Starting phenix.real_space_refine on Tue Mar 19 15:41:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6j_15868/03_2024/8b6j_15868_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6j_15868/03_2024/8b6j_15868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6j_15868/03_2024/8b6j_15868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6j_15868/03_2024/8b6j_15868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6j_15868/03_2024/8b6j_15868_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6j_15868/03_2024/8b6j_15868_trim_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.002 sd= 0.149 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: 7 Type Number sf(0) Gaussians Fe 10 7.16 5 P 47 5.49 5 S 169 5.16 5 C 30867 2.51 5 N 7492 2.21 5 O 8434 1.98 5 H 42507 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 89526 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 7587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 7587 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 465} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 7118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 7118 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 7075 Classifications: {'peptide': 426} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 413} Chain: "D" Number of atoms: 4832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4832 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain: "E" Number of atoms: 3893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3893 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 232} Chain: "F" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1372 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "G" Number of atoms: 5474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5474 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 312} Chain: "H" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2138 Classifications: {'peptide': 129} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "I" Number of atoms: 1998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1998 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "J" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 330 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'TRANS': 65} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'UNK:plan-1': 66} Unresolved non-hydrogen planarities: 66 Chain: "K" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1004 Classifications: {'peptide': 58} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "a" Number of atoms: 7587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 7587 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 465} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 7118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 7118 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 7074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 7074 Classifications: {'peptide': 426} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 413} Chain: "d" Number of atoms: 4832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4832 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain: "e" Number of atoms: 3891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3891 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 232} Chain: "f" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1352 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "g" Number of atoms: 5474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5474 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 312} Chain: "h" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2138 Classifications: {'peptide': 129} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "i" Number of atoms: 1998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1998 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "j" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 330 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'TRANS': 65} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'UNK:plan-1': 66} Unresolved non-hydrogen planarities: 66 Chain: "k" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1004 Classifications: {'peptide': 58} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "l" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 535 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 535 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 805 Unusual residues: {'CDL': 4, 'HEM': 2, 'PC1': 3, 'PEE': 1, 'UQ8': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 212 Unusual residues: {'CDL': 1, 'FES': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 200 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 655 Unusual residues: {'CDL': 3, 'HEM': 2, 'PC1': 4, 'UQ8': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "d" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'HEC': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 154 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 200 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29375 SG CYS E 197 100.221 111.028 140.347 1.00126.30 S ATOM 29663 SG CYS E 216 103.262 113.050 141.595 1.00125.15 S ATOM 72195 SG CYS e 197 125.403 46.505 122.429 1.00135.41 S ATOM 72262 SG CYS e 202 124.190 46.862 126.089 1.00134.66 S ATOM 72482 SG CYS e 216 125.096 44.137 125.216 1.00142.42 S ATOM 72511 SG CYS e 218 122.868 43.785 123.855 1.00139.62 S ATOM 72511 SG CYS e 218 122.868 43.785 123.855 1.00139.62 S Time building chain proxies: 30.50, per 1000 atoms: 0.34 Number of scatterers: 89526 At special positions: 0 Unit cell: (172.5, 167.5, 190, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 10 26.01 S 169 16.00 P 47 15.00 O 8434 8.00 N 7492 7.00 C 30867 6.00 H 42507 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM88042 OA2 CDL H1301 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 61.77 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" ND1 HIS E 199 " pdb="FE2 FES E 301 " - pdb=" ND1 HIS E 219 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 197 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 216 " pdb=" FES e 301 " pdb="FE2 FES e 301 " - pdb=" ND1 HIS e 199 " pdb="FE2 FES e 301 " - pdb=" ND1 HIS e 219 " pdb="FE1 FES e 301 " - pdb=" SG CYS e 218 " pdb="FE1 FES e 301 " - pdb=" SG CYS e 202 " pdb="FE1 FES e 301 " - pdb=" SG CYS e 216 " pdb="FE1 FES e 301 " - pdb=" SG CYS e 197 " Number of angles added : 13 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10270 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 221 helices and 14 sheets defined 47.2% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.63 Creating SS restraints... Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.673A pdb=" N VAL A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLU A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A 162 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 163 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 165 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 182 through 193 removed outlier: 3.629A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 230 through 239 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 256 through 269 removed outlier: 4.943A pdb=" N THR A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 385 through 403 removed outlier: 4.950A pdb=" N ASN A 389 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 391 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 392 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 394 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER A 395 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN A 396 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 398 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 399 " --> pdb=" O GLN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 428 through 442 Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 508 through 511 No H-bonds generated for 'chain 'A' and resid 508 through 511' Processing helix chain 'B' and resid 24 through 31 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 160 through 172 Processing helix chain 'B' and resid 177 through 197 removed outlier: 3.594A pdb=" N GLU B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 212 Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 233 through 243 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 259 through 270 removed outlier: 3.892A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 329 removed outlier: 3.771A pdb=" N VAL B 320 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 369 through 388 removed outlier: 5.686A pdb=" N LYS B 373 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 377 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS B 378 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 411 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 432 through 441 removed outlier: 3.749A pdb=" N TYR B 435 " --> pdb=" O HIS B 432 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL B 436 " --> pdb=" O THR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.514A pdb=" N THR B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 481 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 31 through 53 removed outlier: 3.918A pdb=" N PHE C 34 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLY C 35 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 40 " --> pdb=" O PHE C 37 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 46 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 48 " --> pdb=" O GLN C 45 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY C 49 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 72 Proline residue: C 64 - end of helix removed outlier: 3.645A pdb=" N VAL C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 104 removed outlier: 3.522A pdb=" N ASP C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 137 removed outlier: 4.955A pdb=" N ALA C 114 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS C 117 " --> pdb=" O ALA C 114 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER C 118 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE C 121 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 157 removed outlier: 3.799A pdb=" N PHE C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE C 157 " --> pdb=" O TYR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 175 through 206 removed outlier: 3.806A pdb=" N ALA C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR C 194 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR C 205 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASP C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 248 removed outlier: 3.604A pdb=" N ASN C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 247 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 261 removed outlier: 3.733A pdb=" N PHE C 260 " --> pdb=" O TYR C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 Proline residue: C 284 - end of helix Processing helix chain 'C' and resid 295 through 310 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 332 through 336 Processing helix chain 'C' and resid 353 through 369 Processing helix chain 'C' and resid 386 through 398 Processing helix chain 'C' and resid 402 through 405 No H-bonds generated for 'chain 'C' and resid 402 through 405' Processing helix chain 'C' and resid 409 through 425 removed outlier: 3.560A pdb=" N LEU C 414 " --> pdb=" O THR C 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 92 through 95 Processing helix chain 'D' and resid 102 through 111 removed outlier: 4.184A pdb=" N ASP D 111 " --> pdb=" O GLN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 171 through 180 removed outlier: 3.638A pdb=" N ILE D 175 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN D 177 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 178 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER D 179 " --> pdb=" O TYR D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'D' and resid 250 through 282 Proline residue: D 269 - end of helix removed outlier: 4.229A pdb=" N ALA D 277 " --> pdb=" O PHE D 273 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 302 No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 310 through 313 No H-bonds generated for 'chain 'D' and resid 310 through 313' Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 73 through 76 No H-bonds generated for 'chain 'E' and resid 73 through 76' Processing helix chain 'E' and resid 85 through 118 Processing helix chain 'E' and resid 159 through 165 Processing helix chain 'F' and resid 20 through 28 removed outlier: 3.998A pdb=" N LYS F 25 " --> pdb=" O GLU F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 47 Processing helix chain 'F' and resid 59 through 79 removed outlier: 3.751A pdb=" N CYS F 71 " --> pdb=" O CYS F 67 " (cutoff:3.500A) Proline residue: F 74 - end of helix removed outlier: 3.707A pdb=" N ASN F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 12 Processing helix chain 'G' and resid 16 through 18 No H-bonds generated for 'chain 'G' and resid 16 through 18' Processing helix chain 'G' and resid 35 through 47 Processing helix chain 'G' and resid 50 through 58 Processing helix chain 'G' and resid 60 through 66 Processing helix chain 'G' and resid 68 through 78 removed outlier: 3.512A pdb=" N ARG G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.925A pdb=" N LEU G 86 " --> pdb=" O GLU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 97 through 106 Processing helix chain 'G' and resid 109 through 128 removed outlier: 4.000A pdb=" N MET G 115 " --> pdb=" O THR G 111 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG G 119 " --> pdb=" O MET G 115 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR G 122 " --> pdb=" O ARG G 118 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL G 125 " --> pdb=" O ARG G 121 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY G 128 " --> pdb=" O LYS G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 144 removed outlier: 3.662A pdb=" N GLU G 141 " --> pdb=" O TRP G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 164 Processing helix chain 'G' and resid 183 through 186 No H-bonds generated for 'chain 'G' and resid 183 through 186' Processing helix chain 'G' and resid 195 through 199 Processing helix chain 'G' and resid 213 through 219 Processing helix chain 'G' and resid 232 through 248 Processing helix chain 'G' and resid 262 through 272 Processing helix chain 'G' and resid 282 through 296 removed outlier: 3.659A pdb=" N ALA G 296 " --> pdb=" O LEU G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 318 No H-bonds generated for 'chain 'G' and resid 316 through 318' Processing helix chain 'H' and resid 33 through 36 Processing helix chain 'H' and resid 45 through 48 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 79 through 82 No H-bonds generated for 'chain 'H' and resid 79 through 82' Processing helix chain 'H' and resid 97 through 126 removed outlier: 5.986A pdb=" N PHE H 102 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Proline residue: H 103 - end of helix Processing helix chain 'I' and resid 24 through 26 No H-bonds generated for 'chain 'I' and resid 24 through 26' Processing helix chain 'I' and resid 46 through 58 Processing helix chain 'I' and resid 63 through 92 Proline residue: I 84 - end of helix Processing helix chain 'I' and resid 94 through 96 No H-bonds generated for 'chain 'I' and resid 94 through 96' Processing helix chain 'I' and resid 98 through 114 Processing helix chain 'K' and resid 6 through 34 removed outlier: 3.641A pdb=" N GLY K 23 " --> pdb=" O LYS K 19 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR K 24 " --> pdb=" O ARG K 20 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY K 25 " --> pdb=" O TYR K 21 " (cutoff:3.500A) Proline residue: K 26 - end of helix Processing helix chain 'K' and resid 37 through 44 Processing helix chain 'a' and resid 56 through 59 Processing helix chain 'a' and resid 96 through 98 No H-bonds generated for 'chain 'a' and resid 96 through 98' Processing helix chain 'a' and resid 101 through 103 No H-bonds generated for 'chain 'a' and resid 101 through 103' Processing helix chain 'a' and resid 106 through 116 removed outlier: 3.545A pdb=" N ARG a 112 " --> pdb=" O GLN a 108 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU a 115 " --> pdb=" O GLN a 111 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 132 Processing helix chain 'a' and resid 154 through 169 removed outlier: 3.604A pdb=" N VAL a 157 " --> pdb=" O PRO a 154 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU a 158 " --> pdb=" O GLU a 155 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY a 165 " --> pdb=" O ASP a 162 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE a 167 " --> pdb=" O LEU a 164 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU a 168 " --> pdb=" O GLY a 165 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 194 removed outlier: 4.293A pdb=" N GLU a 183 " --> pdb=" O GLU a 179 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA a 184 " --> pdb=" O ALA a 180 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN a 193 " --> pdb=" O ALA a 189 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASN a 194 " --> pdb=" O LEU a 190 " (cutoff:3.500A) Processing helix chain 'a' and resid 196 through 208 Processing helix chain 'a' and resid 213 through 215 No H-bonds generated for 'chain 'a' and resid 213 through 215' Processing helix chain 'a' and resid 222 through 227 removed outlier: 4.224A pdb=" N HIS a 226 " --> pdb=" O ARG a 222 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN a 227 " --> pdb=" O GLU a 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 222 through 227' Processing helix chain 'a' and resid 230 through 240 Processing helix chain 'a' and resid 243 through 245 No H-bonds generated for 'chain 'a' and resid 243 through 245' Processing helix chain 'a' and resid 256 through 267 Processing helix chain 'a' and resid 319 through 328 Processing helix chain 'a' and resid 336 through 338 No H-bonds generated for 'chain 'a' and resid 336 through 338' Processing helix chain 'a' and resid 350 through 357 removed outlier: 3.544A pdb=" N GLU a 354 " --> pdb=" O LEU a 350 " (cutoff:3.500A) Processing helix chain 'a' and resid 385 through 403 removed outlier: 5.358A pdb=" N ASN a 389 " --> pdb=" O ILE a 386 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE a 393 " --> pdb=" O GLN a 390 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU a 394 " --> pdb=" O MET a 391 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER a 395 " --> pdb=" O LEU a 392 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN a 396 " --> pdb=" O PHE a 393 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE a 398 " --> pdb=" O SER a 395 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER a 400 " --> pdb=" O MET a 397 " (cutoff:3.500A) Processing helix chain 'a' and resid 408 through 423 Processing helix chain 'a' and resid 428 through 442 Processing helix chain 'a' and resid 448 through 456 Processing helix chain 'a' and resid 460 through 470 Processing helix chain 'a' and resid 495 through 500 Processing helix chain 'a' and resid 508 through 511 No H-bonds generated for 'chain 'a' and resid 508 through 511' Processing helix chain 'b' and resid 24 through 31 Processing helix chain 'b' and resid 40 through 45 Processing helix chain 'b' and resid 109 through 115 Processing helix chain 'b' and resid 126 through 136 removed outlier: 3.669A pdb=" N VAL b 133 " --> pdb=" O ASN b 129 " (cutoff:3.500A) Processing helix chain 'b' and resid 160 through 172 Processing helix chain 'b' and resid 177 through 197 Processing helix chain 'b' and resid 200 through 212 removed outlier: 3.619A pdb=" N SER b 206 " --> pdb=" O LEU b 202 " (cutoff:3.500A) Processing helix chain 'b' and resid 216 through 218 No H-bonds generated for 'chain 'b' and resid 216 through 218' Processing helix chain 'b' and resid 225 through 230 removed outlier: 3.513A pdb=" N VAL b 228 " --> pdb=" O ARG b 225 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS b 229 " --> pdb=" O GLY b 226 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 243 Processing helix chain 'b' and resid 246 through 248 No H-bonds generated for 'chain 'b' and resid 246 through 248' Processing helix chain 'b' and resid 259 through 270 removed outlier: 3.716A pdb=" N LYS b 269 " --> pdb=" O LEU b 265 " (cutoff:3.500A) Processing helix chain 'b' and resid 319 through 331 Processing helix chain 'b' and resid 333 through 337 Processing helix chain 'b' and resid 372 through 388 removed outlier: 3.862A pdb=" N ILE b 386 " --> pdb=" O GLU b 382 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA b 387 " --> pdb=" O LEU b 383 " (cutoff:3.500A) Processing helix chain 'b' and resid 392 through 411 Processing helix chain 'b' and resid 413 through 426 Processing helix chain 'b' and resid 435 through 441 Processing helix chain 'b' and resid 444 through 456 removed outlier: 3.594A pdb=" N THR b 456 " --> pdb=" O ALA b 452 " (cutoff:3.500A) Processing helix chain 'b' and resid 474 through 481 Processing helix chain 'c' and resid 13 through 21 Processing helix chain 'c' and resid 30 through 53 removed outlier: 4.189A pdb=" N PHE c 34 " --> pdb=" O ASN c 31 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLY c 35 " --> pdb=" O SER c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 60 through 73 Proline residue: c 64 - end of helix removed outlier: 4.099A pdb=" N VAL c 72 " --> pdb=" O GLU c 68 " (cutoff:3.500A) Processing helix chain 'c' and resid 77 through 104 Processing helix chain 'c' and resid 110 through 137 removed outlier: 4.865A pdb=" N ALA c 114 " --> pdb=" O GLU c 111 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS c 117 " --> pdb=" O ALA c 114 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER c 118 " --> pdb=" O ALA c 115 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE c 121 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL c 129 " --> pdb=" O PHE c 126 " (cutoff:3.500A) Processing helix chain 'c' and resid 140 through 155 Processing helix chain 'c' and resid 169 through 171 No H-bonds generated for 'chain 'c' and resid 169 through 171' Processing helix chain 'c' and resid 175 through 206 removed outlier: 3.809A pdb=" N ALA c 193 " --> pdb=" O ALA c 189 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR c 194 " --> pdb=" O PHE c 190 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS c 204 " --> pdb=" O GLY c 200 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR c 205 " --> pdb=" O VAL c 201 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP c 206 " --> pdb=" O ASP c 202 " (cutoff:3.500A) Processing helix chain 'c' and resid 225 through 248 removed outlier: 3.874A pdb=" N ASN c 229 " --> pdb=" O GLU c 225 " (cutoff:3.500A) Processing helix chain 'c' and resid 257 through 261 removed outlier: 3.706A pdb=" N PHE c 260 " --> pdb=" O TYR c 257 " (cutoff:3.500A) Processing helix chain 'c' and resid 280 through 291 Proline residue: c 284 - end of helix Processing helix chain 'c' and resid 295 through 310 Processing helix chain 'c' and resid 312 through 316 Processing helix chain 'c' and resid 332 through 336 Processing helix chain 'c' and resid 354 through 369 Processing helix chain 'c' and resid 386 through 398 Processing helix chain 'c' and resid 409 through 425 Processing helix chain 'd' and resid 34 through 36 No