Starting phenix.real_space_refine on Mon Sep 14 22:12:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8abf_15319/09_2026/8abf_15319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8abf_15319/09_2026/8abf_15319.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 { model { file = "/net/cci-nas-00/data/ceres_data/8abf_15319/09_2026/8abf_15319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8abf_15319/09_2026/8abf_15319.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8abf_15319/09_2026/8abf_15319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8abf_15319/09_2026/8abf_15319.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8abf_15319/09_2026/8abf_15319.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8abf_15319/09_2026/8abf_15319.cif" } 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 129 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 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: 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: "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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'LMT': 1, 'XP4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "N" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 29.402 46.555 29.358 1.00138.94 S ATOM 4207 SG CYS P 187 31.996 44.352 27.417 1.00153.13 S Time building chain proxies: 6.52, per 1000 atoms: 0.20 Number of scatterers: 32540 At special positions: 0 Unit cell: (119.691, 129.735, 165.726, 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=2.04 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=2.06 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 21 sheets defined 61.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 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: 3.761A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 removed outlier: 3.527A 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: 6.910A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.859A 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: 3.791A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.821A 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: 4.138A 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: 3.608A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 92 No H-bonds generated for 'chain 'P' and resid 90 through 92' Processing helix chain 'P' and resid 94 through 100 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: 3.513A 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 84 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 102 through 120 Processing helix chain 'F' and resid 77 through 89 removed outlier: 4.253A 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: 3.579A 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: 3.518A 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: 4.027A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.991A pdb=" N ASN A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.521A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 4.007A 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: 3.637A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.513A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.281A 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: 3.661A 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: 3.598A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.848A 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: 3.564A 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: 3.831A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 333 through 354 Processing helix chain 'B' and resid 354 through 368 removed outlier: 3.639A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.610A pdb=" N VAL B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 134 through 139 removed outlier: 4.007A pdb=" N LEU D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL D 139 " --> pdb=" O TRP D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 139' Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 266 through 283 Processing helix chain 'D' and resid 285 through 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 81 removed outlier: 4.362A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.765A 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: 3.528A 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: 3.563A pdb=" N TRP J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Proline residue: J 33 - end of helix Processing helix chain 'J' and resid 53 through 60 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 66 through 72 removed outlier: 3.747A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.675A 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: 3.770A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.546A 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: 6.907A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.862A 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: 3.792A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.816A 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: 3.639A 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: 3.521A 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: 4.269A 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: 3.579A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 71 through 80 removed outlier: 3.507A 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: 4.020A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 160 removed outlier: 3.574A 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: 3.506A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 4.020A 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: 3.628A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.706A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.258A 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: 3.669A 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: 3.602A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.849A 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: 3.554A 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: 3.839A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.766A 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: 3.892A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.585A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 removed outlier: 3.500A pdb=" N LEU M 393 " --> pdb=" O ALA M 389 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 410 Processing helix chain 'M' and resid 412 through 416 Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 109 through 123 Processing helix chain 'O' and resid 124 through 127 Processing helix chain 'O' and resid 134 through 139 removed outlier: 4.012A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL O 139 " --> pdb=" O TRP O 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 134 through 139' Processing helix chain 'O' and resid 144 through 154 Processing helix chain 'O' and resid 184 through 191 Processing helix chain 'O' and resid 210 through 220 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 320 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.360A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.541A 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: 3.582A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.747A 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: 3.884A 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: 3.515A pdb=" N SER P 192 " --> pdb=" O CYS P 187 " (cutoff:3.500A) removed outlier: 3.631A 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: 6.541A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.328A 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: 3.975A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.860A 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: 4.179A 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: 6.621A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.599A 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: 6.541A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU L 44 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 307 through 308 removed outlier: 3.954A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.840A 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: 4.154A 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: 6.611A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 156 through 158 Processing sheet with id=AC2, first strand: chain 'O' and resid 236 through 237 Processing sheet with id=AC3, first strand: chain 'U' and resid 19 through 20 1886 hydrogen bonds defined for protein. 5319 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: 7.23 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 13535 1.40 - 1.61: 19622 1.61 - 1.82: 163 1.82 - 2.03: 27 2.03 - 2.24: 20 Bond restraints: 33367 Sorted by residual: bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.460 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" C18 XP4 J 101 " pdb=" O7 XP4 J 101 " ideal model delta sigma weight residual 1.328 1.459 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.462 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.461 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " ideal model delta sigma weight residual 1.334 1.449 -0.115 2.00e-02 2.50e+03 3.32e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 43757 3.97 - 7.94: 1413 7.94 - 11.91: 147 11.91 - 15.87: 27 15.87 - 19.84: 8 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 93.83 17.44 1.47e+00 4.63e-01 1.41e+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 91.45 12.88 1.14e+00 7.69e-01 1.28e+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 94.76 16.51 1.47e+00 4.63e-01 1.26e+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 91.40 12.93 1.20e+00 6.94e-01 1.16e+02 angle pdb=" CG ARG O 289 " pdb=" CD ARG O 289 " pdb=" NE ARG O 289 " ideal model delta sigma weight residual 112.00 92.16 19.84 2.20e+00 2.07e-01 8.14e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.82: 18544 31.82 - 63.65: 881 63.65 - 95.47: 88 95.47 - 127.29: 0 127.29 - 159.11: 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 -103.26 -19.34 0 2.50e+00 1.60e-01 5.98e+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 -103.42 -19.18 0 2.50e+00 1.60e-01 5.89e+01 dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -105.01 -17.59 0 2.50e+00 1.60e-01 4.95e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 4690 0.217 - 0.434: 262 0.434 - 0.651: 5 0.651 - 0.868: 3 0.868 - 1.085: 2 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB VAL C 146 " pdb=" CA VAL C 146 " pdb=" CG1 VAL C 146 " pdb=" CG2 VAL C 146 " both_signs ideal model delta sigma weight residual False -2.63 -1.54 -1.08 2.00e-01 2.50e+01 2.94e+01 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 -1.64 -0.93 2.00e-01 2.50e+01 2.17e+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 -1.71 -0.87 2.00e-01 2.50e+01 1.88e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 76 " 0.347 9.50e-02 1.11e+02 1.59e-01 2.72e+01 pdb=" NE ARG R 76 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG R 76 " 0.057 2.00e-02 2.50e+03 pdb=" NH1 ARG R 76 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG R 76 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 76 " -0.341 9.50e-02 1.11e+02 1.56e-01 2.58e+01 pdb=" NE ARG G 76 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG G 76 " -0.054 2.00e-02 2.50e+03 pdb=" NH1 ARG G 76 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG G 76 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 96 " -0.053 2.00e-02 2.50e+03 4.02e-02 2.43e+01 pdb=" CG HIS N 96 " 0.063 2.00e-02 2.50e+03 pdb=" ND1 HIS N 96 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 HIS N 96 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 HIS N 96 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS N 96 " -0.039 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 358 2.64 - 3.21: 29336 3.21 - 3.77: 53732 3.77 - 4.34: 78187 4.34 - 4.90: 121495 Nonbonded interactions: 283108 Sorted by model distance: nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.075 3.080 nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.076 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.076 3.120 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.118 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEM C 502 " model vdw 2.239 3.080 ... (remaining 283103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'L' and resid 26 through 3002) } 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.280 Find NCS groups from input model: 0.540 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: 0.000 Load rotamer database and sin/cos tables:7.