Starting phenix.real_space_refine on Mon Jul 6 07:38:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ac3_15332/07_2026/8ac3_15332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ac3_15332/07_2026/8ac3_15332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ac3_15332/07_2026/8ac3_15332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ac3_15332/07_2026/8ac3_15332.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ac3_15332/07_2026/8ac3_15332.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ac3_15332/07_2026/8ac3_15332.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ac3_15332/07_2026/8ac3_15332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ac3_15332/07_2026/8ac3_15332.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21031 2.51 5 N 5296 2.21 5 O 6073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 34 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'FES': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 298 Unusual residues: {'CDL': 2, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "U" 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 29.060 47.877 30.268 1.00226.78 S ATOM 4207 SG CYS P 187 31.405 45.203 28.735 1.00207.17 S Time building chain proxies: 5.87, per 1000 atoms: 0.18 Number of scatterers: 32540 At special positions: 0 Unit cell: (119.691, 129.735, 164.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 102 16.00 P 30 15.00 O 6073 8.00 N 5296 7.00 C 21031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.04 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=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 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 61.7% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 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: 3.755A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 removed outlier: 3.506A pdb=" N ILE C 119 " --> pdb=" O SER C 115 " (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: 6.829A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.787A 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: 3.763A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.793A 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: 4.112A 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: 3.636A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 92 No H-bonds generated for 'chain 'P' and resid 90 through 92' Processing helix chain 'P' and resid 94 through 101 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: 3.514A 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: 4.199A 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: 3.600A 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: 3.532A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 122 through 136 Processing helix chain 'A' and resid 140 through 155 removed outlier: 3.996A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 5.041A pdb=" N ASN A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.534A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.977A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.662A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.558A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.382A 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: 3.672A 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: 3.595A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.865A 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: 3.596A pdb=" N THR B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.514A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.806A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.837A pdb=" N VAL B 283 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 333 through 354 Processing helix chain 'B' and resid 354 through 368 removed outlier: 3.722A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.595A pdb=" N VAL B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 266 through 283 Processing helix chain 'D' and resid 285 through 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 81 removed outlier: 4.327A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.749A 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: 3.533A 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: 3.511A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.581A 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: 3.834A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.654A 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: 3.756A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.505A pdb=" N ILE N 119 " --> pdb=" O SER N 115 " (cutoff:3.500A) removed outlier: 3.500A 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: 6.825A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 258 Processing helix chain 'N' and resid 272 through 274 No H-bonds generated for 'chain 'N' and resid 272 through 274' Processing helix chain 'N' and resid 275 through 285 removed outlier: 3.763A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.797A 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: 4.108A 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: 3.651A 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: 3.515A 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 84 Processing helix chain 'R' and resid 88 through 92 Processing helix chain 'R' and resid 94 through 98 Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 4.169A 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: 3.604A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 71 through 80 Processing helix chain 'L' and resid 88 through 100 Processing helix chain 'L' and resid 122 through 136 Processing helix chain 'L' and resid 140 through 155 removed outlier: 3.998A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 removed outlier: 5.056A pdb=" N ASN L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 156 through 160' Processing helix chain 'L' and resid 161 through 175 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 removed outlier: 3.533A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 3.990A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 329 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.665A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.649A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.386A 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: 3.668A 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: 3.585A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.868A 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: 3.596A pdb=" N THR M 147 " --> pdb=" O ASP M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 163 Processing helix chain 'M' and resid 