H-bonds generated for 'chain 'd' and resid 34 through 36' Processing helix chain 'd' and resid 67 through 77 Processing helix chain 'd' and resid 92 through 95 Processing helix chain 'd' and resid 102 through 111 removed outlier: 4.286A pdb=" N ASP d 111 " --> pdb=" O GLN d 107 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 118 No H-bonds generated for 'chain 'd' and resid 116 through 118' Processing helix chain 'd' and resid 147 through 153 Processing helix chain 'd' and resid 171 through 180 removed outlier: 3.673A pdb=" N ILE d 175 " --> pdb=" O ILE d 172 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE d 178 " --> pdb=" O ILE d 175 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER d 179 " --> pdb=" O TYR d 176 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 205 No H-bonds generated for 'chain 'd' and resid 203 through 205' Processing helix chain 'd' and resid 228 through 242 Processing helix chain 'd' and resid 250 through 282 Proline residue: d 269 - end of helix removed outlier: 4.308A pdb=" N ALA d 277 " --> pdb=" O PHE d 273 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR d 278 " --> pdb=" O LYS d 274 " (cutoff:3.500A) Processing helix chain 'd' and resid 299 through 302 No H-bonds generated for 'chain 'd' and resid 299 through 302' Processing helix chain 'd' and resid 310 through 313 No H-bonds generated for 'chain 'd' and resid 310 through 313' Processing helix chain 'e' and resid 28 through 33 Processing helix chain 'e' and resid 73 through 76 No H-bonds generated for 'chain 'e' and resid 73 through 76' Processing helix chain 'e' and resid 85 through 118 Processing helix chain 'e' and resid 159 through 166 removed outlier: 3.676A pdb=" N LYS e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU e 164 " --> pdb=" O ASN e 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 14 Processing helix chain 'f' and resid 20 through 47 Proline residue: f 29 - end of helix removed outlier: 3.991A pdb=" N THR f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ALA f 33 " --> pdb=" O PRO f 29 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP f 34 " --> pdb=" O GLN f 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 79 removed outlier: 3.790A pdb=" N CYS f 71 " --> pdb=" O CYS f 67 " (cutoff:3.500A) Proline residue: f 74 - end of helix removed outlier: 3.653A pdb=" N ASN f 79 " --> pdb=" O ALA f 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 8 through 13 Processing helix chain 'g' and resid 16 through 18 No H-bonds generated for 'chain 'g' and resid 16 through 18' Processing helix chain 'g' and resid 35 through 47 Processing helix chain 'g' and resid 50 through 58 Processing helix chain 'g' and resid 60 through 67 Processing helix chain 'g' and resid 69 through 77 Processing helix chain 'g' and resid 83 through 86 No H-bonds generated for 'chain 'g' and resid 83 through 86' Processing helix chain 'g' and resid 90 through 94 Processing helix chain 'g' and resid 97 through 106 Processing helix chain 'g' and resid 109 through 126 removed outlier: 4.810A pdb=" N PHE g 114 " --> pdb=" O THR g 111 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG g 118 " --> pdb=" O MET g 115 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS g 124 " --> pdb=" O ARG g 121 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU g 126 " --> pdb=" O TYR g 123 " (cutoff:3.500A) Processing helix chain 'g' and resid 136 through 144 removed outlier: 3.524A pdb=" N GLU g 141 " --> pdb=" O TRP g 137 " (cutoff:3.500A) Processing helix chain 'g' and resid 147 through 164 removed outlier: 3.807A pdb=" N ASP g 152 " --> pdb=" O SER g 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 183 through 186 No H-bonds generated for 'chain 'g' and resid 183 through 186' Processing helix chain 'g' and resid 195 through 199 Processing helix chain 'g' and resid 213 through 220 removed outlier: 3.625A pdb=" N ASN g 220 " --> pdb=" O LYS g 216 " (cutoff:3.500A) Processing helix chain 'g' and resid 232 through 248 Processing helix chain 'g' and resid 262 through 272 Processing helix chain 'g' and resid 282 through 295 Processing helix chain 'h' and resid 34 through 36 No H-bonds generated for 'chain 'h' and resid 34 through 36' Processing helix chain 'h' and resid 45 through 48 removed outlier: 3.613A pdb=" N TYR h 48 " --> pdb=" O VAL h 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 45 through 48' Processing helix chain 'h' and resid 65 through 67 No H-bonds generated for 'chain 'h' and resid 65 through 67' Processing helix chain 'h' and resid 79 through 82 No H-bonds generated for 'chain 'h' and resid 79 through 82' Processing helix chain 'h' and resid 97 through 126 removed outlier: 5.933A pdb=" N PHE h 102 " --> pdb=" O ARG h 98 " (cutoff:3.500A) Proline residue: h 103 - end of helix Processing helix chain 'i' and resid 46 through 58 Processing helix chain 'i' and resid 63 through 92 Proline residue: i 84 - end of helix Processing helix chain 'i' and resid 94 through 96 No H-bonds generated for 'chain 'i' and resid 94 through 96' Processing helix chain 'i' and resid 98 through 115 Processing helix chain 'k' and resid 6 through 34 removed outlier: 3.604A pdb=" N GLY k 23 " --> pdb=" O LYS k 19 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR k 24 " --> pdb=" O ARG k 20 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY k 25 " --> pdb=" O TYR k 21 " (cutoff:3.500A) Proline residue: k 26 - end of helix Processing helix chain 'k' and resid 37 through 46 Processing helix chain 'l' and resid 5 through 33 Proline residue: l 18 - end of helix Processing helix chain 'L' and resid 5 through 33 Proline residue: L 18 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 65 through 68 removed outlier: 3.875A pdb=" N GLY A 252 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN A 136 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 290 through 295 Processing sheet with id= C, first strand: chain 'B' and resid 68 through 72 removed outlier: 3.532A pdb=" N THR B 148 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 293 through 297 removed outlier: 6.465A pdb=" N PHE B 461 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASN B 296 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA B 463 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER B 368 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE B 345 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 326 through 328 Processing sheet with id= F, first strand: chain 'E' and resid 130 through 132 removed outlier: 3.717A pdb=" N VAL E 132 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL E 252 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 142 through 147 Processing sheet with id= H, first strand: chain 'a' and resid 65 through 68 removed outlier: 3.813A pdb=" N GLY a 252 " --> pdb=" O GLU a 78 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'a' and resid 290 through 295 Processing sheet with id= J, first strand: chain 'b' and resid 68 through 72 removed outlier: 3.575A pdb=" N THR b 78 " --> pdb=" O ILE b 249 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'b' and resid 293 through 297 removed outlier: 6.669A pdb=" N PHE b 461 " --> pdb=" O VAL b 294 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ASN b 296 " --> pdb=" O PHE b 461 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA b 463 " --> pdb=" O ASN b 296 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER b 368 " --> pdb=" O PHE b 345 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE b 345 " --> pdb=" O SER b 368 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'c' and resid 326 through 328 removed outlier: 3.811A pdb=" N ILE c 341 " --> pdb=" O ARG c 327 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'e' and resid 130 through 133 Processing sheet with id= N, first strand: chain 'e' and resid 142 through 147 1740 hydrogen bonds defined for protein. 