angle : 0.548 14.119 45365 Z= 0.265 Chirality : 0.041 0.146 4962 Planarity : 0.004 0.047 5700 Dihedral : 10.455 88.518 4822 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.41 % Allowed : 11.37 % Favored : 87.22 % 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: 1.97 (0.14), residues: 3955 helix: 1.94 (0.11), residues: 2152 sheet: 0.75 (0.26), residues: 369 loop : 0.63 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 236 TYR 0.015 0.001 TYR N 225 PHE 0.020 0.001 PHE L 334 TRP 0.013 0.001 TRP N 142 HIS 0.006 0.001 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (33367) covalent geometry : angle 0.54775 / 0.26 (45352) SS BOND : bond 0.00252 / 0.15 ( 5) SS BOND : angle 0.54465 / 0.28 ( 10) hydrogen bonds : bond 0.04481 / 3.00 ( 1885) hydrogen bonds : angle 4.26408 / 3.07 ( 5304) metal coordination : bond 0.00546 / 0.28 ( 4) metal coordination : angle 2.66694 / 1.34 ( 3) Misc. bond : bond 0.20690 / 11.87 ( 9) *********************** 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 364 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 317 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: P 118 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8536 (pt) REVERT: G 112 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: F 88 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8412 (tp30) REVERT: F 95 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8187 (tttm) REVERT: F 99 ASP cc_start: 0.8811 (m-30) cc_final: 0.8419 (m-30) REVERT: F 107 LYS cc_start: 0.9157 (tttt) cc_final: 0.8845 (tppp) REVERT: F 110 GLU cc_start: 0.8254 (pt0) cc_final: 0.8035 (pp20) REVERT: A 153 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8328 (ttt90) REVERT: A 390 LYS cc_start: 0.9022 (tptt) cc_final: 0.8765 (mttt) REVERT: A 397 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8374 (mt) REVERT: B 354 ASN cc_start: 0.8237 (t0) cc_final: 0.8019 (t0) REVERT: B 388 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: I 30 ASP cc_start: 0.8999 (t70) cc_final: 0.8655 (t70) REVERT: J 10 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8742 (tppt) REVERT: J 73 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8057 (ptt180) REVERT: E 54 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8774 (tppp) REVERT: R 9 LYS cc_start: 0.8743 (mttp) cc_final: 0.8523 (tttm) REVERT: Q 84 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7990 (mm-30) REVERT: Q 115 ASP cc_start: 0.8950 (m-30) cc_final: 0.8589 (t0) REVERT: L 29 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8736 (tptp) REVERT: L 51 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.8889 (p) REVERT: L 153 ARG cc_start: 0.8416 (ttp-110) cc_final: 0.7983 (ttt-90) REVERT: L 422 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8380 (mt-10) REVERT: M 83 LYS cc_start: 0.9275 (mmtm) cc_final: 0.9073 (mmtp) REVERT: M 101 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9140 (tttt) REVERT: M 353 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: O 146 ASP cc_start: 0.8932 (m-30) cc_final: 0.8709 (m-30) REVERT: S 76 LYS cc_start: 0.9160 (tptp) cc_final: 0.8918 (tppt) REVERT: U 11 LYS cc_start: 0.9019 (ptmm) cc_final: 0.8736 (ptpp) REVERT: U 55 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8468 (ttp-110) REVERT: U 58 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8199 (mp10) outliers start: 47 outliers final: 10 residues processed: 345 average time/residue: 0.8094 time to fit residues: 325.3168 Evaluate side-chains 329 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 304 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 353 GLU Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 58 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 99 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 287 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 294 optimal weight: 0.9990 chunk 369 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 321 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS Q 109 GLN Q 137 ASN U 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.076087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.057278 restraints weight = 