174 through 186 Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'M' and resid 199 through 211 removed outlier: 3.515A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.817A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.836A 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: 3.858A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.592A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 Processing helix chain 'M' and resid 406 through 410 Processing helix chain 'M' and resid 412 through 416 Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 109 through 123 Processing helix chain 'O' and resid 124 through 127 Processing helix chain 'O' and resid 134 through 139 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: 4.332A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.529A 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: 3.561A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.839A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.657A 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: 3.893A 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: 3.613A 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: 6.523A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.303A 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: 4.022A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE H 24 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.559A pdb=" N LYS B 24 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLY B 195 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 26 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.634A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.200A 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: 6.500A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.318A 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: 4.021A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 16 through 20 removed outlier: 6.553A pdb=" N LYS M 24 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLY M 195 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA M 26 " --> pdb=" O GLY M 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.634A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 156 through 158 Processing sheet with id=AC2, first strand: chain 'O' and resid 236 through 237 Processing sheet with id=AC3, first strand: chain 'U' and resid 19 through 20 1885 hydrogen bonds defined for protein. 5292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.30 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 13594 1.41 - 1.61: 19567 1.61 - 1.82: 169 1.82 - 2.03: 19 2.03 - 2.24: 18 Bond restraints: 33367 Sorted by residual: bond pdb=" C18 XP4 U 102 " pdb=" O7 XP4 U 102 " ideal model delta sigma weight residual 1.328 1.472 -0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.589 -0.131 1.90e-02 2.77e+03 4.73e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.587 -0.129 1.90e-02 2.77e+03 4.60e+01 bond pdb=" C18 XP4 A3003 " pdb=" O7 XP4 A3003 " ideal model delta sigma weight residual 1.328 1.462 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C2A HEC O 401 " pdb=" C3A HEC O 401 " ideal model delta sigma weight residual 1.334 1.452 -0.118 2.00e-02 2.50e+03 3.48e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 43039 3.44 - 6.89: 2020 6.89 - 10.33: 244 10.33 - 13.77: 42 13.77 - 17.22: 7 Bond angle restraints: 45352 Sorted by residual: angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.21 11.12 1.14e+00 7.69e-01 9.52e+01 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 97.64 13.63 1.47e+00 4.63e-01 8.59e+01 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.32 11.01 1.20e+00 6.94e-01 8.41e+01 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 99.55 11.72 1.47e+00 4.63e-01 6.35e+01 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 94.78 17.22 2.20e+00 2.07e-01 6.12e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.63: 18550 32.63 - 65.25: 882 65.25 - 97.88: 81 97.88 - 130.50: 1 130.50 - 163.13: 1 Dihedral angle restraints: 19515 sinusoidal: 7896 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -105.76 -16.84 0 2.50e+00 1.60e-01 4.54e+01 dihedral pdb=" C ARG H 51 " pdb=" N ARG H 51 " pdb=" CA ARG H 51 " pdb=" CB ARG H 51 " ideal model delta harmonic sigma weight residual -122.60 -138.29 15.69 0 2.50e+00 1.60e-01 3.94e+01 dihedral pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " pdb=" CAB HEC O 401 " pdb=" CBB HEC O 401 " ideal model delta sinusoidal sigma weight residual 60.00 -3.07 63.07 2 1.00e+01 1.00e-02 3.82e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 4509 0.190 - 0.379: 424 0.379 - 0.569: 23 0.569 - 0.758: 2 0.758 - 0.948: 4 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.63 -0.95 2.00e-01 2.50e+01 2.24e+01 chirality pdb=" CB4 CDL S 101 " pdb=" CB3 CDL S 101 " pdb=" CB6 CDL S 101 " pdb=" OB6 CDL S 101 " both_signs ideal model delta sigma weight residual False -2.57 -1.64 -0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" CB4 CDL N 506 " pdb=" CB3 CDL N 506 " pdb=" CB6 CDL N 506 " pdb=" OB6 CDL N 506 " both_signs ideal model delta sigma weight residual False -2.57 -1.73 -0.85 2.00e-01 2.50e+01 1.80e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS N 96 " -0.044 2.00e-02 2.50e+03 3.59e-02 1.93e+01 pdb=" CG HIS N 96 " 0.063 2.00e-02 2.50e+03 pdb=" ND1 HIS N 96 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS N 96 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS N 96 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS N 96 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM C 502 " -0.023 2.00e-02 2.50e+03 2.74e-02 1.69e+01 pdb=" C2A HEM C 502 " 0.027 2.00e-02 2.50e+03 pdb=" C3A HEM C 502 " 0.010 2.00e-02 2.50e+03 pdb=" C4A HEM C 502 " -0.031 2.00e-02 2.50e+03 pdb=" CAA HEM C 502 " -0.015 2.00e-02 2.50e+03 pdb=" CHA HEM C 502 " 0.036 2.00e-02 2.50e+03 pdb=" CHB HEM C 502 " 0.039 2.00e-02 2.50e+03 pdb=" CMA HEM C 502 " -0.006 2.00e-02 2.50e+03 pdb=" NA HEM C 502 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEC D 401 " -0.014 2.00e-02 2.50e+03 2.73e-02 1.68e+01 pdb=" C2A HEC D 401 " -0.034 2.00e-02 2.50e+03 pdb=" C3A HEC D 401 " -0.013 2.00e-02 2.50e+03 pdb=" C4A HEC D 401 " -0.036 2.00e-02 2.50e+03 pdb=" CAA HEC D 401 " 0.041 2.00e-02 2.50e+03 pdb=" CHA HEC D 401 " 0.012 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " 0.045 2.00e-02 2.50e+03 pdb=" CMA HEC D 401 " -0.003 2.00e-02 2.50e+03 pdb=" NA HEC D 401 " 0.003 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 221 2.62 - 3.19: 28411 3.19 - 3.76: 53306 3.76 - 4.33: 78541 4.33 - 4.90: 121727 Nonbonded interactions: 282206 Sorted by model distance: nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.054 