4671 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: 28.33 Time building geometry restraints manager: 64.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.12: 42461 1.12 - 1.40: 20060 1.40 - 1.68: 27895 1.68 - 1.96: 274 1.96 - 2.24: 32 Bond restraints: 90722 Sorted by residual: bond pdb=" OA3 CDL g 801 " pdb=" PA1 CDL g 801 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.00e-02 1.00e+04 2.67e+01 bond pdb=" OA3 CDL c 507 " pdb=" PA1 CDL c 507 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.00e-02 1.00e+04 2.66e+01 bond pdb=" OA3 CDL E 304 " pdb=" PA1 CDL E 304 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.00e-02 1.00e+04 2.61e+01 bond pdb=" OA3 CDL H1302 " pdb=" PA1 CDL H1302 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.00e-02 1.00e+04 2.61e+01 bond pdb=" OB3 CDL c 503 " pdb=" PB2 CDL c 503 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.00e-02 1.00e+04 2.61e+01 ... (remaining 90717 not shown) Histogram of bond angle deviations from ideal: 87.98 - 106.30: 1721 106.30 - 124.63: 155440 124.63 - 142.95: 3929 142.95 - 161.27: 0 161.27 - 179.59: 12 Bond angle restraints: 161102 Sorted by residual: angle pdb="FE1 FES e 301 " pdb=" S2 FES e 301 " pdb="FE2 FES e 301 " ideal model delta sigma weight residual 75.66 89.63 -13.97 1.14e+00 7.69e-01 1.50e+02 angle pdb=" S1 FES e 301 " pdb="FE2 FES e 301 " pdb=" S2 FES e 301 " ideal model delta sigma weight residual 104.33 90.36 13.97 1.14e+00 7.69e-01 1.50e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 90.70 13.63 1.14e+00 7.69e-01 1.43e+02 angle pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " pdb="FE2 FES E 301 " ideal model delta sigma weight residual 75.66 89.27 -13.61 1.14e+00 7.69e-01 1.42e+02 angle pdb="FE1 FES e 301 " pdb=" S1 FES e 301 " pdb="FE2 FES e 301 " ideal model delta sigma weight residual 75.66 89.60 -13.94 1.20e+00 6.94e-01 1.35e+02 ... (remaining 161097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 42286 34.80 - 69.60: 1739 69.60 - 104.41: 50 104.41 - 139.21: 9 139.21 - 174.01: 6 Dihedral angle restraints: 44090 sinusoidal: 23992 harmonic: 20098 Sorted by residual: dihedral pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " pdb=" CBB HEC D 401 " ideal model delta sinusoidal sigma weight residual -120.00 -55.81 -64.19 2 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" C36 UQ8 C 510 " pdb=" C37 UQ8 C 510 " pdb=" C38 UQ8 C 510 " pdb=" C39 UQ8 C 510 " ideal model delta sinusoidal sigma weight residual 112.38 -73.61 -174.01 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 UQ8 c 508 " pdb=" C27 UQ8 c 508 " pdb=" C28 UQ8 c 508 " pdb=" C29 UQ8 c 508 " ideal model delta sinusoidal sigma weight residual 101.99 -71.89 173.88 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 44087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 5626 0.051 - 0.102: 781 0.102 - 0.152: 180 0.152 - 0.203: 1 0.203 - 0.254: 2 Chirality restraints: 6590 Sorted by residual: chirality pdb=" C2 PEE L 401 " pdb=" C1 PEE L 401 " pdb=" C3 PEE L 401 " pdb=" O2 PEE L 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C2 PEE C 512 " pdb=" C1 PEE C 512 " pdb=" C3 PEE C 512 " pdb=" O2 PEE C 512 " both_signs ideal model delta sigma weight residual False -2.33 -2.55 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE B 80 " pdb=" N ILE B 80 " pdb=" C ILE B 80 " pdb=" CB ILE B 80 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 6587 not shown) Planarity restraints: 13133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ8 c 508 " -0.005 2.00e-02 2.50e+03 1.36e-01 5.59e+02 pdb=" C1M UQ8 c 508 " 0.020 2.00e-02 2.50e+03 pdb=" C2 UQ8 c 508 " -0.043 2.00e-02 2.50e+03 pdb=" C3 UQ8 c 508 " 0.027 2.00e-02 2.50e+03 pdb=" C4 UQ8 c 508 " 0.052 2.00e-02 2.50e+03 pdb=" C5 UQ8 c 508 " -0.080 2.00e-02 2.50e+03 pdb=" C6 UQ8 c 508 " 0.056 2.00e-02 2.50e+03 pdb=" C7 UQ8 c 508 " 0.211 2.00e-02 2.50e+03 pdb=" O2 UQ8 c 508 " -0.137 2.00e-02 2.50e+03 pdb=" O3 UQ8 c 508 " 0.041 2.00e-02 2.50e+03 pdb=" O4 UQ8 c 508 " 0.187 2.00e-02 2.50e+03 pdb=" O5 UQ8 c 508 " -0.329 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ8 C 511 " -0.032 2.00e-02 2.50e+03 4.42e-02 5.87e+01 pdb=" C1M UQ8 C 511 " -0.076 2.00e-02 2.50e+03 pdb=" C2 UQ8 C 511 " -0.004 2.00e-02 2.50e+03 pdb=" C3 UQ8 C 511 " 0.004 2.00e-02 2.50e+03 pdb=" C4 UQ8 C 511 " -0.007 2.00e-02 2.50e+03 pdb=" C5 UQ8 C 511 " -0.014 2.00e-02 2.50e+03 pdb=" C6 UQ8 C 511 " 0.024 2.00e-02 2.50e+03 pdb=" C7 UQ8 C 511 " 0.103 2.00e-02 2.50e+03 pdb=" O2 UQ8 C 511 " 0.024 2.00e-02 2.50e+03 pdb=" O3 UQ8 C 511 " 0.045 2.00e-02 2.50e+03 pdb=" O4 UQ8 C 511 " -0.019 2.00e-02 2.50e+03 pdb=" O5 UQ8 C 511 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ8 C 510 " 0.002 2.00e-02 2.50e+03 3.47e-02 3.60e+01 pdb=" C1M UQ8 C 510 " 0.017 2.00e-02 2.50e+03 pdb=" C2 UQ8 C 510 " -0.018 2.00e-02 2.50e+03 pdb=" C3 UQ8 C 510 " 0.001 2.00e-02 2.50e+03 pdb=" C4 UQ8 C 510 " 0.004 2.00e-02 2.50e+03 pdb=" C5 UQ8 C 510 " -0.021 2.00e-02 2.50e+03 pdb=" C6 UQ8 C 510 " 0.015 2.00e-02 2.50e+03 pdb=" C7 UQ8 C 510 " 0.049 2.00e-02 2.50e+03 pdb=" O2 UQ8 C 510 " -0.054 2.00e-02 2.50e+03 pdb=" O3 UQ8 C 510 " 0.043 2.00e-02 2.50e+03 pdb=" O4 UQ8 C 510 " 0.034 2.00e-02 2.50e+03 pdb=" O5 UQ8 C 510 " -0.070 2.00e-02 2.50e+03 ... (remaining 13130 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.89: 518 1.89 - 2.57: 82250 2.57 - 3.25: 278824 3.25 - 3.92: 350178 3.92 - 4.60: 569237 Nonbonded interactions: 1281007 Sorted by model distance: nonbonded pdb=" HG1 THR G 176 " pdb=" O ASP G 185 " model vdw 1.214 1.850 nonbonded pdb=" HG SER A 428 " pdb=" OE2 GLU B 411 " model vdw 1.242 1.850 nonbonded pdb=" HZ1 LYS B 403 " pdb=" OD1 ASP B 440 " model vdw 1.258 1.850 nonbonded pdb=" HG1 THR g 176 " pdb=" O ASP g 185 " model vdw 1.314 1.850 nonbonded pdb=" HH TYR D 65 " pdb=" OD1 ASN D 240 " model vdw 1.334 1.850 ... (remaining 1281002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 513) selection = (chain 'a' and resid 32 through 513) } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = (chain 'C' and (resid 1 through 278 or (resid 279 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 280 through 426 or resid 501 through 503)) selection = (chain 'c' and (resid 1 through 426 or resid 501 through 503)) } ncs_group { reference = (chain 'D' and resid 25 through 319) selection = (chain 'd' and resid 25 through 319) } ncs_group { reference = (chain 'E' and (resid 25 through 201 or (resid 202 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 203 through 217 or (resid 218 and (name N or name CA or name C or na \ me O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or res \ id 219 through 269 or resid 301)) selection = chain 'e' } ncs_group { reference = (chain 'F' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 3 through 86 \ )) selection = chain 'f' } ncs_group { reference = chain 'G' selection = (chain 'g' and resid 2 through 328) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = (chain 'L' and resid 3 through 34) selection = chain 'l' } 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: 5.740 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: 1.020 Extract box with map and model: 24.830 Check model and map are aligned: 1.010 Set scattering table: 0.630 Process input model: 243.630 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.730 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 290.