56053.554| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 1.64 r_work: 0.2605 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9379 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.359 33385 Z= 0.116 Angle : 0.528 13.828 45365 Z= 0.255 Chirality : 0.040 0.146 4962 Planarity : 0.004 0.048 5700 Dihedral : 10.060 88.000 4818 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.41 % Allowed : 11.52 % Favored : 87.07 % 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: 2.17 (0.14), residues: 3955 helix: 2.11 (0.11), residues: 2150 sheet: 0.87 (0.26), residues: 369 loop : 0.70 (0.18), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 236 TYR 0.017 0.001 TYR B 170 PHE 0.019 0.001 PHE L 334 TRP 0.012 0.001 TRP C 142 HIS 0.005 0.001 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (33367) covalent geometry : angle 0.52678 / 0.25 (45352) SS BOND : bond 0.00248 / 0.15 ( 5) SS BOND : angle 0.50261 / 0.26 ( 10) hydrogen bonds : bond 0.04223 / 2.82 ( 1885) hydrogen bonds : angle 4.17461 / 3.00 ( 5304) metal coordination : bond 0.00362 / 0.19 ( 4) metal coordination : angle 4.73514 / 2.38 ( 3) Misc. bond : bond 0.19396 / 10.83 ( 9) *********************** 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 369 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 322 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: P 118 ILE cc_start: 0.8858 (mp) cc_final: 0.8519 (pt) REVERT: G 66 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8645 (mm-30) REVERT: F 95 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8151 (tttm) REVERT: F 99 ASP cc_start: 0.8791 (m-30) cc_final: 0.8383 (m-30) REVERT: F 107 LYS cc_start: 0.9174 (tttt) cc_final: 0.8816 (tppp) REVERT: F 110 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8042 (pp20) REVERT: A 153 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8403 (ttt90) REVERT: A 390 LYS cc_start: 0.9027 (tptt) cc_final: 0.8761 (mttt) REVERT: A 397 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8393 (mt) REVERT: B 354 ASN cc_start: 0.8223 (t0) cc_final: 0.7987 (t0) REVERT: B 388 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: I 30 ASP cc_start: 0.8986 (t70) cc_final: 0.8651 (t70) REVERT: I 54 ARG cc_start: 0.8968 (ttm-80) cc_final: 0.8721 (ttm110) REVERT: J 10 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8752 (tppt) REVERT: J 73 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8020 (ptt180) REVERT: R 9 LYS cc_start: 0.8716 (mttp) cc_final: 0.8509 (tttm) REVERT: R 16 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8182 (mptt) REVERT: Q 84 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8029 (mm-30) REVERT: Q 115 ASP cc_start: 0.8941 (m-30) cc_final: 0.8602 (t0) REVERT: L 29 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8740 (tptp) REVERT: L 153 ARG cc_start: 0.8401 (ttp-110) cc_final: 0.7971 (ttt-90) REVERT: L 422 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8365 (mt-10) REVERT: M 101 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9098 (tttt) REVERT: O 146 ASP cc_start: 0.8930 (m-30) cc_final: 0.8701 (m-30) REVERT: S 76 LYS cc_start: 0.9148 (tptp) cc_final: 0.8920 (tppt) REVERT: U 10 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8507 (tmmt) REVERT: U 55 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8475 (ttp-110) REVERT: U 58 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8157 (mp10) outliers start: 47 outliers final: 15 residues processed: 354 average time/residue: 0.7852 time to fit residues: 323.8390 Evaluate side-chains 335 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 307 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 58 GLN Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 297 optimal weight: 0.8980 chunk 266 optimal weight: 0.0570 chunk 352 optimal weight: 0.0870 chunk 153 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 289 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS P 115 ASN Q 109 GLN Q 137 ASN L 102 HIS L 317 GLN M 92 HIS M 121 GLN M 184 GLN M 377 ASN U 80 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.059098 restraints weight = 56088.741| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 1.66 r_work: 0.2648 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9348 