Starting phenix.real_space_refine on Mon Jul 6 07:23:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o3h_12706/07_2026/7o3h_12706.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o3h_12706/07_2026/7o3h_12706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7o3h_12706/07_2026/7o3h_12706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o3h_12706/07_2026/7o3h_12706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o3h_12706/07_2026/7o3h_12706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o3h_12706/07_2026/7o3h_12706.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7o3h_12706/07_2026/7o3h_12706.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o3h_12706/07_2026/7o3h_12706.cif" } resolution = 2.6 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= 0.014 sd= 0.029 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 10 7.16 5 P 22 5.49 5 S 165 5.16 5 C 21602 2.51 5 N 5687 2.21 5 O 6214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.14s 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: 33700 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3466 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "B" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3154 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 408} Chain: "C" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3046 Classifications: {'peptide': 380} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 357} Chain: "D" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1919 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 218} Chain: "E" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1512 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "F" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 900 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "G" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 674 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 6, 'TRANS': 73} Chain: "H" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 563 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "J" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 495 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "K" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 421 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "L" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3460 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain: "M" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3154 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 408} Chain: "N" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3046 Classifications: {'peptide': 380} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 357} Chain: "O" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1909 Classifications: {'peptide': 240} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 217} Chain: "P" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1512 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "Q" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 894 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "R" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 637 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "S" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 563 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "U" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 495 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "V" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 438 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "T" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 554 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 9, 'TRANS': 68} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 82 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'3PE': 1, 'HEM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'3PE': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "G" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 102 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "L" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "N" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 169 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 68 Chain: "O" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 123 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 71 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'FES': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "R" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12675 SG CYS E 139 85.672 47.390 143.327 1.00170.07 S ATOM 12811 SG CYS E 158 83.776 47.338 146.469 1.00162.86 S ATOM 28809 SG CYS P 139 40.774 84.279 144.186 1.00172.91 S ATOM 28945 SG CYS P 158 42.637 85.385 147.222 1.00155.24 S Time building chain proxies: 6.50, per 1000 atoms: 0.19 Number of scatterers: 33700 At special positions: 0 Unit cell: (127.453, 133.45, 168.437, 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 10 26.01 S 165 16.00 P 22 15.00 O 6214 8.00 N 5687 7.00 C 21602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 160 " distance=2.03 Simple disulfide: pdb=" SG CYS H 38 " - pdb=" SG CYS H 52 " distance=2.02 Simple disulfide: pdb=" SG CYS P 144 " - pdb=" SG CYS P 160 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 66 " distance=2.03 Simple disulfide: pdb=" SG CYS S 38 " - pdb=" SG CYS S 52 " distance=2.04 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 202 " pdb="FE1 FES E 202 " - pdb=" SG CYS E 158 " pdb="FE1 FES E 202 " - pdb=" SG CYS E 139 " pdb=" FES P 201 " pdb="FE2 FES P 201 " - pdb=" NE2 HIS P 161 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 139 " pdb="FE2 FES P 201 " - pdb=" ND1 HIS P 141 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 158 " Number of angles added : 6 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7766 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 19 sheets defined 57.0% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 72 through 82 removed outlier: 4.178A pdb=" N GLU A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 119 Processing helix chain 'A' and resid 124 through 142 Processing helix chain 'A' and resid 145 through 158 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.572A pdb=" N TYR A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 265 through 278 removed outlier: 4.197A pdb=" N THR A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 330 through 348 Processing helix chain 'A' and resid 350 through 369 Processing helix chain 'A' and resid 371 through 385 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 403 through 415 Processing helix chain 'A' and resid 433 through 441 Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.542A pdb=" N GLU B 58 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.665A pdb=" N VAL B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 129 Processing helix chain 'B' and resid 133 through 152 removed outlier: 4.715A pdb=" N SER B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 removed outlier: 3.870A pdb=" N ARG B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 212 through 224 removed outlier: 3.693A pdb=" N LEU B 216 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 removed outlier: 3.828A pdb=" N ASN B 270 " --> pdb=" O ASN B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 332 through 349 removed outlier: 4.057A pdb=" N VAL B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 372 Processing helix chain 'B' and resid 376 through 389 Processing helix chain 'B' and resid 394 through 404 Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.578A pdb=" N VAL B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 19 removed outlier: 3.608A pdb=" N ILE C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 32 through 53 Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 75 through 103 Processing helix chain 'C' and resid 111 through 133 Processing helix chain 'C' and resid 136 through 151 Processing helix chain 'C' and resid 156 through 166 Processing helix chain 'C' and resid 171 through 202 Proline residue: C 186 - end of helix Processing helix chain 'C' and resid 222 through 244 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 271 through 282 removed outlier: 3.707A pdb=" N LEU