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 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 : 0.004 0.058 48215 Z= 0.221 Angle : 0.536 13.970 64895 Z= 0.278 Chirality : 0.038 0.254 6590 Planarity : 0.004 0.136 8046 Dihedral : 15.549 174.009 18675 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.67 % Allowed : 4.37 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.12), residues: 5265 helix: 1.72 (0.11), residues: 2534 sheet: 0.46 (0.26), residues: 408 loop : -0.07 (0.13), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 360 HIS 0.004 0.001 HIS i 79 PHE 0.011 0.001 PHE h 100 TYR 0.016 0.001 TYR h 108 ARG 0.003 0.000 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Evaluate side-chains 1442 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1411 time to evaluate : 5.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.6689 (tttt) cc_final: 0.6466 (tptt) REVERT: A 438 GLN cc_start: 0.7545 (mt0) cc_final: 0.7269 (mt0) REVERT: B 184 VAL cc_start: 0.7919 (t) cc_final: 0.7652 (p) REVERT: C 34 PHE cc_start: 0.7708 (m-80) cc_final: 0.6908 (m-80) REVERT: C 105 LEU cc_start: 0.6700 (mt) cc_final: 0.6476 (mt) REVERT: C 373 LEU cc_start: 0.4431 (OUTLIER) cc_final: 0.4220 (tp) REVERT: D 89 TYR cc_start: 0.5942 (m-10) cc_final: 0.5401 (m-10) REVERT: E 161 GLU cc_start: 0.5636 (mt-10) cc_final: 0.4776 (mm-30) REVERT: G 16 LYS cc_start: 0.7689 (mttt) cc_final: 0.7248 (mptt) REVERT: H 93 TYR cc_start: 0.6467 (t80) cc_final: 0.6109 (t80) REVERT: I 79 HIS cc_start: 0.5774 (OUTLIER) cc_final: 0.5382 (m-70) REVERT: K 2 TYR cc_start: 0.5553 (t80) cc_final: 0.5237 (t80) REVERT: a 48 GLU cc_start: 0.5645 (tp30) cc_final: 0.5367 (mm-30) REVERT: b 118 LEU cc_start: 0.6661 (mt) cc_final: 0.5969 (mt) REVERT: b 159 ASP cc_start: 0.6194 (m-30) cc_final: 0.5903 (m-30) REVERT: c 286 MET cc_start: 0.5723 (tmm) cc_final: 0.5513 (mpt) REVERT: d 100 TYR cc_start: 0.5969 (m-80) cc_final: 0.5736 (m-80) REVERT: d 112 PHE cc_start: 0.7036 (m-80) cc_final: 0.6825 (m-80) REVERT: e 258 LYS cc_start: 0.8308 (mttt) cc_final: 0.7768 (mtpt) REVERT: g 45 ASN cc_start: 0.7228 (m-40) cc_final: 0.7008 (m-40) REVERT: g 115 MET cc_start: 0.7750 (mmm) cc_final: 0.7530 (mmp) REVERT: h 48 TYR cc_start: 0.7724 (m-80) cc_final: 0.7054 (m-80) REVERT: i 2 VAL cc_start: 0.7623 (m) cc_final: 0.7411 (m) REVERT: k 42 ASN cc_start: 0.7044 (m-40) cc_final: 0.6799 (m110) REVERT: k 53 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7310 (mtm-85) outliers start: 31 outliers final: 5 residues processed: 1432 average time/residue: 2.3829 time to fit residues: 4405.2694 Evaluate side-chains 713 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 706 time to evaluate : 5.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain e residue 59 ASN Chi-restraints excluded: chain l residue 14 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 449 optimal weight: 10.0000 chunk 403 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 416 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 253 optimal weight: 10.0000 chunk 310 optimal weight: 2.9990 chunk 483 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 170 ASN A 396 GLN B 423 ASN C 18 GLN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 140 HIS C 209 ASN ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN D 53 HIS D 118 HIS ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 HIS ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN a 281 ASN a 485 HIS b 135 GLN b 188 GLN b 247 ASN b 331 ASN b 432 HIS c 112 GLN c 321 GLN e 59 ASN ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 261 HIS f 10 GLN g 48 ASN g 195 ASN g 217 GLN g 273 ASN h 67 ASN h 90 GLN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.157 48215 Z= 0.405 Angle : 0.830 19.836 64895 Z= 0.409 Chirality : 0.047 0.366 6590 Planarity : 0.006 0.096 8046 Dihedral : 17.175 176.601 8397 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 3.68 % Allowed : 14.44 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.11), residues: 5265 helix: 0.39 (0.10), residues: 2556 sheet: 0.09 (0.26), residues: 376 loop : -0.72 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 158 HIS 0.015 0.002 HIS C 199 PHE 0.055 0.003 PHE d 145 TYR 0.027 0.002 TYR a 382 ARG 0.018 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Evaluate side-chains 961 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 790 time to evaluate : 5.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7279 (ttp) cc_final: 0.6878 (ttp) REVERT: A 315 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7584 (t70) REVERT: B 126 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7169 (tp30) REVERT: C 162 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8122 (mtmt) REVERT: C 203 MET cc_start: 0.8907 (pp-130) cc_final: 0.8694 (pp-130) REVERT: C 234 MET cc_start: 0.7442 (ttt) cc_final: 0.7219 (ttt) REVERT: D 34 PHE cc_start: 0.8249 (t80) cc_final: 0.7938 (t80) REVERT: D 209 MET cc_start: 0.8689 (ttp) cc_final: 0.8482 (ttp) REVERT: D 219 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7447 (m-30) REVERT: D 254 MET cc_start: 0.8142 (tpt) cc_final: 0.7720 (tpt) REVERT: E 37 LYS cc_start: 0.7047 (mttt) cc_final: 0.6444 (tttp) REVERT: E 46 ASP cc_start: 0.6741 (t70) cc_final: 0.6381 (t0) REVERT: E 161 GLU cc_start: 0.5888 (mt-10) cc_final: 0.4845 (mp0) REVERT: E 183 SER cc_start: 0.6032 (m) cc_final: 0.5582 (p) REVERT: F 58 MET cc_start: 0.7952 (ttm) cc_final: 0.7650 (tmm) REVERT: G 16 LYS cc_start: 0.8097 (mttt) cc_final: 0.7618 (mptt) REVERT: G 85 SER cc_start: 0.8202 (t) cc_final: 0.7912 (p) REVERT: G 184 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8553 (mt) REVERT: H 42 ASN cc_start: 0.7748 (t0) cc_final: 0.7288 (t0) REVERT: H 116 ARG cc_start: 0.6333 (tpt170) cc_final: 0.5324 (ptt90) REVERT: I 79 HIS cc_start: 0.6352 (OUTLIER) cc_final: 0.5866 (m90) REVERT: I 89 TYR cc_start: 0.7435 (t80) cc_final: 0.7218 (t80) REVERT: I 97 SER cc_start: 0.8042 (m) cc_final: 0.7775 (p) REVERT: I 110 LYS cc_start: 0.7642 (ttmt) cc_final: 0.6992 (tppt) REVERT: K 45 TYR cc_start: 0.8791 (m-80) cc_final: 0.8416 (m-80) REVERT: a 35 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6003 (tpt-90) REVERT: a 60 TYR cc_start: 0.7757 (m-80) cc_final: 0.7474 (m-80) REVERT: a 274 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: a 299 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7225 (mtp) REVERT: a 344 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7657 (p) REVERT: a 350 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8182 (mm) REVERT: a 410 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7476 (mm-30) REVERT: b 261 GLU cc_start: 0.6517 (tp30) cc_final: 0.6251 (tp30) REVERT: b 390 VAL cc_start: 0.7534 (m) cc_final: 0.7306 (m) REVERT: c 25 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8512 (p) REVERT: c 86 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8497 (tpp-160) REVERT: c 299 LEU cc_start: 0.8836 (tp) cc_final: 0.8605 (tt) REVERT: d 103 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7155 (mt) REVERT: d 127 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7101 (mt0) REVERT: d 128 GLU cc_start: 0.6917 (mp0) cc_final: 0.6501 (pm20) REVERT: d 205 MET cc_start: 0.7177 (mtt) cc_final: 0.6871 (mtt) REVERT: d 231 MET cc_start: 0.8311 (ttp) cc_final: 0.8069 (mtm) REVERT: g 57 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7215 (mtt90) REVERT: g 129 LEU cc_start: 0.6426 (tp) cc_final: 0.6198 (tt) REVERT: h 48 TYR cc_start: 0.8248 (m-80) cc_final: 0.7922 (m-80) REVERT: h 66 SER cc_start: 0.8551 (m) cc_final: 0.8123 (p) REVERT: h 114 THR cc_start: 0.6346 (p) cc_final: 0.6066 (p) REVERT: i 58 ASN cc_start: 0.7653 (m-40) cc_final: 0.7101 (m-40) REVERT: i 99 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6293 (mm-30) REVERT: k 53 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7451 (mtm-85) REVERT: l 6 PHE cc_start: 0.8496 (m-80) cc_final: 0.8272 (m-80) outliers start: 171 outliers final: 46 residues processed: 916 average time/residue: 2.2585 time to fit residues: 2711.1996 Evaluate side-chains 643 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 580 time to evaluate : 5.