3.080 nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.064 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.113 3.120 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.114 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEM C 502 " model vdw 2.219 3.080 ... (remaining 282201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 26 through 3002) selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and resid 1 through 503) selection = (chain 'N' and resid 1 through 503) } ncs_group { reference = (chain 'D' and resid 85 through 401) selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and (resid 9 through 93 or (resid 701 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) selection = (chain 'S' and (resid 9 through 93 or (resid 101 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = (chain 'U' and resid 8 through 101) } 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: 3.560 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: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 31.120 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9444 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.200 33382 Z= 0.641 Angle : 1.743 17.216 45365 Z= 1.085 Chirality : 0.117 0.948 4962 Planarity : 0.007 0.039 5700 Dihedral : 17.684 163.126 12014 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.40 % Rotamer: Outliers : 3.85 % Allowed : 7.43 % Favored : 88.72 % Cbeta Deviations : 1.18 % 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: -1.48 (0.12), residues: 3955 helix: -1.14 (0.09), residues: 2109 sheet: 0.03 (0.25), residues: 356 loop : -0.71 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG B 128 TYR 0.050 0.007 TYR G 101 PHE 0.047 0.006 PHE B 107 TRP 0.038 0.007 TRP A 474 HIS 0.024 0.004 HIS Q 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01060 / 0.64 (33367) covalent geometry : angle 1.73988 / 1.08 (45352) SS BOND : bond 0.02362 / 1.39 ( 5) SS BOND : angle 2.62893 / 1.33 ( 10) hydrogen bonds : bond 0.18786 / 12.49 ( 1885) hydrogen bonds : angle 6.98731 / 4.98 ( 5292) metal coordination : bond 0.09147 / 4.53 ( 4) metal coordination : angle 13.17569 / 7.25 ( 3) Misc. bond : bond 0.13875 / 7.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 373 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8885 (tptp) REVERT: C 369 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8920 (mtp) REVERT: C 374 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8957 (mt-10) REVERT: P 116 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.8034 (m) REVERT: P 134 GLU cc_start: 0.9284 (mm-30) cc_final: 0.9058 (mm-30) REVERT: P 222 LEU cc_start: 0.9563 (pp) cc_final: 0.9247 (pt) REVERT: G 76 ARG cc_start: 0.9490 (OUTLIER) cc_final: 0.8733 (ttm170) REVERT: G 116 LYS cc_start: 0.8810 (tttm) cc_final: 0.8597 (ttmm) REVERT: G 120 ASP cc_start: 0.9382 (m-30) cc_final: 0.9165 (m-30) REVERT: G 123 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8705 (tm-30) REVERT: F 88 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8682 (mm-30) REVERT: F 109 GLN cc_start: 0.9203 (mt0) cc_final: 0.8995 (mt0) REVERT: F 125 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8861 (tt0) REVERT: A 87 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7408 (mtp85) REVERT: A 97 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.9101 (tp30) REVERT: A 397 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6816 (mt) REVERT: A 402 TYR cc_start: 0.9151 (m-80) cc_final: 0.8830 (m-80) REVERT: B 170 TYR cc_start: 0.8551 (p90) cc_final: 0.8230 (p90) REVERT: B 345 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9242 (mtpp) REVERT: D 160 GLU cc_start: 0.9420 (mm-30) cc_final: 0.9214 (pt0) REVERT: D 166 ASN cc_start: 0.8959 (m110) cc_final: 0.8439 (m-40) REVERT: D 224 GLU cc_start: 0.9310 (tt0) cc_final: 0.8986 (pp20) REVERT: D 248 MET cc_start: 0.9369 (ttp) cc_final: 0.8881 (ttp) REVERT: H 75 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8827 (tm-30) REVERT: H 88 GLU cc_start: 0.9133 (mp0) cc_final: 0.8851 (mp0) REVERT: I 7 PHE cc_start: 0.9035 (t80) cc_final: 0.8827 (m-80) REVERT: J 10 LYS cc_start: 0.9502 (tttm) cc_final: 0.9248 (tptp) REVERT: J 55 ARG cc_start: 0.9154 (ttm-80) cc_final: 0.8932 (tpp80) REVERT: N 250 LYS cc_start: 0.9240 (ttmt) cc_final: 0.9024 (ttmm) REVERT: E 55 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8548 (p0) REVERT: Q 88 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8463 (mm-30) REVERT: Q 122 ASP cc_start: 0.8486 (p0) cc_final: 0.8276 (p0) REVERT: L 397 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7303 (mp) REVERT: M 19 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8760 (tm-30) REVERT: S 75 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8766 (tm-30) REVERT: S 78 GLU cc_start: 0.9357 (tt0) cc_final: 0.9028 (pp20) REVERT: U 10 LYS cc_start: 0.9399 (tttm) cc_final: 0.8999 (mppt) outliers start: 128 outliers final: 13 residues processed: 465 average time/residue: 0.8033 time to fit residues: 431.1491 Evaluate side-chains 302 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 278 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 0.0070 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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 F 97 HIS F 132 HIS A 64 ASN A 135 GLN A 222 HIS A 332 ASN A 371 ASN B 87 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 215 GLN B 316 GLN N 14 ASN N 202 HIS N 332 ASN E 90 ASN Q 132 HIS L 50 GLN L 135 GLN L 177 ASN L 332 ASN L 371 ASN M 87 HIS ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 196 ASN M 215 GLN M 241 ASN M 316 GLN M 377 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.064866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.048213 restraints weight = 81909.402| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.23 r_work: 0.2576 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9264 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.448 33382 Z= 0.135 Angle : 0.626 15.552 45365 Z= 0.310 Chirality : 0.042 0.206 4962 Planarity : 0.004 0.044 5700 Dihedral : 12.006 139.045 4876 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.62 % Allowed : 11.04 % Favored : 87.34 % 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: 0.83 (0.13), residues: 3955 helix: 0.99 (0.11), residues: 2169 sheet: 0.54 (0.27), residues: 365 loop : 0.03 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 201 TYR 0.019 0.002 TYR O 237 PHE 0.021 0.001 PHE A 334 TRP 0.026 0.001 TRP C 156 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (33367) covalent geometry : angle 0.62380 / 0.31 (45352) SS BOND : bond 0.00307 / 0.19 ( 5) SS BOND : angle 0.72558 / 0.37 ( 10) hydrogen bonds : bond 0.04960 / 3.24 ( 1885) hydrogen bonds : angle 4.70619 / 3.36 ( 5292) metal coordination : bond 0.02267 / 1.15 ( 4) metal coordination : angle 6.54110 / 3.58 ( 3) Misc. bond : bond 0.29277 / 17.