C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA C 277 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 304 removed outlier: 5.126A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 removed outlier: 3.960A pdb=" N HIS C 308 " --> pdb=" O PRO C 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 305 through 308' Processing helix chain 'C' and resid 318 through 340 removed outlier: 3.744A pdb=" N GLY C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 364 Processing helix chain 'C' and resid 364 through 377 Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 37 through 40 removed outlier: 3.510A pdb=" N CYS D 40 " --> pdb=" O CYS D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 37 through 40' Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 178 through 195 Processing helix chain 'D' and resid 197 through 229 Proline residue: D 217 - end of helix Processing helix chain 'E' and resid 1 through 5 Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.696A pdb=" N LEU E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 62 Processing helix chain 'E' and resid 65 through 73 removed outlier: 4.067A pdb=" N LYS E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 111 Processing helix chain 'F' and resid 10 through 23 Processing helix chain 'F' and resid 33 through 37 removed outlier: 3.685A pdb=" N LEU F 37 " --> pdb=" O ASP F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 49 Processing helix chain 'F' and resid 51 through 71 Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 90 through 110 removed outlier: 3.738A pdb=" N LYS F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 70 Proline residue: G 35 - end of helix removed outlier: 5.323A pdb=" N LEU G 46 " --> pdb=" O ARG G 42 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG G 47 " --> pdb=" O GLU G 43 " (cutoff:3.500A) Proline residue: G 50 - end of helix Processing helix chain 'H' and resid 13 through 22 removed outlier: 3.762A pdb=" N THR H 17 " --> pdb=" O ASP H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 44 removed outlier: 3.642A pdb=" N SER H 44 " --> pdb=" O ASN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 69 Processing helix chain 'J' and resid 4 through 13 Processing helix chain 'J' and resid 16 through 47 Processing helix chain 'J' and resid 51 through 56 Processing helix chain 'J' and resid 57 through 59 No H-bonds generated for 'chain 'J' and resid 57 through 59' Processing helix chain 'K' and resid 8 through 35 Proline residue: K 19 - end of helix Processing helix chain 'K' and resid 38 through 43 removed outlier: 3.611A pdb=" N ASP K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 52 removed outlier: 3.812A pdb=" N GLY K 50 " --> pdb=" O TYR K 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 44 through 48 Processing helix chain 'L' and resid 54 through 63 Processing helix chain 'L' and resid 73 through 81 Processing helix chain 'L' and resid 105 through 117 Processing helix chain 'L' and resid 123 through 142 Processing helix chain 'L' and resid 144 through 158 Processing helix chain 'L' and resid 170 through 175 Processing helix chain 'L' and resid 178 through 190 Processing helix chain 'L' and resid 204 through 216 Processing helix chain 'L' and resid 265 through 278 removed outlier: 4.063A pdb=" N THR L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 302 Processing helix chain 'L' and resid 330 through 348 Processing helix chain 'L' and resid 350 through 369 Processing helix chain 'L' and resid 371 through 386 removed outlier: 3.506A pdb=" N VAL L 375 " --> pdb=" O GLY L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 391 through 401 Processing helix chain 'L' and resid 403 through 415 Processing helix chain 'L' and resid 433 through 441 Processing helix chain 'M' and resid 54 through 58 removed outlier: 3.603A pdb=" N GLU M 58 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 72 Processing helix chain 'M' and resid 81 through 93 Processing helix chain 'M' and resid 115 through 129 removed outlier: 3.950A pdb=" N LEU M 119 " --> pdb=" O ASP M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 152 removed outlier: 4.824A pdb=" N SER M 142 " --> pdb=" O ALA M 138 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLN M 143 " --> pdb=" O ALA M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 168 removed outlier: 4.145A pdb=" N ARG M 158 " --> pdb=" O ASN M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 199 Processing helix chain 'M' and resid 212 through 224 removed outlier: 3.612A pdb=" N LEU M 216 " --> pdb=" O SER M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 280 removed outlier: 4.050A pdb=" N ASN M 270 " --> pdb=" O ASN M 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 removed outlier: 3.897A pdb=" N LYS M 301 " --> pdb=" O GLN M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 349 Processing helix chain 'M' and resid 353 through 372 Processing helix chain 'M' and resid 374 through 389 Processing helix chain 'M' and resid 394 through 404 Processing helix chain 'M' and resid 406 through 420 Processing helix chain 'N' and resid 3 through 8 Processing helix chain 'N' and resid 10 through 19 removed outlier: 3.667A pdb=" N ILE N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 31 Processing helix chain 'N' and resid 32 through 52 Processing helix chain 'N' and resid 61 through 72 Processing helix chain 'N' and resid 75 through 103 Processing helix chain 'N' and resid 111 through 133 Processing helix chain 'N' and resid 136 through 152 Processing helix chain 'N' and resid 156 through 166 Processing helix chain 'N' and resid 171 through 204 Proline residue: N 186 - end of helix Processing helix chain 'N' and resid 222 through 245 Processing helix chain 'N' and resid 252 through 257 removed outlier: 3.501A pdb=" N MET N 257 " --> pdb=" O ASP N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 273 No H-bonds generated for 'chain 'N' and resid 271 through 273' Processing helix chain 'N' and resid 274 through 284 removed outlier: 4.069A pdb=" N ILE N 284 " --> pdb=" O ILE N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 304 Processing helix chain 'N' and resid 305 through 308 removed outlier: 3.970A pdb=" N HIS N 308 " --> pdb=" O PRO N 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 305 through 308' Processing helix chain 'N' and resid 318 through 340 removed outlier: 3.762A pdb=" N GLY N 340 " --> pdb=" O THR N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 346 through 364 Processing helix chain 'N' and resid 364 through 377 Processing helix chain 'O' and resid 22 through 36 Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 48 through 52 Processing helix chain 'O' and resid 57 through 67 Processing helix chain 'O' and resid 97 through 105 Processing helix chain 'O' and resid 123 through 132 Processing helix chain 'O' and resid 178 through 195 Processing helix chain 'O' and resid 197 through 232 Proline residue: O 217 - end of helix removed outlier: 4.724A pdb=" N VAL O 229 " --> pdb=" O HIS O 225 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU O 230 " --> pdb=" O LYS O 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 5 removed outlier: 3.768A pdb=" N VAL P 5 " --> pdb=" O HIS P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 19 removed outlier: 3.511A pdb=" N LEU P 19 " --> pdb=" O ALA P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 63 Processing helix chain 'P' and resid 65 through 73 removed outlier: 3.853A pdb=" N LYS P 73 " --> pdb=" O LEU P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 110 Processing helix chain 'P' and resid 122 through 127 removed outlier: 3.519A pdb=" N ARG P 126 " --> pdb=" O HIS P 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 23 Processing helix chain 'Q' and resid 33 through 37 removed outlier: 3.771A pdb=" N LEU Q 37 " --> pdb=" O ASP Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 49 Processing helix chain 'Q' and resid 51 through 71 Processing helix chain 'Q' and resid 76 through 80 Processing helix chain 'Q' and resid 82 through 86 Processing helix chain 'Q' and resid 90 through 110 Processing helix chain 'R' and resid 20 through 23 removed outlier: 3.830A pdb=" N GLN R 23 " --> pdb=" O PRO R 