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.340 33385 Z= 0.097 Angle : 0.495 12.260 45365 Z= 0.239 Chirality : 0.039 0.140 4962 Planarity : 0.004 0.048 5700 Dihedral : 9.560 88.430 4817 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.17 % Allowed : 12.03 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.14), residues: 3955 helix: 2.27 (0.11), residues: 2152 sheet: 1.02 (0.26), residues: 367 loop : 0.77 (0.18), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 236 TYR 0.016 0.001 TYR B 170 PHE 0.017 0.001 PHE L 334 TRP 0.011 0.001 TRP C 142 HIS 0.004 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (33367) covalent geometry : angle 0.49463 / 0.24 (45352) SS BOND : bond 0.00199 / 0.13 ( 5) SS BOND : angle 0.45497 / 0.24 ( 10) hydrogen bonds : bond 0.03780 / 2.52 ( 1885) hydrogen bonds : angle 4.05088 / 2.91 ( 5304) metal coordination : bond 0.00660 / 0.32 ( 4) metal coordination : angle 3.59782 / 1.80 ( 3) Misc. bond : bond 0.16837 / 8.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 319 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: F 95 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8443 (tttp) REVERT: F 99 ASP cc_start: 0.8754 (m-30) cc_final: 0.8513 (m-30) REVERT: F 107 LYS cc_start: 0.9147 (tttt) cc_final: 0.8823 (tppp) REVERT: F 110 GLU cc_start: 0.8261 (pt0) cc_final: 0.8039 (pp20) REVERT: A 153 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8487 (ttt-90) REVERT: A 390 LYS cc_start: 0.9019 (tptt) cc_final: 0.8762 (mttt) REVERT: A 397 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8334 (mt) REVERT: I 30 ASP cc_start: 0.8947 (t70) cc_final: 0.8617 (t70) REVERT: I 54 ARG cc_start: 0.8910 (ttm-80) cc_final: 0.8687 (ttm110) REVERT: J 10 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8747 (tptt) REVERT: J 73 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8021 (ptt180) REVERT: E 54 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8715 (tppp) REVERT: R 9 LYS cc_start: 0.8683 (mttp) cc_final: 0.8480 (tttm) REVERT: Q 84 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8004 (mm-30) REVERT: Q 115 ASP cc_start: 0.8909 (m-30) cc_final: 0.8614 (t0) REVERT: L 29 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8739 (tptp) REVERT: L 99 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8509 (tmm) REVERT: L 153 ARG cc_start: 0.8445 (ttp-110) cc_final: 0.8002 (ttt-90) REVERT: L 422 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8314 (mt-10) REVERT: O 146 ASP cc_start: 0.8910 (m-30) cc_final: 0.8688 (m-30) REVERT: S 76 LYS cc_start: 0.9154 (tptp) cc_final: 0.8918 (tppt) REVERT: U 11 LYS cc_start: 0.9059 (ptmm) cc_final: 0.8789 (ptpp) REVERT: U 55 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8410 (ttp-110) REVERT: U 58 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8147 (mp10) outliers start: 39 outliers final: 11 residues processed: 346 average time/residue: 0.7861 time to fit residues: 316.6125 Evaluate side-chains 329 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 308 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 58 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 132 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 304 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS P 115 ASN B 215 GLN N 11 ASN Q 137 ASN M 377 ASN U 80 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.075608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.056592 restraints weight = 56271.461| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 1.67 r_work: 0.2592 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9389 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.345 33385 Z= 0.141 Angle : 0.543 14.903 45365 Z= 0.261 Chirality : 0.041 0.149 4962 Planarity : 0.004 0.047 5700 Dihedral : 9.687 88.913 4817 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.23 % Allowed : 12.30 % Favored : 86.47 % 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: 2.35 (0.14), residues: 3955 helix: 2.23 (0.11), residues: 2156 sheet: 0.99 (0.26), residues: 369 loop : 0.79 (0.18), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 201 TYR 0.022 0.001 TYR B 170 PHE 0.021 0.001 