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 297 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8748 (tptp) REVERT: C 374 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8692 (mt-10) REVERT: P 222 LEU cc_start: 0.9280 (pp) cc_final: 0.9036 (tp) REVERT: G 116 LYS cc_start: 0.8552 (tttm) cc_final: 0.8324 (ttmm) REVERT: G 120 ASP cc_start: 0.8981 (m-30) cc_final: 0.8652 (m-30) REVERT: G 123 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: F 100 GLU cc_start: 0.8594 (pt0) cc_final: 0.8339 (mt-10) REVERT: F 125 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8436 (tt0) REVERT: F 138 THR cc_start: 0.9028 (m) cc_final: 0.8804 (m) REVERT: A 97 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.9020 (tp30) REVERT: A 397 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7029 (mt) REVERT: A 402 TYR cc_start: 0.8893 (m-80) cc_final: 0.8572 (m-80) REVERT: D 166 ASN cc_start: 0.8833 (m110) cc_final: 0.8241 (m-40) REVERT: H 51 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.6980 (ptm160) REVERT: H 88 GLU cc_start: 0.8579 (mp0) cc_final: 0.8365 (mp0) REVERT: J 13 SER cc_start: 0.9044 (t) cc_final: 0.8653 (p) REVERT: J 55 ARG cc_start: 0.8912 (ttm-80) cc_final: 0.8585 (tpp80) REVERT: N 250 LYS cc_start: 0.9147 (ttmt) cc_final: 0.8889 (ttmm) REVERT: E 55 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7849 (p0) REVERT: R 112 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8555 (tp30) REVERT: Q 122 ASP cc_start: 0.8261 (p0) cc_final: 0.7963 (p0) REVERT: M 60 PHE cc_start: 0.9595 (OUTLIER) cc_final: 0.9099 (t80) REVERT: M 292 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8911 (p) REVERT: S 78 GLU cc_start: 0.9072 (tt0) cc_final: 0.8741 (tm-30) REVERT: S 88 GLU cc_start: 0.8894 (mp0) cc_final: 0.8683 (mp0) REVERT: U 10 LYS cc_start: 0.9255 (tttm) cc_final: 0.8993 (mppt) outliers start: 54 outliers final: 10 residues processed: 335 average time/residue: 0.8092 time to fit residues: 314.7443 Evaluate side-chains 282 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 275 optimal weight: 0.9990 chunk 317 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 377 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 43 optimal weight: 0.0060 chunk 292 optimal weight: 4.9990 chunk 384 optimal weight: 10.0000 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS A 317 GLN B 121 GLN L 317 GLN M 92 HIS M 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.048508 restraints weight = 83037.362| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.24 r_work: 0.2597 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9273 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.383 33382 Z= 0.127 Angle : 0.552 13.732 45365 Z= 0.270 Chirality : 0.040 0.174 4962 Planarity : 0.004 0.051 5700 Dihedral : 10.693 112.209 4835 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.47 % Allowed : 12.15 % Favored : 86.38 % 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: 1.68 (0.14), residues: 3955 helix: 1.69 (0.11), residues: 2163 sheet: 0.85 (0.27), residues: 363 loop : 0.43 (0.18), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 144 TYR 0.018 0.001 TYR R 31 PHE 0.018 0.001 PHE L 334 TRP 0.012 0.001 TRP N 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (33367) covalent geometry : angle 0.55029 / 0.27 (45352) SS BOND : bond 0.00217 / 0.13 ( 5) SS BOND : angle 0.65579 / 0.32 ( 10) hydrogen bonds : bond 0.04207 / 2.74 ( 1885) hydrogen bonds : angle 4.34914 / 3.10 ( 5292) metal coordination : bond 0.01438 / 0.72 ( 4) metal coordination : angle 5.47468 / 3.16 ( 3) Misc. bond : bond 0.26028 / 15.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 290 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9051 (ttmt) cc_final: 0.8715 (tptp) REVERT: C 263 MET cc_start: 0.9318 (mmm) cc_final: 0.9102 (mmm) REVERT: C 374 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8686 (mt-10) REVERT: P 222 LEU cc_start: 0.9288 (pp) cc_final: 0.9041 (tp) REVERT: G 120 ASP cc_start: 0.9017 (m-30) cc_final: 0.8735 (m-30) REVERT: G 123 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: F 100 GLU cc_start: 0.8653 (pt0) cc_final: 0.8115 (mt-10) REVERT: F 125 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8388 (tt0) REVERT: A 97 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8999 (tp30) REVERT: A 402 TYR cc_start: 0.8880 (m-80) cc_final: 0.8497 (m-80) REVERT: H 57 LEU cc_start: 0.9088 (tp) cc_final: 0.8769 (tp) REVERT: H 88 GLU cc_start: 0.8570 (mp0) cc_final: 0.8352 (mp0) REVERT: J 11 LYS cc_start: 0.8679 (tmtt) cc_final: 0.8391 (tptp) REVERT: J 13 SER cc_start: 0.9097 (t) cc_final: 0.8727 (p) REVERT: J 55 ARG cc_start: 0.8986 (ttm-80) cc_final: 0.8615 (tpp80) REVERT: J 59 ASP cc_start: 0.9027 (m-30) cc_final: 0.8797 (m-30) REVERT: N 250 LYS cc_start: 0.9145 (ttmt) cc_final: 0.8891 (ttmm) REVERT: N 287 ASP cc_start: 0.8103 (t0) cc_final: 0.7749 (t0) REVERT: E 47 ASP cc_start: 0.8787 (t70) cc_final: 0.8555 (t0) REVERT: E 55 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7920 (p0) REVERT: R 16 LYS cc_start: 0.7911 (pptt) cc_final: 0.7692 (pptt) REVERT: Q 100 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8672 (mm-30) REVERT: Q 122 ASP cc_start: 0.8359 (p0) cc_final: 0.8060 (p0) REVERT: M 60 PHE cc_start: 0.9578 (OUTLIER) cc_final: 0.9045 (t80) REVERT: O 163 ASP cc_start: 0.9186 (m-30) cc_final: 0.8615 (p0) REVERT: S 78 GLU cc_start: 0.9091 (tt0) cc_final: 0.8742 (tm-30) REVERT: S 88 GLU cc_start: 0.8849 (mp0) cc_final: 0.8629 (mp0) REVERT: U 10 LYS cc_start: 0.9229 (tttm) cc_final: 0.9009 (mppt) outliers start: 49 outliers final: 9 residues processed: 324 average time/residue: 0.7587 time to fit residues: 287.6321 Evaluate side-chains 274 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 261 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 364 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 220 optimal weight: 0.9990 chunk 384 optimal weight: 0.8980 chunk 337 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS F 97 HIS A 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.047102 restraints weight = 83224.268| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.24 r_work: 0.2562 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9300 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.404 33382 Z= 0.175 Angle : 0.571 15.893 45365 Z= 0.274 Chirality : 0.042 0.150 4962 Planarity : 0.004 0.053 5700 Dihedral : 10.271 99.490 4829 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.41 % Allowed : 13.38 % Favored : 85.20 % 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: 1.88 (0.14), residues: 3955 helix: 1.86 (0.11), residues: 2167 sheet: 0.85 (0.27), residues: 369 loop : 0.54 (0.18), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 201 TYR 0.018 0.001 TYR C 225 PHE 0.019 0.001 PHE A 334 TRP 0.014 0.001 TRP N 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (33367) covalent geometry : angle 0.56809 / 0.27 (45352) SS BOND : bond 0.00251 / 0.13 ( 5) SS BOND : angle 0.73006 / 0.36 ( 10) hydrogen bonds : bond 0.04308 / 2.81 ( 1885) hydrogen bonds : angle 4.27382 / 3.04 ( 5292) metal coordination : bond 0.02118 / 1.07 ( 4) metal coordination : angle 6.90580 / 3.94 ( 3) Misc. bond : bond 0.29358 / 17.