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 20 through 23' Processing helix chain 'R' and resid 33 through 70 removed outlier: 5.178A pdb=" N LEU R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ARG R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) Proline residue: R 50 - end of helix Processing helix chain 'S' and resid 13 through 24 removed outlier: 3.896A pdb=" N THR S 17 " --> pdb=" O ASP S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 44 removed outlier: 3.508A pdb=" N SER S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 71 removed outlier: 3.515A pdb=" N LYS S 70 " --> pdb=" O CYS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 75 removed outlier: 3.511A pdb=" N LEU S 75 " --> pdb=" O PHE S 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 72 through 75' Processing helix chain 'U' and resid 4 through 13 Processing helix chain 'U' and resid 16 through 47 Processing helix chain 'U' and resid 51 through 56 removed outlier: 3.623A pdb=" N ILE U 55 " --> pdb=" O LEU U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 59 No H-bonds generated for 'chain 'U' and resid 57 through 59' Processing helix chain 'V' and resid 7 through 36 Proline residue: V 19 - end of helix Processing helix chain 'V' and resid 38 through 43 Processing helix chain 'V' and resid 46 through 51 removed outlier: 3.669A pdb=" N ASN V 49 " --> pdb=" O PRO V 46 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY V 50 " --> pdb=" O TYR V 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 8 Processing helix chain 'T' and resid 51 through 56 Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.011A pdb=" N ARG E 126 " --> pdb=" O HIS E 122 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 127' Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'G' and resid 20 through 23 removed outlier: 3.731A pdb=" N GLN G 23 " --> pdb=" O PRO G 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 20 through 23' Processing helix chain 'K' and resid 2 through 6 removed outlier: 4.103A pdb=" N PHE K 5 " --> pdb=" O LEU K 2 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU K 6 " --> pdb=" O SER K 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 2 through 6' Processing helix chain 'L' and resid 327 through 329 No H-bonds generated for 'chain 'L' and resid 327 through 329' Processing helix chain 'N' and resid 212 through 215 removed outlier: 4.377A pdb=" N ALA N 215 " --> pdb=" O ASN N 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 212 through 215' Processing helix chain 'Q' and resid 26 through 30 Processing helix chain 'T' and resid 11 through 16 removed outlier: 3.853A pdb=" N LEU T 15 " --> pdb=" O PHE T 11 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 6.739A pdb=" N ARG A 24 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ALA A 199 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 26 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLY A 201 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLU A 28 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 281 Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.529A pdb=" N VAL B 34 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLY B 208 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA B 36 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU B 96 " --> pdb=" O GLY T 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 242 through 247 removed outlier: 6.540A pdb=" N GLY B 242 " --> pdb=" O MET B 424 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ALA B 426 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B 244 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLY B 428 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLU B 246 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 320 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 72 Processing sheet with id=AA8, first strand: chain 'E' and resid 86 through 91 Processing sheet with id=AA9, first strand: chain 'E' and resid 147 through 148 removed outlier: 3.915A pdb=" N LYS E 173 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AB2, first strand: chain 'L' and resid 15 through 18 removed outlier: 6.632A pdb=" N ARG L 24 " --> pdb=" O LEU L 197 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA L 199 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA L 26 " --> pdb=" O ALA L 199 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLY L 201 " --> pdb=" O ALA L 26 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU L 28 " --> pdb=" O GLY L 201 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 279 through 281 Processing sheet with id=AB4, first strand: chain 'M' and resid 25 through 28 removed outlier: 6.549A pdb=" N VAL M 34 " --> pdb=" O LEU M 206 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLY M 208 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA M 36 " --> pdb=" O GLY M 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 242 through 247 Processing sheet with id=AB6, first strand: chain 'N' and resid 22 through 24 Processing sheet with id=AB7, first strand: chain 'O' and resid 69 through 72 Processing sheet with id=AB8, first strand: chain 'P' and resid 86 through 91 Processing sheet with id=AB9, first strand: chain 'P' and resid 147 through 148 removed outlier: 7.846A pdb=" N HIS P 164 " --> pdb=" O ARG P 172 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 185 through 186 removed outlier: 3.761A pdb=" N GLU P 186 " --> pdb=" O VAL P 194 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL P 194 " --> pdb=" O GLU P 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 168 through 170 removed outlier: 7.009A pdb=" N LYS B 238 " --> pdb=" O LYS B 169 " (cutoff:3.500A) 1883 hydrogen bonds defined for protein. 5397 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 14122 1.40 - 1.60: 20097 1.60 - 1.80: 247 1.80 - 2.01: 31 2.01 - 2.21: 23 Bond restraints: 34520 Sorted by residual: bond pdb=" OB3 CDL A 502 " pdb=" PB2 CDL A 502 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.00e-02 1.00e+04 2.66e+01 bond pdb=" OB3 CDL N 404 " pdb=" PB2 CDL N 404 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.00e-02 1.00e+04 2.66e+01 bond pdb=" OB3 CDL R 101 " pdb=" PB2 CDL R 101 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.00e-02 1.00e+04 2.59e+01 bond pdb=" OB3 CDL G 101 " pdb=" PB2 CDL G 101 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.55e+01 bond pdb=" OB3 CDL G 102 " pdb=" PB2 CDL G 102 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.54e+01 ... (remaining 34515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 46365 3.57 - 7.15: 399 7.15 - 10.72: 48 10.72 - 14.29: 5 14.29 - 17.87: 1 Bond angle restraints: 46818 Sorted by residual: angle pdb=" CA LEU E 78 " pdb=" CB LEU E 78 " pdb=" CG LEU E 78 " ideal model delta sigma weight residual 116.30 134.17 -17.87 3.50e+00 8.16e-02 2.61e+01 angle pdb=" N GLU M 121 " pdb=" CA GLU M 121 " pdb=" CB GLU M 121 " ideal model delta sigma weight residual 110.28 117.85 -7.57 1.55e+00 4.16e-01 2.39e+01 angle pdb=" N ALA G 49 " pdb=" CA ALA G 49 " pdb=" C ALA G 49 " ideal model delta sigma weight residual 113.16 119.94 -6.78 1.42e+00 4.96e-01 2.28e+01 angle pdb=" CB MET N 138 " pdb=" CG MET N 138 " pdb=" SD MET N 138 " ideal model delta sigma weight residual 112.70 126.26 -13.56 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C SER L 220 " pdb=" N ARG L 221 " pdb=" CA ARG L 221 " ideal model delta sigma weight residual 121.54 129.72 -8.18 1.91e+00 2.74e-01 1.83e+01 ... (remaining 46813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 18542 17.92 - 35.85: 1516 35.85 - 53.77: 253 53.77 - 71.69: 76 71.69 - 89.62: 41 Dihedral angle restraints: 20428 sinusoidal: 8355 harmonic: 12073 Sorted by residual: dihedral pdb=" C2B HEM N 402 " pdb=" C3B HEM N 402 " pdb=" CAB HEM N 402 " pdb=" CBB HEM N 402 " ideal model delta sinusoidal sigma weight residual -0.00 -82.82 82.82 2 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" C2B HEM C 402 " pdb=" C3B HEM C 402 " pdb=" CAB HEM C 402 " pdb=" CBB HEM C 402 " ideal model delta sinusoidal sigma weight residual 0.00 -80.92 80.92 2 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" C2C HEM N 401 " pdb=" C3C HEM N 401 " pdb=" CAC HEM N 401 " pdb=" CBC HEM N 