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain a residue 35 ARG Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 170 ASN Chi-restraints excluded: chain a residue 274 ASP Chi-restraints excluded: chain a residue 299 MET Chi-restraints excluded: chain a residue 306 VAL Chi-restraints excluded: chain a residue 344 SER Chi-restraints excluded: chain a residue 350 LEU Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain b residue 143 GLU Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 202 LEU Chi-restraints excluded: chain b residue 268 THR Chi-restraints excluded: chain b residue 415 ASP Chi-restraints excluded: chain b residue 420 THR Chi-restraints excluded: chain b residue 439 ILE Chi-restraints excluded: chain c residue 9 MET Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 281 TYR Chi-restraints excluded: chain c residue 292 CYS Chi-restraints excluded: chain c residue 315 ILE Chi-restraints excluded: chain c residue 320 GLU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 127 GLN Chi-restraints excluded: chain d residue 137 CYS Chi-restraints excluded: chain e residue 188 THR Chi-restraints excluded: chain f residue 67 CYS Chi-restraints excluded: chain g residue 57 ARG Chi-restraints excluded: chain g residue 248 ARG Chi-restraints excluded: chain g residue 310 SER Chi-restraints excluded: chain h residue 12 LYS Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain i residue 99 GLU Chi-restraints excluded: chain l residue 14 ILE Chi-restraints excluded: chain l residue 16 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 268 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 402 optimal weight: 1.9990 chunk 328 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 483 optimal weight: 1.9990 chunk 522 optimal weight: 2.9990 chunk 431 optimal weight: 4.9990 chunk 479 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 388 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 122 ASN A 396 GLN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS D 107 GLN ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 ASN ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN I 58 ASN a 219 HIS b 129 ASN ** b 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 299 ASN e 31 ASN e 242 ASN g 258 GLN g 273 ASN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 48215 Z= 0.269 Angle : 0.585 28.799 64895 Z= 0.293 Chirality : 0.041 0.248 6590 Planarity : 0.004 0.050 8046 Dihedral : 16.125 173.923 8390 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.31 % Allowed : 17.93 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.11), residues: 5265 helix: 0.75 (0.10), residues: 2549 sheet: -0.07 (0.26), residues: 374 loop : -0.57 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 222 HIS 0.035 0.002 HIS D 118 PHE 0.014 0.002 PHE G 18 TYR 0.029 0.002 TYR G 133 ARG 0.008 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Evaluate side-chains 749 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 595 time to evaluate : 5.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8407 (mtm) REVERT: A 396 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7270 (mt0) REVERT: B 126 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7090 (tp30) REVERT: B 185 GLU cc_start: 0.7654 (tp30) cc_final: 0.7388 (mm-30) REVERT: B 257 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6874 (mt-10) REVERT: C 286 MET cc_start: 0.6877 (mtt) cc_final: 0.6436 (mtp) REVERT: D 254 MET cc_start: 0.8020 (tpt) cc_final: 0.7714 (tpt) REVERT: E 37 LYS cc_start: 0.7383 (mttt) cc_final: 0.6783 (tttp) REVERT: E 46 ASP cc_start: 0.6830 (t70) cc_final: 0.6441 (t0) REVERT: E 161 GLU cc_start: 0.5881 (mt-10) cc_final: 0.4912 (mm-30) REVERT: F 21 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6549 (pt0) REVERT: G 16 LYS cc_start: 0.8124 (mttt) cc_final: 0.7568 (mmtm) REVERT: G 85 SER cc_start: 0.8527 (t) cc_final: 0.8218 (p) REVERT: I 79 HIS cc_start: 0.6763 (OUTLIER) cc_final: 0.6505 (m90) REVERT: I 110 LYS cc_start: 0.7791 (ttmt) cc_final: 0.7092 (tppt) REVERT: K 45 TYR cc_start: 0.8765 (m-80) cc_final: 0.8418 (m-80) REVERT: K 47 ASP cc_start: 0.7468 (m-30) cc_final: 0.7213 (m-30) REVERT: a 35 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.5942 (tpt-90) REVERT: a 299 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7302 (mtp) REVERT: a 344 SER cc_start: 0.8058 (OUTLIER) cc_final: 0.7759 (p) REVERT: a 350 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8009 (mm) REVERT: a 505 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: b 79 ILE cc_start: 0.8204 (mm) cc_final: 0.7982 (mp) REVERT: b 80 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8101 (mm) REVERT: b 92 MET cc_start: 0.7377 (mtp) cc_final: 0.6999 (mtp) REVERT: b 101 ASP cc_start: 0.7561 (m-30) cc_final: 0.7322 (m-30) REVERT: b 141 GLU cc_start: 0.7207 (tt0) cc_final: 0.7003 (tm-30) REVERT: c 9 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8201 (tpp) REVERT: c 25 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8456 (p) REVERT: c 203 MET cc_start: 0.7865 (pp-130) cc_final: 0.7506 (pp-130) REVERT: c 220 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7752 (mpp) REVERT: c 234 MET cc_start: 0.7525 (tpt) cc_final: 0.6723 (tpt) REVERT: d 103 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7376 (mt) REVERT: d 128 GLU cc_start: 0.7089 (mp0) cc_final: 0.6702 (pm20) REVERT: d 190 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6648 (ttt) REVERT: d 242 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8362 (mmm) REVERT: g 57 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7652 (mtm110) REVERT: g 133 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.6480 (t80) REVERT: g 136 ASP cc_start: 0.7358 (t0) cc_final: 0.6938 (m-30) REVERT: h 114 THR cc_start: 0.6962 (p) cc_final: 0.6714 (p) REVERT: h 115 MET cc_start: 0.8057 (tpt) cc_final: 0.7825 (tpt) REVERT: h 122 CYS cc_start: 0.7854 (t) cc_final: 0.7383 (m) outliers start: 154 outliers final: 66 residues processed: 700 average time/residue: 2.3405 time to fit residues: 2135.9577 Evaluate side-chains 598 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 514 time to evaluate : 5.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 305 ASN Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain a residue 35 ARG Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 162 ASP Chi-restraints excluded: chain a residue 170 ASN Chi-restraints excluded: chain a residue 299 MET Chi-restraints excluded: chain a residue 303 ASN Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 306 VAL Chi-restraints excluded: chain a residue 344 SER Chi-restraints excluded: chain a residue 350 LEU Chi-restraints excluded: chain a residue 351 ILE Chi-restraints excluded: chain a residue 505 TYR Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 99 THR Chi-restraints excluded: chain b residue 143 GLU Chi-restraints excluded: chain b residue 173 GLU Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 304 THR Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 439 ILE Chi-restraints excluded: chain c residue 9 MET Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 108 PHE Chi-restraints excluded: chain c residue 220 MET Chi-restraints excluded: chain c residue 292 CYS Chi-restraints excluded: chain c residue 320 GLU Chi-restraints excluded: chain c residue 325 THR Chi-restraints excluded: chain c residue 350 GLU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 137 CYS Chi-restraints excluded: chain d residue 190 MET Chi-restraints excluded: chain d residue 242 MET Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 188 THR Chi-restraints excluded: chain f residue 57 CYS Chi-restraints excluded: chain f residue 67 CYS Chi-restraints excluded: chain g residue 133 TYR Chi-restraints excluded: chain g residue 248 ARG