PHE L 334 TRP 0.013 0.001 TRP N 142 HIS 0.008 0.001 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (33367) covalent geometry : angle 0.54159 / 0.26 (45352) SS BOND : bond 0.00294 / 0.18 ( 5) SS BOND : angle 0.52032 / 0.27 ( 10) hydrogen bonds : bond 0.04392 / 2.93 ( 1885) hydrogen bonds : angle 4.12184 / 2.96 ( 5304) metal coordination : bond 0.00536 / 0.27 ( 4) metal coordination : angle 4.51674 / 2.29 ( 3) Misc. bond : bond 0.18473 / 9.85 ( 9) *********************** 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 354 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: P 118 ILE cc_start: 0.8866 (mp) cc_final: 0.8550 (pt) REVERT: F 95 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8225 (tttm) REVERT: F 99 ASP cc_start: 0.8754 (m-30) cc_final: 0.8391 (m-30) REVERT: F 107 LYS cc_start: 0.9174 (tttt) cc_final: 0.8752 (tppp) REVERT: F 110 GLU cc_start: 0.8333 (pt0) cc_final: 0.8104 (pp20) REVERT: A 153 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8410 (ttt90) REVERT: A 390 LYS cc_start: 0.9022 (tptt) cc_final: 0.8755 (mttt) REVERT: A 397 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8422 (mt) REVERT: B 388 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: I 30 ASP cc_start: 0.8985 (t70) cc_final: 0.8649 (t70) REVERT: J 10 LYS cc_start: 0.8985 (tptm) cc_final: 0.8747 (tptt) REVERT: J 73 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8062 (ptt180) REVERT: R 9 LYS cc_start: 0.8722 (mttp) cc_final: 0.8522 (tttm) REVERT: Q 84 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7932 (mm-30) REVERT: Q 114 TYR cc_start: 0.8773 (t80) cc_final: 0.8538 (t80) REVERT: Q 115 ASP cc_start: 0.8918 (m-30) cc_final: 0.8633 (t0) REVERT: L 29 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8758 (tptp) REVERT: L 99 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8498 (tmm) REVERT: L 153 ARG cc_start: 0.8415 (ttp-110) cc_final: 0.7964 (ttt-90) REVERT: L 422 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8388 (mt-10) REVERT: M 101 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9090 (tttt) REVERT: O 146 ASP cc_start: 0.8952 (m-30) cc_final: 0.8705 (m-30) REVERT: S 76 LYS cc_start: 0.9160 (tptp) cc_final: 0.8913 (tppt) REVERT: U 11 LYS cc_start: 0.9069 (ptmm) cc_final: 0.8807 (ptpp) REVERT: U 58 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8160 (mp10) outliers start: 41 outliers final: 23 residues processed: 343 average time/residue: 0.7552 time to fit residues: 302.0449 Evaluate side-chains 338 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 306 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 58 GLN Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 344 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 389 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 307 optimal weight: 3.9990 chunk 341 optimal weight: 0.7980 chunk 286 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 294 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS P 115 ASN A 332 ASN Q 137 ASN M 377 ASN U 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.073604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.054531 restraints weight = 56545.445| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 1.66 r_work: 0.2545 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9418 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.374 33385 Z= 0.222 Angle : 0.602 15.371 45365 Z= 0.292 Chirality : 0.044 0.155 4962 Planarity : 0.004 0.049 5700 Dihedral : 10.117 89.202 4817 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.65 % Allowed : 12.06 % Favored : 86.29 % 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: 2.15 (0.14), residues: 3955 helix: 2.06 (0.11), residues: 2163 sheet: 1.01 (0.26), residues: 365 loop : 0.70 (0.18), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 236 TYR 0.029 0.002 TYR B 170 PHE 0.025 0.002 PHE L 334 TRP 0.014 0.001 TRP N 142 HIS 0.010 0.001 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (33367) covalent geometry : angle 0.60002 / 0.29 (45352) SS BOND : bond 0.00374 / 0.22 ( 5) SS BOND : angle 0.60467 / 0.32 ( 10) hydrogen bonds : bond 0.05120 / 3.42 ( 1885) hydrogen bonds : angle 4.29480 / 3.10 ( 