401 " ideal model delta sinusoidal sigma weight residual 0.00 -75.96 75.96 2 1.00e+01 1.00e-02 4.52e+01 ... (remaining 20425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4717 0.102 - 0.205: 321 0.205 - 0.307: 9 0.307 - 0.409: 1 0.409 - 0.512: 4 Chirality restraints: 5052 Sorted by residual: chirality pdb=" C2 3PE R 102 " pdb=" C1 3PE R 102 " pdb=" C3 3PE R 102 " pdb=" O21 3PE R 102 " both_signs ideal model delta sigma weight residual False -2.53 -2.01 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CA4 CDL R 101 " pdb=" CA3 CDL R 101 " pdb=" CA6 CDL R 101 " pdb=" OA6 CDL R 101 " both_signs ideal model delta sigma weight residual False -2.57 -2.09 -0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" CB4 CDL N 404 " pdb=" CB3 CDL N 404 " pdb=" CB6 CDL N 404 " pdb=" OB6 CDL N 404 " both_signs ideal model delta sigma weight residual False -2.57 -2.12 -0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 5049 not shown) Planarity restraints: 5935 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC O 303 " 0.021 2.00e-02 2.50e+03 5.94e-02 7.94e+01 pdb=" C2C HEC O 303 " -0.163 2.00e-02 2.50e+03 pdb=" C3C HEC O 303 " 0.024 2.00e-02 2.50e+03 pdb=" C4C HEC O 303 " 0.002 2.00e-02 2.50e+03 pdb=" CAC HEC O 303 " 0.032 2.00e-02 2.50e+03 pdb=" CHC HEC O 303 " 0.029 2.00e-02 2.50e+03 pdb=" CHD HEC O 303 " -0.003 2.00e-02 2.50e+03 pdb=" CMC HEC O 303 " 0.048 2.00e-02 2.50e+03 pdb=" NC HEC O 303 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 301 " -0.021 2.00e-02 2.50e+03 5.91e-02 7.86e+01 pdb=" C2C HEC D 301 " 0.162 2.00e-02 2.50e+03 pdb=" C3C HEC D 301 " -0.024 2.00e-02 2.50e+03 pdb=" C4C HEC D 301 " -0.003 2.00e-02 2.50e+03 pdb=" CAC HEC D 301 " -0.032 2.00e-02 2.50e+03 pdb=" CHC HEC D 301 " -0.029 2.00e-02 2.50e+03 pdb=" CHD HEC D 301 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC D 301 " -0.048 2.00e-02 2.50e+03 pdb=" NC HEC D 301 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 183 " -0.009 2.00e-02 2.50e+03 2.56e-02 1.15e+01 pdb=" CG PHE N 183 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE N 183 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE N 183 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE N 183 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 183 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE N 183 " 0.003 2.00e-02 2.50e+03 ... (remaining 5932 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 359 2.63 - 3.20: 28191 3.20 - 3.77: 54964 3.77 - 4.33: 76041 4.33 - 4.90: 123942 Nonbonded interactions: 283497 Sorted by model distance: nonbonded pdb=" NE2 HIS C 83 " pdb="FE HEM C 401 " model vdw 2.066 3.080 nonbonded pdb=" NE2 HIS N 182 " pdb="FE HEM N 401 " model vdw 2.070 3.080 nonbonded pdb=" NE2 HIS N 97 " pdb="FE HEM N 402 " model vdw 2.202 3.080 nonbonded pdb=" SD MET D 160 " pdb="FE HEC D 301 " model vdw 2.209 3.360 nonbonded pdb=" SD MET O 160 " pdb="FE HEC O 303 " model vdw 2.211 3.360 ... (remaining 283492 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 2 through 501) selection = (chain 'L' and (resid 2 through 445 or (resid 446 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 501)) } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = (chain 'N' and (resid 1 through 402 or (resid 403 and (name N or name C1 or name \ C11 or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or n \ ame C25 or name C26 or name C27 or name C28 or name C29 or name C2A or name C2B \ or name C2C or name C2D or name C2E or name C2F or name C2G or name C3 or name C \ 31 or name C32 or name C33 or name C34 or name O11 or name O12 or name O13 or na \ me O14 or name O21 or name O22 or name O31 or name O32 or name P )))) } ncs_group { reference = (chain 'D' and resid 1 through 240) selection = (chain 'O' and resid 1 through 240) } ncs_group { reference = (chain 'E' and resid 1 through 196) selection = (chain 'P' and resid 1 through 196) } ncs_group { reference = (chain 'F' and resid 10 through 110) selection = chain 'Q' } ncs_group { reference = (chain 'G' and (resid 1 through 76 or (resid 102 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 C32 or \ name C33 or name C51 or name C52 or name C71 or name C72 or name CA2 or name CA \ 3 or name CA4 or name CA5 or name CA6 or name CA7 or name CB4 or name CB5 or nam \ e 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)) or resid 103)) selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = (chain 'J' and resid 2 through 61) selection = chain 'U' } ncs_group { reference = chain 'K' selection = (chain 'V' and resid 2 through 52) } 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: 1.130 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: 0.010 Extract box with map and model: 1.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 29.570 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 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 : 0.006 0.243 34541 Z= 0.330 Angle : 0.883 17.867 46834 Z= 0.459 Chirality : 0.054 0.512 5052 Planarity : 0.007 0.083 5935 Dihedral : 14.333 89.617 12647 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: -0.68 (0.12), residues: 4119 helix: -0.36 (0.10), residues: 2093 sheet: 0.81 (0.26), residues: 380 loop : -0.70 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 134 TYR 0.031 0.002 TYR F 55 PHE 0.054 0.002 PHE N 183 TRP 0.012 0.001 TRP B 135 HIS 0.009 0.001 HIS N 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.28 (34520) covalent geometry : angle 0.88192 / 0.46 (46818) SS BOND : bond 0.00446 / 0.24 ( 5) SS BOND : angle 2.65233 / 1.40 ( 10) hydrogen bonds : bond 0.13455 / 8.98 ( 1883) hydrogen bonds : angle 5.82946 / 4.15 ( 5397) metal coordination : bond 0.08169 / 4.14 ( 6) metal coordination : angle 2.65336 / 1.39 ( 6) Misc. bond : bond 0.15737 / 9.43 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 687 time to evaluate : 1.343 Fit side-chains REVERT: B 218 GLN cc_start: 0.8415 (pt0) cc_final: 0.8201 (pt0) REVERT: B 246 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8468 (mm-30) REVERT: C 111 GLU cc_start: 0.8485 (mp0) cc_final: 0.8238 (mt-10) REVERT: D 77 ASP cc_start: 0.7968 (p0) cc_final: 0.7249 (p0) REVERT: E 23 LYS cc_start: 0.8607 (tttm) cc_final: 0.8280 (tttp) REVERT: F 42 ASP cc_start: 0.8109 (m-30) cc_final: 0.7764 (m-30) REVERT: F 96 GLU cc_start: 0.8362 (tp30) cc_final: 0.8092 (pt0) REVERT: J 48 GLU cc_start: 0.8182 (pm20) cc_final: 0.7977 (pm20) REVERT: L 115 ASP cc_start: 0.7349 (t70) cc_final: 0.6777 (t70) REVERT: M 218 GLN cc_start: 0.8239 (pp30) cc_final: 0.8034 (pp30) REVERT: P 135 LEU cc_start: 0.7504 (mt) cc_final: 0.7174 (pp) REVERT: T 47 ARG cc_start: 0.8328 (ptp-110) cc_final: 0.7698 (ttm-80) outliers start: 0 outliers final: 1 residues processed: 687 average time/residue: 0.7338 time to fit residues: 588.6116 Evaluate side-chains 510 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 509 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 251 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 20.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 GLN A 21 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN A 400 GLN A 430 GLN A 435 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN F 73 GLN G 73 ASN K 16 ASN L 6 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 301 ASN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 270 ASN O 97 ASN V 16 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.108196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.083314 restraints weight = 54041.998| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.98 r_work: 0.2972 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.348 34541 Z= 0.156 Angle : 0.628 14.012 46834 Z= 0.310 Chirality : 0.043 0.190 5052 Planarity : 0.005 0.060 5935 Dihedral : 9.693 87.856 4928 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.59 % Allowed : 11.13 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 0.65 (0.13), residues: 4119 helix: 0.98 (0.11), residues: 2123 sheet: 0.70 (0.26), residues: 384 loop : -0.26 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 15 TYR 0.024 0.001 TYR N 224 PHE 0.018 0.001 PHE P 89 TRP 0.013 0.001 TRP C 141 HIS 0.009 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (34520) covalent geometry : angle 0.62333 / 0.31 (46818) SS BOND : bond 0.00226 / 0.12 ( 5) SS BOND : angle 1.64475 / 0.89 ( 10) hydrogen bonds : bond 0.05136 / 3.42 ( 1883) hydrogen bonds : angle 4.58945 / 3.26 ( 5397) metal coordination : bond 0.01926 / 1.09 ( 6) metal coordination : angle 6.54534 / 3.16 ( 6) Misc. bond : bond 0.22434 / 12.24 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 533 time to evaluate : 1.346 Fit side-chains REVERT: A 365 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8707 (mp) REVERT: B 246 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8555 (mm-30) REVERT: C 111 GLU cc_start: 0.8518 (mp0) cc_final: 0.8276 (mt-10) REVERT: D 77 ASP cc_start: 0.8304 (p0) cc_final: 0.7971 (p0) REVERT: E 23 LYS cc_start: 0.8652 (tttm) cc_final: 0.8450 (tttp) REVERT: E 87 MET cc_start: 0.6161 (ptm) cc_final: 0.5640 (ptt) REVERT: F 42 ASP cc_start: 0.8199 (m-30) cc_final: 0.7888 (m-30) REVERT: F 96 GLU cc_start: 0.8315 (tp30) cc_final: 0.8014 (pt0) REVERT: H 50 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: K 37 ASP cc_start: 0.7574 (m-30) cc_final: 0.7313 (m-30) REVERT: L 176 ARG cc_start: 0.8400 (ppt170) cc_final: 0.8177 (ppt170) REVERT: M 110 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: M 218 GLN cc_start: 0.8266 (pp30) cc_final: 0.8032 (pp30) REVERT: P 135 LEU cc_start: 0.7100 (mt) cc_final: 0.6757 (pp) REVERT: Q 101 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8136 (tmm160) REVERT: V 16 ASN cc_start: 0.7415 (m110) cc_final: 0.7214 (m-40) REVERT: T 47 ARG cc_start: 0.8062 (ptp-110) cc_final: 0.7731 (ttm-80) outliers start: 56 outliers final: 22 residues processed: 556 average time/residue: 0.7132 time to fit residues: 463.6966 Evaluate side-chains 517 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 491 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 367 SER Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 228 optimal weight: 6.9990 chunk 307 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 351 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 398 optimal weight: 50.0000 chunk 91 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN B 218 GLN E 141 HIS F 73 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.081357 restraints weight = 53916.623| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.91 r_work: 0.2931 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.349 34541 Z= 0.171 Angle : 0.620 14.125 46834 Z= 0.306 Chirality : 0.043 0.180 5052 Planarity : 0.004 0.060 5935 Dihedral : 9.366 88.051 4926 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.53 % Allowed : 12.18 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.18 (0.13), residues: 4119 helix: 1.51 (0.11), residues: 2118 sheet: 0.68 (0.26), residues: 384 loop : -0.06 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 8 TYR 0.024 0.001 TYR N 224 PHE 0.017 0.002 PHE Q 60 TRP 0.014 0.001 TRP C 141 HIS 0.009 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (34520) covalent geometry : angle 0.61563 / 0.31 (46818) SS BOND : bond 0.00426 / 0.21 ( 5) SS BOND : angle 1.82925 / 1.08 ( 10) hydrogen bonds : bond 0.05226 / 3.48 ( 1883) hydrogen bonds : angle 4.44660 / 3.15 ( 5397) metal coordination : bond 0.01771 / 0.96 ( 6) metal coordination : angle 6.47460 / 3.16 ( 6) Misc. bond : bond 0.20133 / 10.99 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 528 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: A 365 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8712 (mp) REVERT: C 111 GLU cc_start: 0.8571 (mp0) cc_final: 0.8335 (mt-10) REVERT: D 77 ASP cc_start: 0.8171 (p0) cc_final: 0.7936 (p0) REVERT: E 23 LYS cc_start: 0.8654 (tttm) cc_final: 0.8416 (tttp) REVERT: E 87 MET cc_start: 0.6069 (ptm) cc_final: 0.5491 (ptt) REVERT: F 42 ASP cc_start: 0.8245 (m-30) cc_final: 0.7914 (m-30) REVERT: F 96 GLU cc_start: 0.8353 (tp30) cc_final: 0.8012 (pt0) REVERT: L 176 ARG cc_start: 0.8435 (ppt170) cc_final: 0.8169 (ppt170) REVERT: M 110 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: M 147 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8581 (t70) REVERT: N 172 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8358 (tptm) REVERT: P 135 LEU cc_start: 0.7296 (mt) cc_final: 0.6992 (pp) REVERT: Q 32 MET cc_start: 0.9207 (mmm) cc_final: 0.9003 (mtp) REVERT: Q 78 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8616 (p0) REVERT: Q 101 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8070 (tmm160) REVERT: U 16 ARG cc_start: 0.8159 (mtm110) cc_final: 0.7814 (mmm160) REVERT: V 16 ASN cc_start: 0.7470 (m110) cc_final: 0.7250 (m-40) outliers start: 89 outliers final: 38 residues processed: 571 average time/residue: 0.7176 time to fit residues: 481.3429 Evaluate side-chains 530 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 486 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 367 SER Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 147 ASP Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 172 LYS Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 78 ASP Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 37 GLN Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 408 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 312 optimal weight: 0.0570 chunk 128 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 358 optimal weight: 40.0000 chunk 366 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 384 optimal weight: 5.9990 chunk 319 optimal weight: 20.0000 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 400 GLN D 71 GLN F 73 GLN G 36 ASN G 73 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 289 ASN ** N 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 71 GLN Q 73 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.106372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.081855 restraints weight = 53698.092| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.89 r_work: 0.2939 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.349 34541 Z= 0.145 Angle : 0.591 13.001 46834 Z= 0.291 Chirality : 0.042 0.164 5052 Planarity : 0.004 0.056 5935 Dihedral : 9.061 89.278 4926 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.42 % Allowed : 13.61 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.46 (0.13), residues: 4119 helix: 1.75 (0.11), residues: 2122 sheet: 0.71 (0.26), residues: 381 loop : 0.06 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 8 TYR 0.020 0.001 TYR C 224 PHE 0.016 0.001 PHE Q 60 TRP 0.013 0.001 TRP C 141 HIS 0.008 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (34520) covalent geometry : angle 0.58518 / 0.29 (46818) SS BOND : bond 0.00296 / 0.15 ( 5) SS BOND : angle 1.68391 / 1.01 ( 10) hydrogen bonds : bond 0.04824 / 3.21 ( 1883) hydrogen bonds : angle 4.33387 / 3.07 ( 5397) metal coordination : bond 0.01602 / 0.85 ( 6) metal coordination : angle 6.75398 / 3.27 ( 6) Misc. bond : bond 0.19426 / 10.90 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 533 time to evaluate : 1.049 Fit side-chains REVERT: A 6 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8420 (mp10) REVERT: A 9 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: A 21 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7839 (p0) REVERT: A 115 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8333 (t0) REVERT: A 365 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8678 (mp) REVERT: B 223 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: C 111 GLU cc_start: 0.8556 (mp0) cc_final: 0.8318 (mt-10) REVERT: D 77 ASP cc_start: 0.8154 (p0) cc_final: 0.7939 (p0) REVERT: E 87 MET cc_start: 0.5990 (ptm) cc_final: 0.5443 (ptt) REVERT: F 96 GLU cc_start: 0.8361 (tp30) cc_final: 0.8003 (pt0) REVERT: L 176 ARG cc_start: 0.8457 (ppt170) cc_final: 0.8196 (ppt170) REVERT: M 110 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: N 14 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9232 (mp) REVERT: N 172 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8350 (tptm) REVERT: N 343 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8749 (m) REVERT: N 377 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8839 (mp) REVERT: O 166 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8702 (m) REVERT: P 135 LEU cc_start: 0.7361 (mt) cc_final: 0.7055 (pp) REVERT: Q 32 MET cc_start: 0.9168 (mmm) cc_final: 