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9494 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 : 0.012 0.682 33385 Z= 0.823 Angle : 1.758 23.722 45365 Z= 1.081 Chirality : 0.114 1.085 4962 Planarity : 0.009 0.159 5700 Dihedral : 17.451 159.114 12014 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.22 % Allowed : 7.22 % Favored : 89.56 % Cbeta Deviations : 1.47 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.12), residues: 3955 helix: -0.78 (0.09), residues: 2145 sheet: 0.05 (0.25), residues: 351 loop : -0.62 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.003 ARG R 76 TYR 0.055 0.008 TYR O 120 PHE 0.063 0.008 PHE B 107 TRP 0.044 0.009 TRP L 474 HIS 0.022 0.005 HIS N 57 Details of bonding type rmsd/Z covalent geometry : bond 0.01042 / 0.64 (33367) covalent geometry : angle 1.75190 / 1.08 (45352) SS BOND : bond 0.02804 / 1.66 ( 5) SS BOND : angle 2.54062 / 1.34 ( 10) hydrogen bonds : bond 0.18287 / 12.34 ( 1886) hydrogen bonds : angle 6.86762 / 5.00 ( 5319) metal coordination : bond 0.07880 / 3.99 ( 4) metal coordination : angle 17.19427 / 9.14 ( 3) Misc. bond : bond 0.32626 / 16.11 ( 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 581 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 474 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: P 106 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6582 (mmmt) REVERT: P 131 THR cc_start: 0.7604 (p) cc_final: 0.7262 (p) REVERT: P 134 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8431 (mm-30) REVERT: P 158 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6965 (mtpt) REVERT: P 178 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7041 (mm-30) REVERT: P 182 PHE cc_start: 0.7567 (m-80) cc_final: 0.7313 (m-80) REVERT: F 84 GLU cc_start: 0.8690 (tt0) cc_final: 0.8280 (tp30) REVERT: F 88 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7858 (mm-30) REVERT: F 131 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8951 (mm-40) REVERT: A 68 TYR cc_start: 0.8770 (m-80) cc_final: 0.8564 (m-80) REVERT: A 153 ARG cc_start: 0.8364 (ttp-110) cc_final: 0.7917 (ttt-90) REVERT: A 390 LYS cc_start: 0.9050 (tptt) cc_final: 0.8658 (mttp) REVERT: B 236 ARG cc_start: 0.8453 (ttm110) cc_final: 0.7768 (tpp-160) REVERT: N 288 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8674 (tttt) REVERT: E 55 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7896 (p0) REVERT: L 48 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8721 (tp) REVERT: L 51 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8947 (p) REVERT: L 87 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8511 (mtt90) REVERT: L 97 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8894 (mm-30) REVERT: L 153 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.7802 (ttt90) REVERT: M 16 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8495 (p) REVERT: M 236 ARG cc_start: 0.8647 (mtt90) cc_final: 0.8243 (mmm160) REVERT: M 356 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8376 (t0) REVERT: S 78 GLU cc_start: 0.8853 (tt0) cc_final: 0.8585 (tm-30) REVERT: U 73 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8742 (mtt180) outliers start: 107 outliers final: 10 residues processed: 539 average time/residue: 0.7812 time to fit residues: 485.8276 Evaluate side-chains 353 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 332 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 288 LYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 356 ASP Chi-restraints excluded: chain U residue 73 ARG 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: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** P 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN A 50 GLN A 74 HIS A 222 HIS A 332 ASN A 371 ASN B 87 HIS B 197 ASN B 377 ASN N 14 ASN N 202 HIS N 332 ASN E 90 ASN R 84 HIS L 50 GLN L 332 ASN L 371 ASN M 87 HIS M 197 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.077785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.058029 restraints weight = 55445.587| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 1.66 r_work: 0.2612 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9363 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.429 33385 Z= 0.140 Angle : 0.633 16.133 45365 Z= 0.311 Chirality : 0.042 0.168 4962 Planarity : 0.004 0.039 5700 Dihedral : 11.991 132.017 4869 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.74 % Allowed : 10.38 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.13), residues: 3955 helix: 1.16 (0.11), residues: 2152 sheet: 0.37 (0.26), residues: 369 loop : 0.12 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 339 TYR 0.020 0.002 TYR D 237 PHE 0.023 0.002 PHE B 107 TRP 0.031 0.002 TRP C 156 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (33367) covalent geometry : angle 0.63179 / 0.31 (45352) SS BOND : bond 0.00228 / 0.13 ( 5) SS BOND : angle 0.62436 / 0.32 ( 10) hydrogen bonds : bond 0.05114 / 3.42 ( 1886) hydrogen bonds : angle 4.66971 / 3.39 ( 5319) metal coordination : bond 0.00518 / 0.26 ( 4) metal coordination : angle 4.71329 / 2.66 ( 3) Misc. bond : bond 0.24507 / 14.15 ( 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 425 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 367 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 158 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6843 (mtpt) REVERT: P 216 PHE cc_start: 0.7109 (m-80) cc_final: 0.6432 (m-80) REVERT: G 115 GLU cc_start: 0.9008 (tt0) cc_final: 0.8798 (tt0) REVERT: F 84 GLU cc_start: 0.8759 (tt0) cc_final: 0.8485 (tp30) REVERT: F 96 HIS cc_start: 0.8870 (t-90) cc_final: 0.8570 (t-170) REVERT: F 103 GLU cc_start: 0.8747 (tp30) cc_final: 0.8458 (tm-30) REVERT: F 126 GLU cc_start: 0.9058 (mp0) cc_final: 0.8851 (mp0) REVERT: A 153 ARG cc_start: 0.8578 (ttp-110) cc_final: 0.8168 (ttt-90) REVERT: A 240 GLN cc_start: 0.8329 (mp10) cc_final: 0.8094 (pm20) REVERT: A 390 LYS cc_start: 0.9035 (tptt) cc_final: 0.8721 (mttp) REVERT: A 397 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8138 (mt) REVERT: B 251 GLU cc_start: 0.8138 (pm20) cc_final: 0.7781 (pm20) REVERT: H 57 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8601 (tt) REVERT: R 33 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8946 (ttpt) REVERT: Q 84 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8422 (mt-10) REVERT: Q 95 LYS cc_start: 0.8779 (tptt) cc_final: 0.8520 (tttp) REVERT: Q 96 HIS cc_start: 0.8857 (t-90) cc_final: 0.8393 (t70) REVERT: Q 107 LYS cc_start: 0.9001 (tttp) cc_final: 0.8752 (mtpt) REVERT: Q 137 ASN cc_start: 0.8974 (m-40) cc_final: 0.8758 (m-40) REVERT: L 51 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8958 (p) REVERT: L 87 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7266 (mtp85) REVERT: L 97 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8785 (mm-30) REVERT: L 153 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.8056 (ttt90) REVERT: M 16 SER cc_start: 