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 268 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8714 (tptp) REVERT: C 263 MET cc_start: 0.9365 (mmm) cc_final: 0.9124 (mmm) REVERT: C 374 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8702 (mt-10) REVERT: G 120 ASP cc_start: 0.9040 (m-30) cc_final: 0.8764 (m-30) REVERT: G 123 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8366 (tm-30) REVERT: F 88 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8393 (tp30) REVERT: F 100 GLU cc_start: 0.8513 (pt0) cc_final: 0.8217 (mt-10) REVERT: F 125 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8369 (tt0) REVERT: A 97 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.8973 (tp30) REVERT: A 402 TYR cc_start: 0.8874 (m-80) cc_final: 0.8499 (m-80) REVERT: A 461 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7669 (p0) REVERT: H 88 GLU cc_start: 0.8587 (mp0) cc_final: 0.8382 (mp0) REVERT: J 13 SER cc_start: 0.9107 (t) cc_final: 0.8774 (p) REVERT: J 55 ARG cc_start: 0.9005 (ttm-80) cc_final: 0.8549 (tpp80) REVERT: J 59 ASP cc_start: 0.9016 (m-30) cc_final: 0.8736 (m-30) REVERT: N 250 LYS cc_start: 0.9150 (ttmt) cc_final: 0.8929 (ttmm) REVERT: N 287 ASP cc_start: 0.8130 (t0) cc_final: 0.7776 (t0) REVERT: E 47 ASP cc_start: 0.8815 (t70) cc_final: 0.8579 (t0) REVERT: R 91 ASP cc_start: 0.8782 (m-30) cc_final: 0.8520 (m-30) REVERT: R 97 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8472 (mp0) REVERT: R 112 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8740 (tp30) REVERT: Q 107 LYS cc_start: 0.9389 (mtpm) cc_final: 0.8955 (mttm) REVERT: Q 122 ASP cc_start: 0.8373 (p0) cc_final: 0.8105 (p0) REVERT: M 60 PHE cc_start: 0.9601 (OUTLIER) cc_final: 0.9031 (t80) REVERT: O 163 ASP cc_start: 0.9219 (m-30) cc_final: 0.8647 (p0) REVERT: O 248 MET cc_start: 0.8848 (ttm) cc_final: 0.8390 (ttm) REVERT: S 78 GLU cc_start: 0.9092 (tt0) cc_final: 0.8763 (tm-30) REVERT: U 10 LYS cc_start: 0.9213 (tttm) cc_final: 0.8976 (mppt) outliers start: 47 outliers final: 19 residues processed: 305 average time/residue: 0.7743 time to fit residues: 276.3091 Evaluate side-chains 277 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE 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: 2.9990 chunk 167 optimal weight: 0.0980 chunk 287 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 369 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 321 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 GLN F 97 HIS E 90 ASN M 121 GLN O 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.064820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.048372 restraints weight = 82860.395| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.23 r_work: 0.2597 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9277 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.374 33382 Z= 0.117 Angle : 0.536 13.087 45365 Z= 0.258 Chirality : 0.040 0.224 4962 Planarity : 0.004 0.052 5700 Dihedral : 9.773 88.891 4824 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.44 % Allowed : 13.35 % Favored : 85.20 % 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: 2.08 (0.14), residues: 3955 helix: 2.01 (0.11), residues: 2174 sheet: 0.92 (0.27), residues: 369 loop : 0.64 (0.18), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 128 TYR 0.021 0.001 TYR F 114 PHE 0.018 0.001 PHE A 334 TRP 0.012 0.001 TRP N 142 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (33367) covalent geometry : angle 0.53392 / 0.26 (45352) SS BOND : bond 0.00203 / 0.12 ( 5) SS BOND : angle 0.55115 / 0.27 ( 10) hydrogen bonds : bond 0.03870 / 2.51 ( 1885) hydrogen bonds : angle 4.17413 / 2.97 ( 5292) metal coordination : bond 0.00896 / 0.45 ( 4) metal coordination : angle 5.88769 / 3.27 ( 3) Misc. bond : bond 0.25215 / 15.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8691 (tptp) REVERT: P 222 LEU cc_start: 0.9179 (pt) cc_final: 0.8671 (tp) REVERT: G 120 ASP cc_start: 0.9001 (m-30) cc_final: 0.8714 (m-30) REVERT: G 123 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8163 (tm-30) REVERT: F 100 GLU cc_start: 0.8516 (pt0) cc_final: 0.8286 (mt-10) REVERT: A 97 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8943 (tp30) REVERT: A 267 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: A 402 TYR cc_start: 0.8849 (m-80) cc_final: 0.8471 (m-80) REVERT: A 461 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7352 (p0) REVERT: D 90 HIS cc_start: 0.9296 (OUTLIER) cc_final: 0.9070 (m-70) REVERT: J 11 LYS cc_start: 0.8612 (tmtt) cc_final: 0.8307 (tptp) REVERT: J 13 SER cc_start: 0.9133 (t) cc_final: 0.8744 (p) REVERT: J 15 LYS cc_start: 0.9150 (ptmm) cc_final: 0.8943 (pttt) REVERT: J 55 ARG cc_start: 0.8987 (ttm-80) cc_final: 0.8543 (tpp80) REVERT: J 59 ASP cc_start: 0.9033 (m-30) cc_final: 0.8767 (m-30) REVERT: N 250 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8901 (ttmm) REVERT: N 287 ASP cc_start: 0.8035 (t0) cc_final: 0.7634 (t0) REVERT: E 55 ASP cc_start: 0.8502 (p0) cc_final: 0.8205 (p0) REVERT: R 112 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8742 (tp30) REVERT: Q 122 ASP cc_start: 0.8405 (p0) cc_final: 0.8113 (p0) REVERT: M 236 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8293 (mtp85) REVERT: M 364 MET cc_start: 0.9170 (mmm) cc_final: 0.8915 (mmm) REVERT: O 163 ASP cc_start: 0.9196 (m-30) cc_final: 0.8677 (p0) REVERT: S 57 LEU cc_start: 0.8925 (tp) cc_final: 0.8659 (tt) REVERT: S 78 GLU cc_start: 0.9092 (tt0) cc_final: 0.8763 (tm-30) outliers start: 48 outliers final: 17 residues processed: 315 average time/residue: 0.7505 time to fit residues: 275.6512 Evaluate side-chains 280 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 258 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG 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: 7.9990 chunk 352 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 289 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 HIS F 97 HIS F 109 GLN R 84 HIS O 