0.8909 (mtp) REVERT: Q 91 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: Q 99 ARG cc_start: 0.8311 (ttp-110) cc_final: 0.8032 (ttp-110) REVERT: Q 101 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7988 (tmm160) REVERT: R 68 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7696 (mp10) REVERT: U 16 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7757 (mmm160) REVERT: V 16 ASN cc_start: 0.7444 (m110) cc_final: 0.7180 (m-40) outliers start: 85 outliers final: 34 residues processed: 578 average time/residue: 0.6921 time to fit residues: 471.8983 Evaluate side-chains 546 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 497 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 367 SER Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 172 LYS Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 43 MET Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 370 optimal weight: 0.8980 chunk 372 optimal weight: 5.9990 chunk 345 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 282 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 246 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN O 71 GLN Q 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.082138 restraints weight = 54006.896| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.90 r_work: 0.2940 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.342 34541 Z= 0.140 Angle : 0.585 13.106 46834 Z= 0.288 Chirality : 0.042 0.160 5052 Planarity : 0.004 0.054 5935 Dihedral : 8.906 89.223 4926 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.65 % Allowed : 14.83 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.13), residues: 4119 helix: 1.85 (0.11), residues: 2126 sheet: 0.70 (0.26), residues: 381 loop : 0.11 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 8 TYR 0.021 0.001 TYR N 224 PHE 0.016 0.001 PHE Q 60 TRP 0.013 0.001 TRP M 135 HIS 0.008 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (34520) covalent geometry : angle 0.58183 / 0.29 (46818) SS BOND : bond 0.00483 / 0.22 ( 5) SS BOND : angle 1.82797 / 1.04 ( 10) hydrogen bonds : bond 0.04745 / 3.16 ( 1883) hydrogen bonds : angle 4.29293 / 3.05 ( 5397) metal coordination : bond 0.01231 / 0.61 ( 6) metal coordination : angle 4.70358 / 2.48 ( 6) Misc. bond : bond 0.18214 / 10.02 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 524 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8221 (mt0) REVERT: A 21 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8081 (p0) REVERT: A 115 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8330 (t0) REVERT: A 365 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8660 (mp) REVERT: B 223 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: C 111 GLU cc_start: 0.8568 (mp0) cc_final: 0.8328 (mt-10) REVERT: E 87 MET cc_start: 0.5922 (ptm) cc_final: 0.5373 (ptt) REVERT: F 32 MET cc_start: 0.9169 (mmm) cc_final: 0.8925 (mtp) REVERT: F 42 ASP cc_start: 0.8236 (m-30) cc_final: 0.8034 (m-30) REVERT: F 96 GLU cc_start: 0.8361 (tp30) cc_final: 0.8050 (pt0) REVERT: L 176 ARG cc_start: 0.8471 (ppt170) cc_final: 0.8229 (ppt170) REVERT: M 110 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: N 14 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9222 (mp) REVERT: N 377 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8809 (mp) REVERT: P 87 MET cc_start: 0.5255 (OUTLIER) cc_final: 0.2757 (pp-130) REVERT: P 135 LEU cc_start: 0.7366 (mt) cc_final: 0.7083 (pp) REVERT: Q 32 MET cc_start: 0.9169 (mmm) cc_final: 0.8940 (mtp) REVERT: Q 91 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: Q 99 ARG cc_start: 0.8322 (ttp-110) cc_final: 0.8051 (ttp-110) REVERT: Q 101 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.7920 (tmm160) REVERT: R 68 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: S 11 LEU cc_start: 0.8062 (tt) cc_final: 0.7761 (tp) REVERT: U 16 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7678 (mmm160) REVERT: V 16 ASN cc_start: 0.7443 (m110) cc_final: 0.7175 (m-40) outliers start: 93 outliers final: 42 residues processed: 571 average time/residue: 0.6702 time to fit residues: 451.1097 Evaluate side-chains 548 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 494 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 218 GLN Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 43 MET Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 253 optimal weight: 20.0000 chunk 252 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 246 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 193 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 404 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 374 optimal weight: 9.9990 chunk 322 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN G 73 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN O 71 GLN Q 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.081486 restraints weight = 53913.683| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.93 r_work: 0.2932 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.335 34541 Z= 0.152 Angle : 0.599 13.696 46834 Z= 0.295 Chirality : 0.042 0.162 5052 Planarity : 0.004 0.055 5935 Dihedral : 8.852 87.420 4926 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.76 % Allowed : 15.06 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.61 (0.13), residues: 4119 helix: 1.89 (0.11), residues: 2128 sheet: 0.69 (0.26), residues: 381 loop : 0.15 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 8 TYR 0.021 0.001 TYR N 224 PHE 0.016 0.001 PHE Q 60 TRP 0.013 0.001 TRP C 141 HIS 0.008 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (34520) covalent geometry : angle 0.59643 / 0.30 (46818) SS BOND : bond 0.00488 / 0.22 ( 5) SS BOND : angle 1.70469 / 0.98 ( 10) hydrogen bonds : bond 0.04851 / 3.23 ( 1883) hydrogen bonds : angle 4.29137 / 3.05 ( 5397) metal coordination : bond 0.01192 / 0.60 ( 6) metal coordination : angle 4.87371 / 2.48 ( 6) Misc. bond : bond 0.18707 / 10.07 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 514 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: A 115 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8359 (t0) REVERT: A 365 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8653 (mp) REVERT: B 223 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: B 376 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8743 (pp20) REVERT: C 111 GLU cc_start: 0.8565 (mp0) cc_final: 0.8330 (mt-10) REVERT: E 87 MET cc_start: 0.5919 (ptm) cc_final: 0.5354 (ptt) REVERT: F 32 MET cc_start: 0.9180 (mmm) cc_final: 0.8938 (mtp) REVERT: F 96 GLU cc_start: 0.8357 (tp30) cc_final: 0.7945 (tp30) REVERT: F 99 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8413 (ttm-80) REVERT: L 176 ARG cc_start: 0.8462 (ppt170) cc_final: 0.8240 (ppt170) REVERT: M 110 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: N 12 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8717 (ptmm) REVERT: N 14 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9244 (mp) REVERT: N 377 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8822 (mp) REVERT: P 135 LEU cc_start: 0.7370 (mt) cc_final: 0.7081 (pp) REVERT: Q 32 MET cc_start: 0.9166 (mmm) cc_final: 0.8947 (mtp) REVERT: Q 91 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: Q 99 ARG cc_start: 0.8311 (ttp-110) cc_final: 0.8050 (ttp-110) REVERT: Q 101 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7958 (tmm160) REVERT: S 11 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7686 (tp) REVERT: U 16 ARG cc_start: 0.8180 (mtm110) cc_final: 0.7685 (mmm160) REVERT: V 16 ASN cc_start: 0.7451 (m110) cc_final: 0.7181 (m-40) outliers start: 97 outliers final: 47 residues processed: 563 average time/residue: 0.7119 time to fit residues: 469.6039 Evaluate side-chains 552 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 493 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 218 GLN Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 43 MET Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 47 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 190 optimal weight: 7.9990 chunk 406 optimal weight: 50.0000 chunk 305 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 337 optimal weight: 0.2980 chunk 260 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 338 optimal