0.8285 (m) cc_final: 0.7889 (p) REVERT: M 60 PHE cc_start: 0.9529 (OUTLIER) cc_final: 0.9058 (t80) REVERT: M 170 TYR cc_start: 0.8128 (p90) cc_final: 0.7741 (p90) REVERT: S 78 GLU cc_start: 0.8897 (tt0) cc_final: 0.8341 (tm-30) outliers start: 58 outliers final: 8 residues processed: 407 average time/residue: 0.7511 time to fit residues: 354.7696 Evaluate side-chains 338 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 322 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 230 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 275 optimal weight: 10.0000 chunk 317 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 377 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 292 optimal weight: 6.9990 chunk 384 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 HIS F 137 ASN B 316 GLN B 354 ASN B 377 ASN M 92 HIS M 316 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.055547 restraints weight = 55787.145| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 1.67 r_work: 0.2562 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9398 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.380 33385 Z= 0.199 Angle : 0.618 15.349 45365 Z= 0.303 Chirality : 0.044 0.153 4962 Planarity : 0.004 0.046 5700 Dihedral : 11.081 99.815 4830 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.74 % Allowed : 10.77 % Favored : 87.49 % 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: 1.63 (0.13), residues: 3955 helix: 1.67 (0.11), residues: 2139 sheet: 0.61 (0.26), residues: 363 loop : 0.45 (0.17), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 55 TYR 0.020 0.002 TYR N 225 PHE 0.024 0.002 PHE L 334 TRP 0.016 0.002 TRP N 142 HIS 0.013 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (33367) covalent geometry : angle 0.61499 / 0.30 (45352) SS BOND : bond 0.00273 / 0.15 ( 5) SS BOND : angle 0.66481 / 0.33 ( 10) hydrogen bonds : bond 0.05336 / 3.59 ( 1886) hydrogen bonds : angle 4.46361 / 3.24 ( 5319) metal coordination : bond 0.01134 / 0.57 ( 4) metal coordination : angle 7.89624 / 4.53 ( 3) Misc. bond : bond 0.22783 / 12.85 ( 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 393 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 335 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 116 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7148 (m) REVERT: P 182 PHE cc_start: 0.7515 (m-80) cc_final: 0.7286 (m-80) REVERT: P 194 TYR cc_start: 0.8246 (m-80) cc_final: 0.7862 (m-80) REVERT: P 202 ARG cc_start: 0.7506 (ttp80) cc_final: 0.7298 (ttp80) REVERT: G 112 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: F 84 GLU cc_start: 0.8788 (tt0) cc_final: 0.8519 (tp30) REVERT: F 88 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7873 (mm-30) REVERT: F 109 GLN cc_start: 0.9026 (mt0) cc_final: 0.8753 (mt0) REVERT: F 126 GLU cc_start: 0.9054 (mp0) cc_final: 0.8817 (mp0) REVERT: A 153 ARG cc_start: 0.8614 (ttp-110) cc_final: 0.8115 (ttt-90) REVERT: A 240 GLN cc_start: 0.8333 (mp10) cc_final: 0.7997 (pm20) REVERT: A 390 LYS cc_start: 0.9036 (tptt) cc_final: 0.8695 (mttp) REVERT: A 397 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8091 (mt) REVERT: B 205 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 251 GLU cc_start: 0.8223 (pm20) cc_final: 0.7826 (pm20) REVERT: H 57 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8687 (tt) REVERT: J 10 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8532 (ttmp) REVERT: J 15 LYS cc_start: 0.8822 (mtmm) cc_final: 0.8559 (ptmm) REVERT: E 55 ASP cc_start: 0.8245 (p0) cc_final: 0.7893 (p0) REVERT: Q 84 GLU cc_start: 0.8771 (tp30) cc_final: 0.8548 (tt0) REVERT: Q 95 LYS cc_start: 0.8787 (tptt) cc_final: 0.8541 (tttp) REVERT: Q 96 HIS cc_start: 0.8945 (t-90) cc_final: 0.8519 (t70) REVERT: Q 100 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8163 (mt-10) REVERT: Q 137 ASN cc_start: 0.8887 (m-40) cc_final: 0.8686 (m110) REVERT: L 51 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.8873 (p) REVERT: M 16 SER cc_start: 0.8317 (m) cc_final: 0.7988 (p) REVERT: M 139 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8941 (ttmm) REVERT: M 170 TYR cc_start: 0.8248 (p90) cc_final: 0.7782 (p90) REVERT: M 236 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7956 (mtp85) REVERT: O 248 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8371 (ttm) REVERT: S 78 GLU cc_start: 0.8902 (tt0) cc_final: 0.8372 (tm-30) outliers start: 58 outliers final: 19 residues processed: 376 average time/residue: 0.7849 time to fit residues: 341.3988 Evaluate side-chains 341 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 314 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain P residue 192 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 139 LYS Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 248 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 364 optimal weight: 0.9990 chunk 175 optimal weight: 8.9990 chunk 166 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.5693 > 50:) chunk 295 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 289 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 chunk 384 optimal weight: 8.9990 chunk 337 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS P 85 GLN A 317 GLN B 377 ASN L 102 HIS L 159 ASN M 215 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.058349 restraints weight = 55641.180| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 1.67 r_work: 0.2628 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9355 moved from start: 0.2461 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= 0.111 Angle : 0.520 12.600 45365 Z= 0.255 Chirality : 0.040 0.160 4962 Planarity : 0.004 0.048 5700 Dihedral : 10.283 89.712 4823 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.35 % Allowed : 11.37 % Favored : 87.28 % 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: 2.02 (0.14), residues: 3955 helix: 1.98 (0.11), residues: 2142 sheet: 0.78 (0.26), residues: 369 loop : 0.64 (0.18), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 128 TYR 0.013 0.001 TYR N 225 PHE 0.020 0.001 PHE L 334 TRP 0.014 0.001 TRP C 156 HIS 0.004 0.001 HIS M 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (33367) covalent geometry : angle 0.51759 / 0.25 (45352) SS BOND : bond 0.00242 / 0.14 ( 5) SS BOND : angle 0.51738 / 0.25 ( 10) hydrogen bonds : bond 0.04141 / 2.76 ( 1886) hydrogen bonds : angle 4.23781 / 3.08 ( 5319) metal coordination : bond 0.00554 / 0.28 ( 4) metal coordination : angle 5.58393 / 3.22 ( 3) Misc. bond : bond 0.18194 / 9.29 ( 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 