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.061757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.045216 restraints weight = 84257.435| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 2.22 r_work: 0.2512 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9344 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.465 33382 Z= 0.296 Angle : 0.654 17.036 45365 Z= 0.312 Chirality : 0.045 0.167 4962 Planarity : 0.004 0.054 5700 Dihedral : 9.866 86.931 4824 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.50 % Allowed : 13.92 % Favored : 84.57 % 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: 1.89 (0.14), residues: 3955 helix: 1.87 (0.11), residues: 2161 sheet: 0.90 (0.27), residues: 365 loop : 0.53 (0.18), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 201 TYR 0.022 0.002 TYR C 225 PHE 0.023 0.002 PHE N 240 TRP 0.016 0.001 TRP N 142 HIS 0.012 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.29 (33367) covalent geometry : angle 0.64933 / 0.31 (45352) SS BOND : bond 0.00327 / 0.17 ( 5) SS BOND : angle 0.90857 / 0.45 ( 10) hydrogen bonds : bond 0.04814 / 3.14 ( 1885) hydrogen bonds : angle 4.33654 / 3.10 ( 5292) metal coordination : bond 0.02222 / 1.13 ( 4) metal coordination : angle 9.11952 / 5.14 ( 3) Misc. bond : bond 0.35544 / 19.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8735 (tptp) REVERT: C 322 SER cc_start: 0.9499 (OUTLIER) cc_final: 0.9224 (m) REVERT: G 120 ASP cc_start: 0.9068 (m-30) cc_final: 0.8795 (m-30) REVERT: G 123 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8242 (tm-30) REVERT: A 97 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.9037 (tp30) REVERT: A 402 TYR cc_start: 0.8897 (m-80) cc_final: 0.8481 (m-80) REVERT: A 461 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.7727 (p0) REVERT: J 13 SER cc_start: 0.9147 (t) cc_final: 0.8820 (p) REVERT: J 55 ARG cc_start: 0.9025 (ttm-80) cc_final: 0.8560 (tpp80) REVERT: J 59 ASP cc_start: 0.9045 (m-30) cc_final: 0.8778 (m-30) REVERT: N 287 ASP cc_start: 0.8063 (t0) cc_final: 0.7659 (t0) REVERT: E 55 ASP cc_start: 0.8779 (p0) cc_final: 0.8488 (p0) REVERT: E 92 SER cc_start: 0.9266 (OUTLIER) cc_final: 0.8894 (p) REVERT: R 85 LYS cc_start: 0.9303 (mtpt) cc_final: 0.9042 (mtmm) REVERT: R 91 ASP cc_start: 0.8828 (m-30) cc_final: 0.8553 (m-30) REVERT: R 97 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8547 (mp0) REVERT: R 112 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8758 (tp30) REVERT: R 123 GLU cc_start: 0.9119 (tt0) cc_final: 0.8907 (pt0) REVERT: Q 107 LYS cc_start: 0.9395 (mtpm) cc_final: 0.9067 (mtmm) REVERT: Q 112 GLU cc_start: 0.8204 (tp30) cc_final: 0.7998 (tp30) REVERT: Q 122 ASP cc_start: 0.8420 (p0) cc_final: 0.8127 (p0) REVERT: O 85 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8899 (ptm) REVERT: O 163 ASP cc_start: 0.9229 (m-30) cc_final: 0.8673 (p0) REVERT: S 78 GLU cc_start: 0.9110 (tt0) cc_final: 0.8792 (tm-30) outliers start: 50 outliers final: 19 residues processed: 300 average time/residue: 0.7256 time to fit residues: 253.1273 Evaluate side-chains 276 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 132 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 304 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 109 GLN N 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.047213 restraints weight = 83548.531| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.24 r_work: 0.2570 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9299 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.397 33382 Z= 0.134 Angle : 0.562 14.346 45365 Z= 0.270 Chirality : 0.040 0.159 4962 Planarity : 0.004 0.054 5700 Dihedral : 9.491 88.942 4824 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.99 % Allowed : 14.29 % Favored : 84.72 % 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 (0.14), residues: 3955 helix: 2.00 (0.11), residues: 2169 sheet: 0.94 (0.27), residues: 365 loop : 0.62 (0.18), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 201 TYR 0.022 0.001 TYR Q 114 PHE 0.018 0.001 PHE L 334 TRP 0.013 0.001 TRP N 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (33367) covalent geometry : angle 0.55884 / 0.27 (45352) SS BOND : bond 0.00209 / 0.12 ( 5) SS BOND : angle 0.56958 / 0.28 ( 10) hydrogen bonds : bond 0.04051 / 2.63 ( 1885) hydrogen bonds : angle 4.20324 / 2.99 ( 5292) metal coordination : bond 0.00916 / 0.46 ( 4) metal coordination : angle 7.86638 / 4.25 ( 3) Misc. bond : bond 0.28383 / 16.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8711 (tptp) REVERT: C 322 SER cc_start: 0.9481 (OUTLIER) cc_final: 0.9235 (m) REVERT: C 374 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8536 (mt-10) REVERT: P 76 SER cc_start: 0.9218 (m) cc_final: 0.8946 (p) REVERT: G 120 ASP cc_start: 0.9024 (m-30) cc_final: 0.8764 (m-30) REVERT: G 123 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 97 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8949 (tp30) REVERT: A 402 TYR cc_start: 0.8867 (m-80) cc_final: 0.8469 (m-80) REVERT: A 461 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7510 (p0) REVERT: J 11 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8285 (tptp) REVERT: J 13 SER cc_start: 0.9154 (t) cc_final: 0.8782 (p) REVERT: J 55 ARG cc_start: 0.9021 (ttm-80) cc_final: 0.8584 (tpp80) REVERT: J 59 ASP cc_start: 0.9023 (m-30) cc_final: 0.8752 (m-30) REVERT: N 287 ASP cc_start: 0.8029 (t0) cc_final: 0.7647 (t0) REVERT: N 288 LYS cc_start: 0.8156 (tptt) cc_final: 0.7900 (tttt) REVERT: E 55 ASP cc_start: 0.8737 (p0) cc_final: 0.8406 (p0) REVERT: E 92 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.8969 (p) REVERT: R 85 LYS cc_start: 0.9280 (mtpt) cc_final: 0.9024 (mtmm) REVERT: R 112 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8754 (tp30) REVERT: R 123 GLU cc_start: 0.9120 (tt0) cc_final: 0.8855 (pt0) REVERT: Q 112 GLU cc_start: 0.8240 (tp30) cc_final: 0.8032 (tp30) REVERT: Q 122 ASP cc_start: 0.8421 (p0) cc_final: 0.8126 (p0) REVERT: M 364 MET cc_start: 0.9157 (mmm) cc_final: 0.8798 (mmm) REVERT: O 85 MET cc_start: 0.9118 (ptp) cc_final: 0.8881 (ptm) REVERT: O 163 ASP cc_start: 0.9177 (m-30) cc_final: 0.8681 (p0) REVERT: S 57 LEU cc_start: 0.8971 (tp) cc_final: 0.8703 (tt) REVERT: S 78 GLU cc_start: 0.9122 (tt0) cc_final: 0.8807 (tm-30) REVERT: T 34 GLU cc_start: 0.8859 (tt0) cc_final: 0.8282 (pt0) outliers start: 33 outliers final: 17 residues processed: 298 average time/residue: 0.7342 time to fit residues: 255.1856 Evaluate side-chains 280 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 259 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 344 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 389 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 307 optimal