weight: 3.9990 chunk 359 optimal weight: 40.0000 chunk 234 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN A 400 GLN G 36 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN O 71 GLN Q 73 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.106168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.081744 restraints weight = 53771.958| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.88 r_work: 0.2930 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.335 34541 Z= 0.151 Angle : 0.601 14.555 46834 Z= 0.297 Chirality : 0.042 0.175 5052 Planarity : 0.004 0.061 5935 Dihedral : 8.776 87.391 4926 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.85 % Allowed : 15.57 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.65 (0.13), residues: 4119 helix: 1.92 (0.11), residues: 2122 sheet: 0.70 (0.26), residues: 381 loop : 0.17 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG J 8 TYR 0.021 0.001 TYR N 224 PHE 0.016 0.001 PHE Q 60 TRP 0.013 0.001 TRP M 135 HIS 0.008 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (34520) covalent geometry : angle 0.59779 / 0.30 (46818) SS BOND : bond 0.00473 / 0.22 ( 5) SS BOND : angle 1.67021 / 0.98 ( 10) hydrogen bonds : bond 0.04839 / 3.22 ( 1883) hydrogen bonds : angle 4.28593 / 3.04 ( 5397) metal coordination : bond 0.01115 / 0.57 ( 6) metal coordination : angle 4.91390 / 2.46 ( 6) Misc. bond : bond 0.19193 / 10.61 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 505 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: A 115 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8354 (t0) REVERT: A 365 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8658 (mp) REVERT: B 223 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: B 376 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8741 (pp20) REVERT: C 111 GLU cc_start: 0.8573 (mp0) cc_final: 0.8322 (mt-10) REVERT: E 87 MET cc_start: 0.5914 (ptm) cc_final: 0.5333 (ptt) REVERT: F 32 MET cc_start: 0.9189 (mmm) cc_final: 0.8953 (mtp) REVERT: F 96 GLU cc_start: 0.8357 (tp30) cc_final: 0.8028 (pt0) REVERT: F 99 ARG cc_start: 0.8653 (ttp80) cc_final: 0.8429 (ttm-80) REVERT: L 176 ARG cc_start: 0.8472 (ppt170) cc_final: 0.8266 (ppt170) REVERT: M 44 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8667 (mp) REVERT: M 110 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: N 14 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9239 (mp) REVERT: N 377 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8822 (mp) REVERT: P 87 MET cc_start: 0.5232 (OUTLIER) cc_final: 0.2707 (pp-130) REVERT: P 135 LEU cc_start: 0.7412 (mt) cc_final: 0.7156 (pp) REVERT: Q 32 MET cc_start: 0.9174 (mmm) cc_final: 0.8963 (mtp) REVERT: Q 91 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: Q 101 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7984 (tmm160) REVERT: S 11 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7787 (tp) REVERT: U 16 ARG cc_start: 0.8195 (mtm110) cc_final: 0.7698 (mmm160) REVERT: V 16 ASN cc_start: 0.7462 (m110) cc_final: 0.7182 (m-40) REVERT: T 20 ARG cc_start: 0.8712 (ptp-110) cc_final: 0.8246 (mtm-85) REVERT: T 53 GLU cc_start: 0.8657 (mp0) cc_final: 0.8445 (mm-30) outliers start: 100 outliers final: 49 residues processed: 556 average time/residue: 0.7710 time to fit residues: 502.9490 Evaluate side-chains 553 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 491 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 218 GLN Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 43 MET Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 47 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 71 optimal weight: 30.0000 chunk 297 optimal weight: 5.9990 chunk 288 optimal weight: 30.0000 chunk 279 optimal weight: 10.0000 chunk 358 optimal weight: 0.7980 chunk 245 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 292 optimal weight: 20.0000 chunk 342 optimal weight: 6.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN G 36 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN N 331 ASN O 71 GLN Q 73 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.080857 restraints weight = 53904.644| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.96 r_work: 0.2922 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9136 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.334 34541 Z= 0.158 Angle : 0.611 14.839 46834 Z= 0.303 Chirality : 0.042 0.171 5052 Planarity : 0.004 0.079 5935 Dihedral : 8.744 87.501 4926 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.65 % Allowed : 16.00 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.66 (0.13), residues: 4119 helix: 1.93 (0.11), residues: 2123 sheet: 0.71 (0.26), residues: 381 loop : 0.17 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG J 8 TYR 0.021 0.001 TYR N 224 PHE 0.016 0.001 PHE Q 60 TRP 0.013 0.001 TRP C 141 HIS 0.008 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (34520) covalent geometry : angle 0.60801 / 0.30 (46818) SS BOND : bond 0.00481 / 0.22 ( 5) SS BOND : angle 1.64658 / 0.99 ( 10) hydrogen bonds : bond 0.04919 / 3.27 ( 1883) hydrogen bonds : angle 4.29767 / 3.05 ( 5397) metal coordination : bond 0.01157 / 0.59 ( 6) metal coordination : angle 4.81091 / 2.38 ( 6) Misc. bond : bond 0.18653 / 10.50 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 499 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8353 (t0) REVERT: A 365 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8660 (mp) REVERT: B 223 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: B 376 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8731 (pp20) REVERT: C 111 GLU cc_start: 0.8572 (mp0) cc_final: 0.8332 (mt-10) REVERT: E 87 MET cc_start: 0.5837 (ptm) cc_final: 0.5246 (ptt) REVERT: F 32 MET cc_start: 0.9194 (mmm) cc_final: 0.8964 (mtp) REVERT: F 96 GLU cc_start: 0.8353 (tp30) cc_final: 0.8026 (pt0) REVERT: F 99 ARG cc_start: 0.8640 (ttp80) cc_final: 0.8411 (ttm-80) REVERT: M 44 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8677 (mp) REVERT: M 110 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: N 14 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9237 (mp) REVERT: N 377 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8862 (mp) REVERT: P 87 MET cc_start: 0.5183 (OUTLIER) cc_final: 0.2711 (pp-130) REVERT: P 135 LEU cc_start: 0.7364 (mt) cc_final: 0.7090 (pp) REVERT: Q 32 MET cc_start: 0.9177 (mmm) cc_final: 0.8967 (mtp) REVERT: Q 91 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: Q 101 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.7999 (tmm160) REVERT: S 11 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7855 (tp) REVERT: U 16 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7753 (mmm160) REVERT: V 16 ASN cc_start: 0.7487 (m110) cc_final: 0.7213 (m-40) REVERT: T 20 ARG cc_start: 0.8750 (ptp-110) cc_final: 0.8280 (mtm-85) REVERT: T 53 GLU cc_start: 0.8666 (mp0) cc_final: 0.8448 (mm-30) REVERT: T 62 ARG cc_start: 0.8495 (mmm160) cc_final: 0.8252 (mtt180) outliers start: 93 outliers final: 54 residues processed: 549 average time/residue: 0.7704 time to fit residues: 496.7229 Evaluate side-chains 554 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 488 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 218 GLN Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 43 MET Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain V residue 18 ILE Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 102 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 265 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 354 optimal weight: 20.0000 chunk 369 optimal weight: 10.0000 chunk 348 optimal weight: 9.9990 chunk 336 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN D 106 ASN G 36 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN N 331 ASN O 71 GLN Q 73 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.105779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.081064 restraints weight = 54123.551| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.94 r_work: 0.2924 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.339 34541 Z= 0.157 Angle : 0.618 14.562 46834 Z= 0.306 Chirality : 0.042 0.173 5052 Planarity : 0.004 0.084 5935 Dihedral : 8.710 87.496 4926 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.65 % Allowed : 16.40 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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 (0.13), residues: 4119 helix: 1.94 (0.11), residues: 2120 sheet: 0.71 (0.26), residues: 381 loop : 0.19 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG J 8 TYR 0.021 0.001 TYR N 224 PHE 0.015 0.001 PHE Q 60 TRP 0.013 0.001 TRP M 135 HIS 0.008 0.001 HIS N 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (34520) covalent geometry : angle 0.61535 / 0.31 (46818) SS BOND : bond 0.00573 / 0.27 ( 5) SS BOND : angle 1.68207 / 0.94 ( 10) hydrogen bonds : bond 0.04913 / 3.27 ( 1883) hydrogen bonds : angle 4.30177 / 3.06 ( 5397) metal coordination : bond 0.01143 / 0.59 ( 6) metal coordination : angle 4.75561 / 2.33 ( 6) Misc. bond : bond 0.19497 / 10.84 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 508 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8337 (t0) REVERT: A 365 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8659 (mp) REVERT: B 223 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: B 376 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8723 (pp20) REVERT: C 111 GLU cc_start: 0.8579 (mp0) cc_final: 0.8344 (mt-10) REVERT: E 87 MET cc_start: 0.5835 (ptm) cc_final: 0.5320 (ptt) REVERT: F 32 MET cc_start: 0.9196 (mmm) cc_final: 0.8966 (mtp) REVERT: F 96 GLU cc_start: 0.8359 (tp30) cc_final: 0.8035 (pt0) REVERT: F 99 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8416 (ttm-80) REVERT: M 44 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8666 (mp) REVERT: M 110 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: N 377 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8844 (mp) REVERT: P 135 LEU cc_start: 0.7384 (mt) cc_final: 0.7118 (pp) REVERT: Q 32 MET cc_start: 0.9170 (mmm) cc_final: 0.8961 (mtp) REVERT: Q 91 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: Q 99 ARG cc_start: 0.8317 (ttp-110) cc_final: 0.8049 (ttp-110) REVERT: Q 101 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8012 (tmm160) REVERT: U 16 ARG cc_start: 0.8196 (mtm110) cc_final: 0.7741 (mmm160) REVERT: V 16 ASN cc_start: 0.7493 (m110) cc_final: 0.7215 (m-40) REVERT: T 20 ARG cc_start: 0.8763 (ptp-110) cc_final: 0.8294 (mtm-85) REVERT: T 53 GLU cc_start: 0.8663 (mp0) cc_final: 0.8443 (mm-30) REVERT: T 62 ARG cc_start: 0.8506 (mmm160) cc_final: 0.8279 (mtt180) outliers start: 93 outliers final: 55 residues processed: 557 average time/residue: 0.7096 time to fit residues: 463.9929 Evaluate side-chains 564 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 500 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 218 GLN Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 240 MET Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 43 MET Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain V residue 18 ILE Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 126 optimal weight: 30.0000 chunk 360 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 376 optimal weight: 30.0000 chunk 287 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN D 106 ASN G 36 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN O 71 GLN Q 73 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.081881 restraints weight = 54339.988| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.91 r_work: 0.2935 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.338 34541 Z= 0.141 Angle : 0.613 14.158 46834 Z= 0.303 Chirality : 0.042 0.170 5052 Planarity : 0.004 0.089 5935 Dihedral : 8.613 87.363 4926 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.05 % Allowed : 17.14 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.69 (0.13), residues: 4119 helix: 1.95 (0.11), residues: 2127 sheet: 0.72 (0.26), residues: 381 loop : 0.19 (0.17), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG J 8 TYR 0.020 0.001 TYR N 224 PHE 0.015 0.001 PHE L 307 TRP 0.014 0.001 TRP M 135 HIS 0.008 0.001 HIS N 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (34520) covalent geometry : angle 0.60987 / 0.30 (46818) SS BOND : bond 0.00540 / 0.25 ( 5) SS BOND : angle 1.65555 / 0.92 ( 10) hydrogen bonds : bond 0.04721 / 3.14 ( 1883) hydrogen bonds : angle 4.26688 / 3.03 ( 5397) metal coordination : bond 0.01073 / 0.55 ( 6) metal coordination : angle 4.77205 / 2.34 ( 6) Misc. bond : bond 0.18646 / 10.49 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8238 Ramachandran restraints generated. 4119 Oldfield, 0 Emsley, 4119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 516 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8339 (t0) REVERT: A 365 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8638 (mp) REVERT: B 223 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: B 376 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8712 (pp20) REVERT: C 111 GLU cc_start: 0.8557 (mp0) cc_final: 0.8320 (mt-10) REVERT: E 87 MET cc_start: 0.5940 (ptm) cc_final: 0.5295 (ptt) REVERT: F 32 MET cc_start: 0.9173 (mmm) cc_final: 0.8943 (mtp) REVERT: F 96 GLU cc_start: 0.8345 (tp30) cc_final: 0.8030 (pt0) REVERT: F 99 ARG cc_start: 0.8649 (ttp80) cc_final: 0.8419 (ttm-80) REVERT: M 44 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8638 (mp) REVERT: M 110 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: M 221 GLU cc_start: 0.7837 (pp20) cc_final: 0.7574 (pt0) REVERT: N 377 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8833 (mp) REVERT: P 135 LEU cc_start: 0.7410 (mt) cc_final: 0.7143 (pp) REVERT: Q 32 MET cc_start: 0.9168 (mmm) cc_final: 0.8963 (mtp) REVERT: Q 91 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: Q 99 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.8083 (ttp-110) REVERT: Q 101 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8003 (tmm160) REVERT: U 16 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7885 (mtp180) REVERT: V 16 ASN cc_start: 0.7513 (m110) cc_final: 0.7223 (m-40) REVERT: T 20 ARG cc_start: 0.8758 (ptp-110) cc_final: 0.8288 (mtm-85) REVERT: T 62 ARG cc_start: 0.8510 (mmm160) cc_final: 0.8282 (mtt180) outliers start: 72 outliers final: 45 residues processed: 552 average time/residue: 0.8153 time to fit residues: 527.9451 Evaluate side-chains 546 residues out of total 3513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 492 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain O residue 43 MET Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 6 LYS Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain Q residue 101 ARG Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 130 optimal weight: 30.0000 chunk 405 optimal weight: 0.0870 chunk 207 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 370 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 298 optimal weight: 20.0000 chunk 324 optimal weight: 6.9990 chunk 318 optimal weight: 8.9990 chunk 177 optimal weight: 30.0000 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN D 106 ASN G 36 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN O 71 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.081322 restraints weight = 53833.276| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.89 r_work: 0.2928 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.344 34541 Z= 0.155 Angle : 0.625 15.273 46834 Z= 0.309 Chirality : 0.042 0.172 5052 Planarity : 0.004 0.091 5935 Dihedral : 8.633 87.603 4926 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.08 % Allowed : 17.45 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 1.69 (0.13), residues: 4119 helix: 1.95 (0.11), residues: 2122 sheet: 0.73 (0.26), residues: 381 loop : 0.20 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG J 8 TYR 0.021 0.001 TYR N 224 PHE 0.015 0.001 PHE Q 60 TRP 0.013 0.001 TRP M 135 HIS 0.009 0.001 HIS N 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (34520) covalent geometry : angle 0.62222 / 0.31 (46818) SS BOND : bond 0.00580 / 0.27 ( 5) SS BOND : angle 1.67828 / 0.97 ( 10) hydrogen bonds : bond 0.04847 / 3.22 ( 1883) hydrogen bonds : angle 4.28892 / 3.05 ( 5397) metal coordination : bond 0.01083 / 0.56 ( 6) metal coordination : angle 4.68399 / 2.32 ( 6) Misc. bond : bond 0.18629 / 10.66 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14590.19 seconds wall clock time: 248 minutes 9.99 seconds (14889.99 seconds total)