388 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 343 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 322 SER cc_start: 0.9507 (OUTLIER) cc_final: 0.9250 (m) REVERT: P 194 TYR cc_start: 0.8346 (m-80) cc_final: 0.7537 (m-80) REVERT: F 84 GLU cc_start: 0.8782 (tt0) cc_final: 0.8505 (tp30) REVERT: F 88 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7948 (mm-30) REVERT: F 103 GLU cc_start: 0.8717 (tp30) cc_final: 0.8447 (tm-30) REVERT: F 109 GLN cc_start: 0.9042 (mt0) cc_final: 0.8781 (mt0) REVERT: F 126 GLU cc_start: 0.9023 (mp0) cc_final: 0.8795 (mp0) REVERT: A 153 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8129 (ttt-90) REVERT: A 240 GLN cc_start: 0.8298 (mp10) cc_final: 0.7970 (pm20) REVERT: A 390 LYS cc_start: 0.9007 (tptt) cc_final: 0.8689 (mttp) REVERT: A 397 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8023 (mt) REVERT: B 205 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8088 (tm-30) REVERT: B 251 GLU cc_start: 0.8238 (pm20) cc_final: 0.7957 (pm20) REVERT: H 57 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8692 (tt) REVERT: E 55 ASP cc_start: 0.8244 (p0) cc_final: 0.7923 (p0) REVERT: R 85 LYS cc_start: 0.8896 (mttp) cc_final: 0.8684 (mtpp) REVERT: Q 84 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: Q 95 LYS cc_start: 0.8743 (tptt) cc_final: 0.8533 (tttp) REVERT: Q 96 HIS cc_start: 0.8872 (t-90) cc_final: 0.8445 (t70) REVERT: Q 100 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8096 (mt-10) REVERT: Q 137 ASN cc_start: 0.8866 (m-40) cc_final: 0.8637 (m-40) REVERT: M 16 SER cc_start: 0.8342 (m) cc_final: 0.8037 (p) REVERT: M 60 PHE cc_start: 0.9518 (OUTLIER) cc_final: 0.8972 (t80) REVERT: M 170 TYR cc_start: 0.8234 (p90) cc_final: 0.7764 (p90) REVERT: O 248 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8569 (ttm) REVERT: S 78 GLU cc_start: 0.8858 (tt0) cc_final: 0.8340 (tm-30) outliers start: 45 outliers final: 8 residues processed: 371 average time/residue: 0.7721 time to fit residues: 331.1310 Evaluate side-chains 335 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 321 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 99 optimal weight: 0.9980 chunk 167 optimal weight: 0.0670 chunk 287 optimal weight: 0.0670 chunk 275 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 369 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 321 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS P 129 HIS F 137 ASN A 102 HIS B 354 ASN B 377 ASN L 317 GLN M 121 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.059410 restraints weight = 55751.190| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.67 r_work: 0.2654 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9340 moved from start: 0.2665 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= 0.100 Angle : 0.497 12.554 45365 Z= 0.242 Chirality : 0.039 0.155 4962 Planarity : 0.004 0.045 5700 Dihedral : 9.616 89.023 4817 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.29 % Allowed : 11.58 % Favored : 87.13 % 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: 2.30 (0.14), residues: 3955 helix: 2.20 (0.11), residues: 2152 sheet: 0.94 (0.27), residues: 369 loop : 0.78 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 201 TYR 0.014 0.001 TYR C 225 PHE 0.018 0.001 PHE L 334 TRP 0.014 0.001 TRP P 161 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (33367) covalent geometry : angle 0.49621 / 0.24 (45352) SS BOND : bond 0.00229 / 0.13 ( 5) SS BOND : angle 0.55948 / 0.27 ( 10) hydrogen bonds : bond 0.03884 / 2.58 ( 1886) hydrogen bonds : angle 4.10178 / 2.98 ( 5319) metal coordination : bond 0.00704 / 0.36 ( 4) metal coordination : angle 4.18167 / 2.39 ( 3) Misc. bond : bond 0.16715 / 8.24 ( 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 371 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 328 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 322 SER cc_start: 0.9504 (OUTLIER) cc_final: 0.9235 (m) REVERT: P 194 TYR cc_start: 0.8367 (m-80) cc_final: 0.7595 (m-80) REVERT: G 112 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: F 84 GLU cc_start: 0.8787 (tt0) cc_final: 0.8503 (tp30) REVERT: F 103 GLU cc_start: 0.8658 (tp30) cc_final: 0.8422 (mm-30) REVERT: F 109 GLN cc_start: 0.9003 (mt0) cc_final: 0.8738 (mt0) REVERT: F 126 GLU cc_start: 0.9073 (mp0) cc_final: 0.8827 (mp0) REVERT: A 153 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8153 (ttt-90) REVERT: A 240 GLN cc_start: 0.8362 (mp10) cc_final: 0.8036 (pm20) REVERT: A 397 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8019 (mt) REVERT: B 31 GLN cc_start: 0.8833 (mt0) cc_final: 0.8472 (mm110) REVERT: B 205 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8154 (tm-30) REVERT: H 57 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8702 (tt) REVERT: J 15 LYS cc_start: 0.8867 (ptmm) cc_final: 0.8620 (ptmt) REVERT: E 55 ASP cc_start: 0.8255 (p0) cc_final: 0.7932 (p0) REVERT: Q 84 GLU cc_start: 0.8720 (tp30) cc_final: 0.8363 (mt-10) REVERT: Q 95 LYS cc_start: 0.8699 (tptt) cc_final: 0.8498 (tttp) REVERT: Q 96 HIS cc_start: 0.8840 (t-90) cc_final: 0.8368 (t-170) REVERT: Q 100 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8078 (mt-10) REVERT: Q 137 ASN cc_start: 0.8841 (m-40) cc_final: 0.8600 (m-40) REVERT: L 48 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8589 (tp) REVERT: M 16 SER cc_start: 0.8418 (m) cc_final: 0.8177 (p) REVERT: M 60 PHE cc_start: 0.9494 (OUTLIER) cc_final: 0.8969 (t80) REVERT: M 170 TYR cc_start: 0.8264 (p90) cc_final: 0.7785 (p90) REVERT: M 236 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7902 (mtp85) REVERT: S 76 LYS cc_start: 0.9075 (tptp) cc_final: 0.8818 (tptt) REVERT: S 78 GLU cc_start: 0.8924 (tt0) cc_final: 0.8391 (tm-30) REVERT: U 10 LYS cc_start: 0.9236 (tppt) cc_final: 0.9000 (tppt) outliers start: 43 outliers final: 8 residues processed: 353 average time/residue: 0.7548 time to fit residues: 309.7144 Evaluate side-chains 330 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 315 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 297 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 352 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 289 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN B 354 ASN B 377 ASN N 11 ASN M 121 GLN M 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.074526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.054721 restraints weight = 56126.560| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 1.67 r_work: 0.2546 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9408 