5304) metal coordination : bond 0.00739 / 0.38 ( 4) metal coordination : angle 5.76252 / 2.94 ( 3) Misc. bond : bond 0.21418 / 11.85 ( 9) *********************** 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 358 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 303 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 118 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8561 (pt) REVERT: P 193 HIS cc_start: 0.5506 (OUTLIER) cc_final: 0.4489 (m90) REVERT: G 112 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: F 95 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8215 (tttm) REVERT: F 99 ASP cc_start: 0.8783 (m-30) cc_final: 0.8393 (m-30) REVERT: F 107 LYS cc_start: 0.9178 (tttt) cc_final: 0.8741 (tppp) REVERT: F 110 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8058 (pp20) REVERT: A 153 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8347 (ttt90) REVERT: A 390 LYS cc_start: 0.9011 (tptt) cc_final: 0.8752 (mttt) REVERT: A 397 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8485 (mt) REVERT: B 388 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: I 30 ASP cc_start: 0.9047 (t70) cc_final: 0.8656 (t70) REVERT: J 10 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8730 (tptt) REVERT: J 73 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8091 (ptt180) REVERT: N 283 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8467 (mtp180) REVERT: E 54 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8774 (tppp) REVERT: Q 84 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7987 (mm-30) REVERT: Q 114 TYR cc_start: 0.8768 (t80) cc_final: 0.8508 (t80) REVERT: Q 115 ASP cc_start: 0.8937 (m-30) cc_final: 0.8658 (t0) REVERT: L 29 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8645 (tptp) REVERT: L 153 ARG cc_start: 0.8368 (ttp-110) cc_final: 0.7906 (ttt-90) REVERT: L 422 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8441 (mt-10) REVERT: M 101 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9157 (tttt) REVERT: M 353 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: O 146 ASP cc_start: 0.8994 (m-30) cc_final: 0.8739 (m-30) REVERT: S 76 LYS cc_start: 0.9194 (tptp) cc_final: 0.8984 (tppt) REVERT: U 11 LYS cc_start: 0.9064 (ptmm) cc_final: 0.8808 (ptpp) REVERT: U 58 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8184 (mp10) outliers start: 55 outliers final: 24 residues processed: 342 average time/residue: 0.8028 time to fit residues: 319.3072 Evaluate side-chains 337 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 297 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 193 HIS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 353 GLU Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 58 GLN Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 266 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 362 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 294 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 250 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS P 115 ASN M 377 ASN U 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.075056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.056076 restraints weight = 56059.371| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 1.67 r_work: 0.2579 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9397 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.367 33385 Z= 0.135 Angle : 0.550 14.671 45365 Z= 0.265 Chirality : 0.041 0.147 4962 Planarity : 0.004 0.047 5700 Dihedral : 9.828 88.527 4817 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.20 % Allowed : 12.48 % Favored : 86.32 % 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: 2.28 (0.14), residues: 3955 helix: 2.16 (0.11), residues: 2156 sheet: 1.05 (0.26), residues: 365 loop : 0.78 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 201 TYR 0.030 0.001 TYR B 170 PHE 0.021 0.001 PHE L 334 TRP 0.013 0.001 TRP N 142 HIS 0.006 0.001 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (33367) covalent geometry : angle 0.54851 / 0.27 (45352) SS BOND : bond 0.00268 / 0.16 ( 5) SS BOND : angle 0.49439 / 0.25 ( 10) hydrogen bonds : bond 0.04477 / 2.99 ( 1885) hydrogen bonds : angle 4.20064 / 3.02 ( 5304) metal coordination : bond 0.00527 / 0.27 ( 4) metal coordination : angle 5.39395 / 2.75 ( 3) Misc. bond : bond 0.19808 / 10.57 ( 9) *********************** 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 347 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 307 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: P 118 ILE cc_start: 0.8906 (mp) cc_final: 0.8609 (pt) REVERT: P 193 HIS cc_start: 0.5436 (OUTLIER) cc_final: 0.4556 (m90) REVERT: F 95 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8160 (tttm) REVERT: F 99 ASP cc_start: 0.8757 (m-30) cc_final: 0.8345 (m-30) REVERT: F 107 LYS cc_start: 0.9184 (tttt) cc_final: 0.8782 (tppp) REVERT: F 110 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8069 (pp20) REVERT: A 153 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8368 (ttt90) REVERT: A 390 LYS cc_start: 0.9012 (tptt) cc_final: 0.8763 (mttt) REVERT: A 397 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8382 (mt) REVERT: B 388 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: I 30 ASP cc_start: 0.9002 (t70) cc_final: 0.8630 (t70) REVERT: J 10 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8734 (tptt) REVERT: J 55 ARG cc_start: 0.9156 (ttm110) cc_final: 0.8930 (ttm110) REVERT: J 73 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8076 (ptt180) REVERT: E 54 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8749 (tppp) REVERT: Q 84 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7996 (mm-30) REVERT: Q 114 TYR cc_start: 0.8770 (t80) cc_final: 0.8515 (t80) REVERT: Q 115 ASP cc_start: 0.8909 (m-30) cc_final: 0.8659 (t0) REVERT: L 29 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8646 (tptp) REVERT: L 153 ARG cc_start: 0.8365 (ttp-110) cc_final: 0.7908 (ttt-90) REVERT: L 422 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8429 (mt-10) REVERT: M 101 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9116 (tttt) REVERT: O 146 ASP cc_start: 0.8958 (m-30) cc_final: 0.8715 (m-30) REVERT: S 76 LYS cc_start: 0.9168 (tptp) cc_final: 0.8955 (tppt) REVERT: U 11 LYS cc_start: 0.9071 (ptmm) cc_final: 0.8819 (ptpp) REVERT: U 55 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7917 (ttp-110) REVERT: U 58 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8138 (mp10) outliers start: 40 outliers final: 19 residues processed: 336 average time/residue: 0.7349 time to fit residues: 287.5492 Evaluate side-chains 334 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 193 HIS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 58 GLN 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: 3.9990 chunk 162 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS P 115 ASN Q 137 ASN M 377 ASN U 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.075092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.056114 restraints weight = 56508.026| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 1.67 r_work: 0.2580 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9396 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.357 33385 Z= 0.145 Angle : 0.554 14.656 45365 Z= 0.267 Chirality : 0.041 0.148 4962 Planarity : 0.004 0.047 5700 Dihedral : 9.706 89.035 4817 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.02 % Allowed : 12.69 % Favored : 86.29 % 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: 2.28 (0.14), residues: 3955 helix: 2.15 (0.11), residues: 2168 sheet: 0.99 (0.26), residues: 369 loop : 0.79 (0.18), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 236 TYR 0.032 0.002 TYR B 170 PHE 0.021 0.001 PHE L 334 TRP 0.012 0.001 TRP C 142 HIS 0.007 0.001 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (33367) covalent geometry : angle 0.55194 / 0.27 (45352) SS BOND : bond 0.00277 / 0.17 ( 5) SS BOND : angle 0.50558 / 0.26 ( 10) hydrogen bonds : bond 0.04495 / 3.00 ( 1885) hydrogen bonds : angle 4.18943 / 3.01 ( 5304) metal coordination : bond 0.00529 / 0.27 ( 4) metal coordination : angle 5.40254 / 2.77 ( 3) Misc. bond : bond 0.19493 / 10.59 ( 9) ********************** 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 346 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 312 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: P 118 ILE cc_start: 0.8898 (mp) cc_final: 0.8585 (pt) REVERT: P 182 PHE cc_start: 0.8345 (m-10) cc_final: 0.8045 (m-10) REVERT: P 193 HIS cc_start: 0.5405 (OUTLIER) cc_final: 0.4380 (m90) REVERT: P 201 ARG cc_start: 0.7269 (mtp85) cc_final: 0.5237 (mmm160) REVERT: F 95 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8185 (tttm) REVERT: F 99 ASP cc_start: 0.8745 (m-30) cc_final: 0.8400 (m-30) REVERT: F 107 LYS cc_start: 0.9208 (tttt) cc_final: 0.8795 (tppp) REVERT: F 110 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8073 (pp20) REVERT: A 153 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8349 (ttt90) REVERT: A 390 LYS cc_start: 0.9017 (tptt) cc_final: 0.8764 (mttt) REVERT: A 397 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8388 (mt) REVERT: B 388 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: I 30 ASP cc_start: 0.8987 (t70) cc_final: 0.8651 (t70) REVERT: J 10 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8730 (tptt) REVERT: J 55 ARG cc_start: 0.9159 (ttm110) cc_final: 0.8934 (ttm110) REVERT: J 73 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8071 (ptt180) REVERT: Q 84 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7985 (mm-30) REVERT: Q 114 TYR cc_start: 0.8761 (t80) cc_final: 0.8500 (t80) REVERT: Q 115 ASP cc_start: 0.8928 (m-30) cc_final: 0.8696 (t0) REVERT: L 29 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8650 (tptp) REVERT: L 153 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.7858 (ttt-90) REVERT: L 422 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8425 (mt-10) REVERT: M 101 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9114 (tttt) REVERT: O 146 ASP cc_start: 0.8966 (m-30) cc_final: 0.8720 (m-30) REVERT: S 76 LYS cc_start: 0.9167 (tptp) cc_final: 0.8939 (tppt) REVERT: U 11 LYS cc_start: 0.9079 (ptmm) cc_final: 0.8834 (ptpp) REVERT: U 55 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7829 (ttp-110) REVERT: U 58 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8128 (mp10) outliers start: 34 outliers final: 19 residues processed: 339 average time/residue: 0.7962 time to fit residues: 313.9474 Evaluate side-chains 334 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 303 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 193 HIS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 58 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 179 optimal weight: 0.9990 chunk 354 optimal weight: 1.9990 chunk 387 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 370 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 377 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS P 115 ASN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 96 HIS Q 137 ASN M 377 ASN U 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.075056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.056068 restraints weight = 56387.886| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 1.67 r_work: 0.2579 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9396 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.358 33385 Z= 0.159 Angle : 0.663 59.200 45365 Z= 0.352 Chirality : 0.042 0.786 4962 Planarity : 0.004 0.067 5700 Dihedral : 9.721 89.060 4817 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.08 % Allowed : 12.69 % Favored : 86.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 2.28 (0.14), residues: 3955 helix: 2.15 (0.11), residues: 2168 sheet: 0.99 (0.26), residues: 369 loop : 0.79 (0.18), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 236 TYR 0.027 0.001 TYR B 170 PHE 0.021 0.001 PHE L 334 TRP 0.012 0.001 TRP N 142 HIS 0.030 0.001 HIS P 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (33367) covalent geometry : angle 0.66113 / 0.35 (45352) SS BOND : bond 0.00260 / 0.16 ( 5) SS BOND : angle 0.49694 / 0.25 ( 10) hydrogen bonds : bond 0.04476 / 2.99 ( 1885) hydrogen bonds : angle 4.18905 / 3.01 ( 5304) metal coordination : bond 0.01037 / 0.52 ( 4) metal coordination : angle 5.34897 / 2.74 ( 3) Misc. bond : bond 0.19806 / 10.87 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12797.06 seconds wall clock time: 218 minutes 20.30 seconds (13100.30 seconds total)