weight: 0.9980 chunk 341 optimal weight: 8.9990 chunk 286 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 294 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 377 ASN O 236 ASN U 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.063935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.047480 restraints weight = 83543.748| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.24 r_work: 0.2577 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9294 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.376 33382 Z= 0.131 Angle : 0.561 13.940 45365 Z= 0.268 Chirality : 0.040 0.156 4962 Planarity : 0.004 0.054 5700 Dihedral : 9.230 89.787 4822 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.99 % Allowed : 14.53 % Favored : 84.48 % 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: 2.16 (0.14), residues: 3955 helix: 2.08 (0.11), residues: 2170 sheet: 0.98 (0.27), residues: 365 loop : 0.66 (0.18), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 144 TYR 0.019 0.001 TYR Q 114 PHE 0.017 0.001 PHE A 334 TRP 0.012 0.001 TRP N 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (33367) covalent geometry : angle 0.55725 / 0.27 (45352) SS BOND : bond 0.00212 / 0.12 ( 5) SS BOND : angle 0.55972 / 0.28 ( 10) hydrogen bonds : bond 0.03946 / 2.56 ( 1885) hydrogen bonds : angle 4.15697 / 2.96 ( 5292) metal coordination : bond 0.01071 / 0.55 ( 4) metal coordination : angle 7.78832 / 4.27 ( 3) Misc. bond : bond 0.26462 / 15.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8714 (tptp) REVERT: C 322 SER cc_start: 0.9456 (OUTLIER) cc_final: 0.9205 (m) REVERT: C 374 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8286 (mt-10) REVERT: P 76 SER cc_start: 0.9209 (m) cc_final: 0.8936 (p) REVERT: G 31 TYR cc_start: 0.9194 (t80) cc_final: 0.8966 (t80) REVERT: G 97 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8684 (mp0) REVERT: G 120 ASP cc_start: 0.9019 (m-30) cc_final: 0.8765 (m-30) REVERT: G 123 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8158 (tm-30) REVERT: F 121 GLU cc_start: 0.8327 (tt0) cc_final: 0.8008 (tt0) REVERT: A 97 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8959 (tp30) REVERT: A 402 TYR cc_start: 0.8860 (m-80) cc_final: 0.8462 (m-80) REVERT: A 461 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7390 (p0) REVERT: B 119 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8025 (mtmt) REVERT: I 30 ASP cc_start: 0.9121 (t70) cc_final: 0.8817 (t0) REVERT: J 11 LYS cc_start: 0.8581 (tmtt) cc_final: 0.8248 (tptp) REVERT: J 13 SER cc_start: 0.9153 (t) cc_final: 0.8788 (p) REVERT: J 55 ARG cc_start: 0.8996 (ttm-80) cc_final: 0.8570 (tpp80) REVERT: J 59 ASP cc_start: 0.9036 (m-30) cc_final: 0.8760 (m-30) REVERT: N 287 ASP cc_start: 0.8039 (t0) cc_final: 0.7654 (t0) REVERT: E 55 ASP cc_start: 0.8775 (p0) cc_final: 0.8459 (p0) REVERT: R 85 LYS cc_start: 0.9255 (mtpt) cc_final: 0.8987 (mtmm) REVERT: R 97 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8553 (mp0) REVERT: R 112 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8784 (tp30) REVERT: R 123 GLU cc_start: 0.9125 (tt0) cc_final: 0.8879 (pt0) REVERT: Q 112 GLU cc_start: 0.8309 (tp30) cc_final: 0.7996 (tp30) REVERT: Q 122 ASP cc_start: 0.8422 (p0) cc_final: 0.8119 (p0) REVERT: M 364 MET cc_start: 0.9122 (mmm) cc_final: 0.8853 (mmm) REVERT: O 85 MET cc_start: 0.9118 (ptp) cc_final: 0.8876 (ptm) REVERT: O 163 ASP cc_start: 0.9205 (m-30) cc_final: 0.8672 (p0) REVERT: S 57 LEU cc_start: 0.8965 (tp) cc_final: 0.8697 (tt) REVERT: S 78 GLU cc_start: 0.9106 (tt0) cc_final: 0.8765 (tm-30) REVERT: T 34 GLU cc_start: 0.8857 (tt0) cc_final: 0.8258 (pt0) outliers start: 33 outliers final: 19 residues processed: 293 average time/residue: 0.7935 time to fit residues: 271.2330 Evaluate side-chains 280 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 257 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE 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: 7.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 255 optimal weight: 0.9990 chunk 362 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 294 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 250 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 150 GLN F 109 GLN ** Q 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.063966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.047559 restraints weight = 82709.975| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.23 r_work: 0.2571 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9280 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.369 33382 Z= 0.132 Angle : 0.561 13.843 45365 Z= 0.268 Chirality : 0.040 0.172 4962 Planarity : 0.004 0.054 5700 Dihedral : 9.063 89.396 4822 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.99 % Allowed : 14.71 % Favored : 84.30 % 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: 2.22 (0.14), residues: 3955 helix: 2.13 (0.11), residues: 2172 sheet: 0.99 (0.27), residues: 365 loop : 0.70 (0.18), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 144 TYR 0.022 0.001 TYR Q 114 PHE 0.017 0.001 PHE A 334 TRP 0.011 0.001 TRP N 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (33367) covalent geometry : angle 0.55762 / 0.27 (45352) SS BOND : bond 0.00221 / 0.13 ( 5) SS BOND : angle 0.57457 / 0.28 ( 10) hydrogen bonds : bond 0.03883 / 2.52 ( 1885) hydrogen bonds : angle 4.11646 / 2.93 ( 5292) metal coordination : bond 0.00997 / 0.51 ( 4) metal coordination : angle 7.55624 / 4.10 ( 3) Misc. bond : bond 0.26552 / 15.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8714 (tptp) REVERT: C 322 SER cc_start: 0.9430 (OUTLIER) cc_final: 0.9178 (m) REVERT: C 374 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8544 (mt-10) REVERT: P 76 SER cc_start: 0.9189 (m) cc_final: 0.8924 (p) REVERT: G 97 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8704 (pt0) REVERT: G 120 ASP cc_start: 0.8981 (m-30) cc_final: 0.8723 (m-30) REVERT: G 123 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8132 (tm-30) REVERT: F 100 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7936 (mp0) REVERT: A 97 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8946 (tp30) REVERT: A 402 TYR cc_start: 0.8892 (m-80) cc_final: 0.8485 (m-80) REVERT: A 461 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7353 (p0) REVERT: B 119 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8026 (mtmt) REVERT: I 30 ASP cc_start: 0.9137 (t70) cc_final: 0.8786 (t0) REVERT: J 13 SER cc_start: 0.9152 (t) cc_final: 0.8800 (p) REVERT: J 55 ARG cc_start: 0.8986 (ttm-80) cc_final: 0.8564 (tpp80) REVERT: J 59 ASP cc_start: 0.9026 (m-30) cc_final: 0.8744 (m-30) REVERT: N 287 ASP cc_start: 0.8025 (t0) cc_final: 0.7645 (t0) REVERT: N 288 LYS cc_start: 0.8116 (tptt) cc_final: 0.7873 (tttt) REVERT: E 55 ASP cc_start: 0.8796 (p0) cc_final: 0.8475 (p0) REVERT: R 85 LYS cc_start: 0.9241 (mtpt) cc_final: 0.9017 (mtmm) REVERT: R 112 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8791 (tp30) REVERT: R 123 GLU cc_start: 0.9137 (tt0) cc_final: 0.8887 (pt0) REVERT: Q 112 GLU cc_start: 0.8388 (tp30) cc_final: 0.8070 (tp30) REVERT: Q 122 ASP cc_start: 0.8431 (p0) cc_final: 0.8121 (p0) REVERT: M 364 MET cc_start: 0.9112 (mmm) cc_final: 0.8862 (mmm) REVERT: O 85 MET cc_start: 0.9084 (ptp) cc_final: 0.8833 (ptm) REVERT: O 163 ASP cc_start: 0.9164 (m-30) cc_final: 0.8596 (p0) REVERT: S 57 LEU cc_start: 0.8963 (tp) cc_final: 0.8704 (tt) REVERT: S 78 GLU cc_start: 0.9046 (tt0) cc_final: 0.8713 (tm-30) REVERT: T 34 GLU cc_start: 0.8825 (tt0) cc_final: 0.8229 (pt0) outliers start: 33 outliers final: 19 residues processed: 296 average time/residue: 0.7891 time to fit residues: 272.7582 Evaluate side-chains 279 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 256 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 151 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 13 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 162 optimal weight: 0.0030 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 138 optimal weight: 0.0670 chunk 203 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 65 optimal weight: 0.0670 chunk 23 optimal weight: 0.9980 overall best weight: 0.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.065383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.049166 restraints weight = 82934.942| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.24 r_work: 0.2616 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9241 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.334 33382 Z= 0.102 Angle : 0.538 12.206 45365 Z= 0.259 Chirality : 0.039 0.179 4962 Planarity : 0.004 0.054 5700 Dihedral : 8.843 88.671 4822 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.60 % Allowed : 15.25 % Favored : 84.15 % 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: 2.34 (0.14), residues: 3955 helix: 2.25 (0.11), residues: 2161 sheet: 0.97 (0.27), residues: 369 loop : 0.76 (0.18), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 144 TYR 0.023 0.001 TYR Q 114 PHE 0.014 0.001 PHE A 334 TRP 0.009 0.001 TRP C 142 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (33367) covalent geometry : angle 0.53513 / 0.26 (45352) SS BOND : bond 0.00209 / 0.12 ( 5) SS BOND : angle 0.47601 / 0.23 ( 10) hydrogen bonds : bond 0.03534 / 2.29 ( 1885) hydrogen bonds : angle 4.04448 / 2.87 ( 5292) metal coordination : bond 0.00560 / 0.28 ( 4) metal coordination : angle 6.25428 / 3.37 ( 3) Misc. bond : bond 0.24451 / 13.82 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 278 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9050 (ttmt) cc_final: 0.8697 (tptp) REVERT: C 322 SER cc_start: 0.9387 (OUTLIER) cc_final: 0.9131 (m) REVERT: C 374 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8561 (mt-10) REVERT: P 202 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7412 (ptt90) REVERT: G 120 ASP cc_start: 0.8972 (m-30) cc_final: 0.8691 (m-30) REVERT: G 123 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8120 (tm-30) REVERT: A 97 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8944 (tp30) REVERT: A 402 TYR cc_start: 0.8874 (m-80) cc_final: 0.8465 (m-80) REVERT: A 461 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7310 (p0) REVERT: D 85 MET cc_start: 0.8574 (pmm) cc_final: 0.8138 (pmm) REVERT: I 30 ASP cc_start: 0.9044 (t70) cc_final: 0.8662 (t0) REVERT: J 13 SER cc_start: 0.9183 (t) cc_final: 0.8783 (p) REVERT: J 55 ARG cc_start: 0.8969 (ttm-80) cc_final: 0.8567 (tpp80) REVERT: J 59 ASP cc_start: 0.8983 (m-30) cc_final: 0.8694 (m-30) REVERT: N 287 ASP cc_start: 0.8019 (t0) cc_final: 0.7643 (t0) REVERT: N 288 LYS cc_start: 0.7994 (tptt) cc_final: 0.7770 (tttt) REVERT: E 55 ASP cc_start: 0.8785 (p0) cc_final: 0.8447 (p0) REVERT: R 85 LYS cc_start: 0.9248 (mtpt) cc_final: 0.9022 (mtmm) REVERT: R 97 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8522 (mp0) REVERT: R 123 GLU cc_start: 0.9117 (tt0) cc_final: 0.8876 (pt0) REVERT: Q 112 GLU cc_start: 0.8361 (tp30) cc_final: 0.8154 (tp30) REVERT: Q 120 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8609 (mmtm) REVERT: Q 122 ASP cc_start: 0.8465 (p0) cc_final: 0.8143 (p0) REVERT: M 364 MET cc_start: 0.9096 (mmm) cc_final: 0.8852 (mmm) REVERT: O 85 MET cc_start: 0.9057 (ptp) cc_final: 0.8849 (ptm) REVERT: O 163 ASP cc_start: 0.9149 (m-30) cc_final: 0.8599 (p0) REVERT: S 57 LEU cc_start: 0.8939 (tp) cc_final: 0.8696 (tt) REVERT: S 78 GLU cc_start: 0.9001 (tt0) cc_final: 0.8660 (tm-30) outliers start: 20 outliers final: 13 residues processed: 296 average time/residue: 0.8075 time to fit residues: 278.1999 Evaluate side-chains 274 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 257 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain Q residue 120 LYS Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 179 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 387 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 370 optimal weight: 0.8980 chunk 229 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 377 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 109 GLN B 92 HIS ** Q 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.048407 restraints weight = 83116.860| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.24 r_work: 0.2594 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9262 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.416 33382 Z= 0.122 Angle : 0.560 12.906 45365 Z= 0.267 Chirality : 0.040 0.168 4962 Planarity : 0.004 0.054 5700 Dihedral : 8.811 89.771 4822 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.54 % Allowed : 15.40 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.14), residues: 3955 helix: 2.26 (0.11), residues: 2163 sheet: 0.98 (0.27), residues: 369 loop : 0.80 (0.18), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 144 TYR 0.023 0.001 TYR Q 114 PHE 0.020 0.001 PHE P 126 TRP 0.010 0.001 TRP N 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (33367) covalent geometry : angle 0.55755 / 0.27 (45352) SS BOND : bond 0.00203 / 0.12 ( 5) SS BOND : angle 0.52447 / 0.26 ( 10) hydrogen bonds : bond 0.03667 / 2.38 ( 1885) hydrogen bonds : angle 4.04062 / 2.87 ( 5292) metal coordination : bond 0.00873 / 0.44 ( 4) metal coordination : angle 6.68167 / 3.71 ( 3) Misc. bond : bond 0.27757 / 14.90 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10927.65 seconds wall clock time: 187 minutes 15.26 seconds (11235.26 seconds total)