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.391 33385 Z= 0.259 Angle : 0.622 14.649 45365 Z= 0.305 Chirality : 0.045 0.157 4962 Planarity : 0.004 0.048 5700 Dihedral : 10.174 89.836 4817 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.35 % Allowed : 11.52 % Favored : 87.13 % 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: 2.04 (0.13), residues: 3955 helix: 1.98 (0.11), residues: 2142 sheet: 0.86 (0.26), residues: 363 loop : 0.67 (0.18), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 201 TYR 0.026 0.002 TYR C 225 PHE 0.027 0.002 PHE C 240 TRP 0.016 0.002 TRP N 142 HIS 0.015 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.26 (33367) covalent geometry : angle 0.61974 / 0.30 (45352) SS BOND : bond 0.00293 / 0.18 ( 5) SS BOND : angle 0.68785 / 0.36 ( 10) hydrogen bonds : bond 0.05412 / 3.64 ( 1886) hydrogen bonds : angle 4.35930 / 3.16 ( 5319) metal coordination : bond 0.01704 / 0.86 ( 4) metal coordination : angle 6.51422 / 3.80 ( 3) Misc. bond : bond 0.21888 / 11.80 ( 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 359 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 314 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 322 SER cc_start: 0.9541 (OUTLIER) cc_final: 0.9271 (m) REVERT: P 150 GLN cc_start: 0.6724 (mt0) cc_final: 0.6465 (mt0) REVERT: P 194 TYR cc_start: 0.8316 (m-80) cc_final: 0.7577 (m-80) REVERT: F 84 GLU cc_start: 0.8804 (tt0) cc_final: 0.8487 (tp30) REVERT: F 88 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8172 (mm-30) REVERT: F 103 GLU cc_start: 0.8693 (tp30) cc_final: 0.8454 (mm-30) REVERT: F 109 GLN cc_start: 0.8973 (mt0) cc_final: 0.8771 (mt0) REVERT: F 126 GLU cc_start: 0.9052 (mp0) cc_final: 0.8784 (mp0) REVERT: A 153 ARG cc_start: 0.8658 (ttp-110) cc_final: 0.8168 (ttt-90) REVERT: A 240 GLN cc_start: 0.8322 (mp10) cc_final: 0.8004 (pm20) REVERT: A 397 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8043 (mt) REVERT: B 205 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8214 (tm-30) REVERT: B 251 GLU cc_start: 0.8010 (pm20) cc_final: 0.7747 (pm20) REVERT: H 57 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8670 (tt) REVERT: J 15 LYS cc_start: 0.8957 (ptmm) cc_final: 0.8731 (ptpp) REVERT: J 69 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6421 (pm20) REVERT: E 55 ASP cc_start: 0.8515 (p0) cc_final: 0.8223 (p0) REVERT: Q 84 GLU cc_start: 0.8751 (tp30) cc_final: 0.8511 (tt0) REVERT: Q 95 LYS cc_start: 0.8781 (tptt) cc_final: 0.8535 (tttp) REVERT: Q 96 HIS cc_start: 0.8848 (t-90) cc_final: 0.8353 (t-170) REVERT: Q 100 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8103 (mt-10) REVERT: M 16 SER cc_start: 0.8412 (m) cc_final: 0.8151 (p) REVERT: M 170 TYR cc_start: 0.8259 (p90) cc_final: 0.7797 (p90) REVERT: M 236 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7971 (mtp85) REVERT: O 248 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.8516 (ttm) REVERT: S 78 GLU cc_start: 0.8912 (tt0) cc_final: 0.8368 (tm-30) outliers start: 45 outliers final: 17 residues processed: 341 average time/residue: 0.7726 time to fit residues: 305.6950 Evaluate side-chains 332 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 309 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 248 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 132 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 304 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN ** Q 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.057699 restraints weight = 55810.135| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 1.68 r_work: 0.2615 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9366 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.370 33385 Z= 0.111 Angle : 0.519 13.353 45365 Z= 0.252 Chirality : 0.040 0.168 4962 Planarity : 0.004 0.048 5700 Dihedral : 9.592 89.877 4817 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.84 % Allowed : 12.15 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.14), residues: 3955 helix: 2.18 (0.11), residues: 2142 sheet: 0.91 (0.27), residues: 369 loop : 0.77 (0.18), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 153 TYR 0.014 0.001 TYR N 225 PHE 0.021 0.001 PHE L 334 TRP 0.016 0.001 TRP P 161 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (33367) covalent geometry : angle 0.51754 / 0.25 (45352) SS BOND : bond 0.00215 / 0.13 ( 5) SS BOND : angle 0.51822 / 0.26 ( 10) hydrogen bonds : bond 0.04169 / 2.78 ( 1886) hydrogen bonds : angle 4.16926 / 3.03 ( 5319) metal coordination : bond 0.00344 / 0.17 ( 4) metal coordination : angle 4.57434 / 2.67 ( 3) Misc. bond : bond 0.19509 / 10.35 ( 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 353 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 325 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.9057 (m-30) cc_final: 0.8772 (m-30) REVERT: C 322 SER cc_start: 0.9519 (OUTLIER) cc_final: 0.9252 (m) REVERT: P 194 TYR cc_start: 0.8277 (m-80) cc_final: 0.7563 (m-80) REVERT: F 84 GLU cc_start: 0.8801 (tt0) cc_final: 0.8489 (tp30) REVERT: F 88 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8100 (mm-30) REVERT: F 103 GLU cc_start: 0.8666 (tp30) cc_final: 0.8444 (mm-30) REVERT: F 109 GLN cc_start: 0.8965 (mt0) cc_final: 0.8764 (mt0) REVERT: F 126 GLU cc_start: 0.9021 (mp0) cc_final: 0.8780 (mp0) REVERT: A 153 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.8209 (ttt-90) REVERT: A 240 GLN cc_start: 0.8309 (mp10) cc_final: 0.8002 (pm20) REVERT: A 397 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7980 (mt) REVERT: B 31 GLN cc_start: 0.8853 (mt0) cc_final: 0.8467 (mm110) REVERT: B 205 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8108 (tm-30) REVERT: B 251 GLU cc_start: 0.8155 (pm20) cc_final: 0.7946 (pm20) REVERT: H 57 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8718 (tt) REVERT: H 78 GLU cc_start: 0.9006 (tt0) cc_final: 0.8793 (tt0) REVERT: J 15 LYS cc_start: 0.8951 (ptmm) cc_final: 0.8741 (ptpp) REVERT: E 55 ASP cc_start: 0.8392 (p0) cc_final: 0.8086 (p0) REVERT: Q 84 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: Q 95 LYS cc_start: 0.8749 (tptt) cc_final: 0.8516 (tttp) REVERT: Q 96 HIS cc_start: 0.8829 (t-90) cc_final: 0.8345 (t-170) REVERT: Q 100 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8011 (mt-10) REVERT: L 48 LEU cc_start: 0.8895 (tp) cc_final: 0.8572 (tp) REVERT: M 16 SER cc_start: 0.8459 (m) cc_final: 0.8217 (p) REVERT: M 170 TYR cc_start: 0.8301 (p90) cc_final: 0.7829 (p90) REVERT: M 236 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7941 (mtp85) REVERT: O 248 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8617 (ttm) REVERT: S 78 GLU cc_start: 0.8896 (tt0) cc_final: 0.8378 (tm-30) outliers start: 28 outliers final: 11 residues processed: 343 average time/residue: 0.7875 time to fit residues: 313.4862 Evaluate side-chains 333 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 316 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain O residue 248 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 344 optimal weight: 0.0170 chunk 130 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 389 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 307 optimal weight: 5.9990 chunk 341 optimal weight: 8.9990 chunk 286 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 316 GLN B 354 ASN B 377 ASN ** Q 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.074440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.054693 restraints weight = 56190.908| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 1.67 r_work: 0.2547 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9408 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.385 33385 Z= 0.256 Angle : 0.618 14.625 45365 Z= 0.302 Chirality : 0.045 0.168 4962 Planarity : 0.004 0.049 5700 Dihedral : 10.003 89.908 4817 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.26 % Allowed : 11.88 % Favored : 86.86 % 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: 2.06 (0.13), residues: 3955 helix: 1.99 (0.11), residues: 2144 sheet: 0.89 (0.26), residues: 363 loop : 0.68 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 153 TYR 0.024 0.002 TYR C 225 PHE 0.026 0.002 PHE L 334 TRP 0.017 0.002 TRP P 161 HIS 0.016 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.25 (33367) covalent geometry : angle 0.61645 / 0.30 (45352) SS BOND : bond 0.00296 / 0.18 ( 5) SS BOND : angle 0.71964 / 0.38 ( 10) hydrogen bonds : bond 0.05331 / 3.58 ( 1886) hydrogen bonds : angle 4.34412 / 3.15 ( 5319) metal coordination : bond 0.01564 / 0.80 ( 4) metal coordination : angle 5.93780 / 3.47 ( 3) Misc. bond : bond 0.21878 / 12.01 ( 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 354 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 312 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 322 SER cc_start: 0.9543 (OUTLIER) cc_final: 0.9273 (m) REVERT: P 194 TYR cc_start: 0.8304 (m-80) cc_final: 0.7542 (m-80) REVERT: F 84 GLU cc_start: 0.8803 (tt0) cc_final: 0.8490 (tp30) REVERT: F 88 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8157 (mm-30) REVERT: F 103 GLU cc_start: 0.8701 (tp30) cc_final: 0.8462 (tm-30) REVERT: F 109 GLN cc_start: 0.8952 (mt0) cc_final: 0.8749 (mt0) REVERT: F 126 GLU cc_start: 0.9044 (mp0) cc_final: 0.8786 (mp0) REVERT: A 153 ARG cc_start: 0.8676 (ttp-110) cc_final: 0.8143 (ttt-90) REVERT: A 240 GLN cc_start: 0.8309 (mp10) cc_final: 0.7995 (pm20) REVERT: A 397 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7990 (mt) REVERT: B 205 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8153 (tm-30) REVERT: B 251 GLU cc_start: 0.8194 (pm20) cc_final: 0.7989 (pm20) REVERT: D 258 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8493 (tp30) REVERT: H 57 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8678 (tt) REVERT: Q 84 GLU cc_start: 0.8749 (tp30) cc_final: 0.8504 (tt0) REVERT: Q 95 LYS cc_start: 0.8805 (tptt) cc_final: 0.8545 (tttp) REVERT: Q 96 HIS cc_start: 0.8857 (t-90) cc_final: 0.8428 (t-170) REVERT: Q 100 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8115 (mt-10) REVERT: L 48 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8547 (tp) REVERT: M 16 SER cc_start: 0.8482 (m) cc_final: 0.8228 (p) REVERT: M 170 TYR cc_start: 0.8263 (p90) cc_final: 0.7788 (p90) REVERT: M 236 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7962 (mtp85) REVERT: O 248 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8510 (ttm) REVERT: S 78 GLU cc_start: 0.8910 (tt0) cc_final: 0.8375 (tm-30) outliers start: 42 outliers final: 20 residues processed: 338 average time/residue: 0.7864 time to fit residues: 307.9963 Evaluate side-chains 334 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 307 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain O residue 248 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 266 optimal weight: 7.9990 chunk 274 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 255 optimal weight: 8.9990 chunk 362 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 chunk 205 optimal weight: 0.6980 chunk 250 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN ** Q 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.055680 restraints weight = 55770.997| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 1.66 r_work: 0.2568 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9396 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.385 33385 Z= 0.181 Angle : 0.573 14.542 45365 Z= 0.280 Chirality : 0.042 0.183 4962 Planarity : 0.004 0.049 5700 Dihedral : 9.836 89.857 4817 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.02 % Allowed : 12.09 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.14), residues: 3955 helix: 2.04 (0.11), residues: 2144 sheet: 0.88 (0.26), residues: 363 loop : 0.72 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 153 TYR 0.021 0.002 TYR N 225 PHE 0.024 0.002 PHE L 334 TRP 0.019 0.001 TRP P 161 HIS 0.013 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (33367) covalent geometry : angle 0.57160 / 0.28 (45352) SS BOND : bond 0.00248 / 0.15 ( 5) SS BOND : angle 0.59971 / 0.31 ( 10) hydrogen bonds : bond 0.04861 / 3.26 ( 1886) hydrogen bonds : angle 4.28897 / 3.11 ( 5319) metal coordination : bond 0.00911 / 0.46 ( 4) metal coordination : angle 5.11619 / 2.99 ( 3) Misc. bond : bond 0.21542 / 11.74 ( 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 348 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 314 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 322 SER cc_start: 0.9534 (OUTLIER) cc_final: 0.9255 (m) REVERT: P 194 TYR cc_start: 0.8294 (m-80) cc_final: 0.7577 (m-80) REVERT: F 84 GLU cc_start: 0.8802 (tt0) cc_final: 0.8495 (tp30) REVERT: F 88 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8129 (mm-30) REVERT: F 103 GLU cc_start: 0.8691 (tp30) cc_final: 0.8449 (tm-30) REVERT: F 109 GLN cc_start: 0.8925 (mt0) cc_final: 0.8708 (mt0) REVERT: F 126 GLU cc_start: 0.9038 (mp0) cc_final: 0.8780 (mp0) REVERT: A 153 ARG cc_start: 0.8674 (ttp-110) cc_final: 0.8137 (ttt-90) REVERT: A 240 GLN cc_start: 0.8322 (mp10) cc_final: 0.8004 (pm20) REVERT: A 397 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7987 (mt) REVERT: B 205 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8182 (tm-30) REVERT: D 258 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8481 (tp30) REVERT: H 57 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8688 (tt) REVERT: J 69 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6409 (pm20) REVERT: E 55 ASP cc_start: 0.8524 (p0) cc_final: 0.8317 (p0) REVERT: Q 84 GLU cc_start: 0.8759 (tp30) cc_final: 0.8498 (tt0) REVERT: Q 95 LYS cc_start: 0.8763 (tptt) cc_final: 0.8497 (tttp) REVERT: Q 96 HIS cc_start: 0.8851 (t-90) cc_final: 0.8431 (t-170) REVERT: L 48 LEU cc_start: 0.8910 (tp) cc_final: 0.8570 (tp) REVERT: M 16 SER cc_start: 0.8468 (m) cc_final: 0.8223 (p) REVERT: M 170 TYR cc_start: 0.8264 (p90) cc_final: 0.7786 (p90) REVERT: M 236 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7949 (mtp85) REVERT: O 248 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8504 (ttm) REVERT: S 78 GLU cc_start: 0.8912 (tt0) cc_final: 0.8376 (tm-30) outliers start: 34 outliers final: 20 residues processed: 338 average time/residue: 0.7925 time to fit residues: 310.0457 Evaluate side-chains 337 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 310 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 364 MET Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 13 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 265 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 354 ASN B 377 ASN ** Q 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.055641 restraints weight = 56117.422| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 1.67 r_work: 0.2568 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9397 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.383 33385 Z= 0.184 Angle : 0.579 14.516 45365 Z= 0.282 Chirality : 0.042 0.181 4962 Planarity : 0.004 0.049 5700 Dihedral : 9.779 89.713 4817 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.90 % Allowed : 12.30 % 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: 2.14 (0.13), residues: 3955 helix: 2.06 (0.11), residues: 2140 sheet: 0.88 (0.26), residues: 363 loop : 0.73 (0.18), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 128 TYR 0.020 0.002 TYR N 225 PHE 0.024 0.002 PHE L 334 TRP 0.020 0.001 TRP P 161 HIS 0.012 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (33367) covalent geometry : angle 0.57729 / 0.28 (45352) SS BOND : bond 0.00250 / 0.15 ( 5) SS BOND : angle 0.63410 / 0.33 ( 10) hydrogen bonds : bond 0.04874 / 3.27 ( 1886) hydrogen bonds : angle 4.28312 / 3.11 ( 5319) metal coordination : bond 0.00935 / 0.48 ( 4) metal coordination : angle 5.01936 / 2.94 ( 3) Misc. bond : bond 0.21477 / 11.70 ( 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 344 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 314 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 322 SER cc_start: 0.9532 (OUTLIER) cc_final: 0.9256 (m) REVERT: P 194 TYR cc_start: 0.8266 (m-80) cc_final: 0.7616 (m-80) REVERT: F 84 GLU cc_start: 0.8780 (tt0) cc_final: 0.8476 (tp30) REVERT: F 88 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8136 (mm-30) REVERT: F 103 GLU cc_start: 0.8692 (tp30) cc_final: 0.8451 (tm-30) REVERT: F 109 GLN cc_start: 0.8922 (mt0) cc_final: 0.8699 (mt0) REVERT: F 126 GLU cc_start: 0.9038 (mp0) cc_final: 0.8781 (mp0) REVERT: A 153 ARG cc_start: 0.8687 (ttp-110) cc_final: 0.8137 (ttt-90) REVERT: A 240 GLN cc_start: 0.8329 (mp10) cc_final: 0.8014 (pm20) REVERT: A 397 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7974 (mt) REVERT: B 205 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8184 (tm-30) REVERT: D 258 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8488 (tp30) REVERT: H 57 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8692 (tt) REVERT: J 69 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6376 (pm20) REVERT: Q 84 GLU cc_start: 0.8761 (tp30) cc_final: 0.8504 (tt0) REVERT: Q 95 LYS cc_start: 0.8794 (tptt) cc_final: 0.8525 (tttp) REVERT: Q 96 HIS cc_start: 0.8848 (t-90) cc_final: 0.8554 (t-90) REVERT: L 48 LEU cc_start: 0.8909 (tp) cc_final: 0.8564 (tp) REVERT: M 16 SER cc_start: 0.8476 (m) cc_final: 0.8231 (p) REVERT: M 170 TYR cc_start: 0.8259 (p90) cc_final: 0.7787 (p90) REVERT: M 236 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7952 (mtp85) REVERT: O 248 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8511 (ttm) REVERT: S 78 GLU cc_start: 0.8905 (tt0) cc_final: 0.8381 (tm-30) outliers start: 30 outliers final: 21 residues processed: 336 average time/residue: 0.8072 time to fit residues: 314.1533 Evaluate side-chains 337 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 309 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 364 MET Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 179 optimal weight: 3.9990 chunk 354 optimal weight: 0.9990 chunk 387 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 370 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 209 optimal weight: 0.5980 chunk 377 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 234 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 316 GLN B 377 ASN ** Q 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.077609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.058131 restraints weight = 55825.738| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 1.67 r_work: 0.2626 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9358 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.364 33385 Z= 0.107 Angle : 0.514 12.594 45365 Z= 0.251 Chirality : 0.040 0.187 4962 Planarity : 0.004 0.046 5700 Dihedral : 9.267 89.440 4817 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.78 % Allowed : 12.54 % Favored : 86.68 % 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: 2.36 (0.14), residues: 3955 helix: 2.24 (0.11), residues: 2142 sheet: 1.00 (0.27), residues: 363 loop : 0.82 (0.18), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 153 TYR 0.013 0.001 TYR N 225 PHE 0.019 0.001 PHE L 334 TRP 0.020 0.001 TRP P 161 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (33367) covalent geometry : angle 0.51326 / 0.25 (45352) SS BOND : bond 0.00200 / 0.12 ( 5) SS BOND : angle 0.48146 / 0.25 ( 10) hydrogen bonds : bond 0.04015 / 2.67 ( 1886) hydrogen bonds : angle 4.12710 / 3.00 ( 5319) metal coordination : bond 0.00190 / 0.09 ( 4) metal coordination : angle 3.53470 / 2.08 ( 3) Misc. bond : bond 0.18309 / 9.41 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13022.78 seconds wall clock time: 222 minutes 11.18 seconds (13331.18 seconds total)