Chi-restraints excluded: chain g residue 278 SER Chi-restraints excluded: chain h residue 12 LYS Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain h residue 124 ASP Chi-restraints excluded: chain h residue 129 SER Chi-restraints excluded: chain k residue 32 SER Chi-restraints excluded: chain l residue 16 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 478 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 324 optimal weight: 0.8980 chunk 485 optimal weight: 3.9990 chunk 514 optimal weight: 4.9990 chunk 253 optimal weight: 10.0000 chunk 460 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 389 ASN B 446 GLN C 322 ASN D 107 GLN D 118 HIS ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 ASN ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 384 ASN b 302 ASN d 54 ASN g 11 GLN g 273 ASN h 35 ASN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.7491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 48215 Z= 0.314 Angle : 0.586 14.210 64895 Z= 0.297 Chirality : 0.040 0.145 6590 Planarity : 0.004 0.054 8046 Dihedral : 15.746 176.917 8388 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.16 % Allowed : 18.85 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 5265 helix: 0.74 (0.10), residues: 2549 sheet: -0.08 (0.26), residues: 374 loop : -0.58 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 34 HIS 0.006 0.001 HIS E 42 PHE 0.017 0.001 PHE a 163 TYR 0.015 0.002 TYR c 281 ARG 0.006 0.001 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Evaluate side-chains 696 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 549 time to evaluate : 5.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7285 (tp30) REVERT: B 285 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6142 (pp20) REVERT: B 301 SER cc_start: 0.8641 (t) cc_final: 0.8421 (m) REVERT: C 234 MET cc_start: 0.7893 (ttt) cc_final: 0.7263 (tpt) REVERT: C 286 MET cc_start: 0.7238 (mtt) cc_final: 0.6765 (mtp) REVERT: D 114 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7790 (tt) REVERT: D 219 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8134 (m-30) REVERT: D 254 MET cc_start: 0.8002 (tpt) cc_final: 0.7690 (tpt) REVERT: D 257 TYR cc_start: 0.7587 (m-10) cc_final: 0.7064 (m-10) REVERT: E 27 LEU cc_start: 0.7487 (mt) cc_final: 0.7264 (mt) REVERT: E 37 LYS cc_start: 0.7453 (mttt) cc_final: 0.6779 (tttp) REVERT: E 68 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8229 (m) REVERT: E 145 MET cc_start: 0.3362 (tpp) cc_final: 0.2714 (tpt) REVERT: E 161 GLU cc_start: 0.5947 (mt-10) cc_final: 0.4818 (mp0) REVERT: F 12 TRP cc_start: 0.7063 (m100) cc_final: 0.6732 (m-10) REVERT: G 16 LYS cc_start: 0.8359 (mttt) cc_final: 0.7837 (mmtm) REVERT: G 136 ASP cc_start: 0.7011 (t70) cc_final: 0.6756 (OUTLIER) REVERT: G 199 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7118 (m-30) REVERT: H 32 LYS cc_start: 0.8314 (mmmt) cc_final: 0.8051 (mmmt) REVERT: H 90 GLN cc_start: 0.8652 (tt0) cc_final: 0.8256 (tt0) REVERT: I 14 TYR cc_start: 0.8124 (t80) cc_final: 0.7833 (t80) REVERT: I 110 LYS cc_start: 0.8064 (ttmt) cc_final: 0.7270 (tppt) REVERT: K 45 TYR cc_start: 0.8853 (m-80) cc_final: 0.8545 (m-80) REVERT: a 35 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.5976 (tpt-90) REVERT: a 299 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7460 (mtp) REVERT: a 350 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8291 (tp) REVERT: a 505 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: b 80 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8282 (mp) REVERT: b 92 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7507 (mtp) REVERT: c 9 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8411 (tpp) REVERT: c 25 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8607 (p) REVERT: c 86 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8460 (tpp-160) REVERT: c 203 MET cc_start: 0.7850 (pp-130) cc_final: 0.7440 (pp-130) REVERT: c 234 MET cc_start: 0.7593 (tpt) cc_final: 0.6827 (tpt) REVERT: c 235 ILE cc_start: 0.6861 (mt) cc_final: 0.6552 (mt) REVERT: c 312 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8553 (tp40) REVERT: d 103 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7554 (mt) REVERT: d 242 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8370 (mmm) REVERT: g 57 ARG cc_start: 0.8293 (mtt90) cc_final: 0.7812 (mtm110) REVERT: g 133 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.6711 (t80) REVERT: g 136 ASP cc_start: 0.7492 (t0) cc_final: 0.7094 (m-30) REVERT: h 76 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8159 (mp) REVERT: h 114 THR cc_start: 0.7007 (p) cc_final: 0.6802 (p) REVERT: h 122 CYS cc_start: 0.7813 (t) cc_final: 0.7469 (m) REVERT: k 53 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7685 (mtp85) outliers start: 147 outliers final: 58 residues processed: 651 average time/residue: 2.3304 time to fit residues: 1981.0206 Evaluate side-chains 529 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 452 time to evaluate : 5.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain a residue 35 ARG Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 167 ILE Chi-restraints excluded: chain a residue 170 ASN Chi-restraints excluded: chain a residue 299 MET Chi-restraints excluded: chain a residue 303 ASN Chi-restraints excluded: chain a residue 350 LEU Chi-restraints excluded: chain a residue 384 ASN Chi-restraints excluded: chain a residue 430 ASP Chi-restraints excluded: chain a residue 505 TYR Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 92 MET Chi-restraints excluded: chain b residue 173 GLU Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 439 ILE Chi-restraints excluded: chain c residue 9 MET Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 108 PHE Chi-restraints excluded: chain c residue 292 CYS Chi-restraints excluded: chain c residue 312 GLN Chi-restraints excluded: chain c residue 315 ILE Chi-restraints excluded: chain c residue 320 GLU Chi-restraints excluded: chain c residue 325 THR Chi-restraints excluded: chain c residue 327 ARG Chi-restraints excluded: chain c residue 339 SER Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 242 MET Chi-restraints excluded: chain e residue 188 THR Chi-restraints excluded: chain f residue 12 TRP Chi-restraints excluded: chain f residue 67 CYS Chi-restraints excluded: chain g residue 133 TYR Chi-restraints excluded: chain g residue 248 ARG Chi-restraints excluded: chain g residue 281 ASP Chi-restraints excluded: chain g residue 310 SER Chi-restraints excluded: chain h residue 12 LYS Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain h residue 124 ASP Chi-restraints excluded: chain i residue 116 GLU Chi-restraints excluded: chain k residue 32 SER Chi-restraints excluded: chain l residue 16 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 428 optimal weight: 9.9990 chunk 291 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 382 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 438 optimal weight: 5.9990 chunk 355 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 262 optimal weight: 0.7980 chunk 461 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN D 118 HIS ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 ASN ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 ASN d 54 ASN ** f 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 273 ASN h 35 ASN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN i 108 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.8058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 48215 Z= 0.273 Angle : 0.545 17.175 64895 Z= 0.279 Chirality : 0.040 0.347 6590 Planarity : 0.004 0.078 8046 Dihedral : 15.400 175.800 8386 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.21 % Allowed : 19.17 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.12), residues: 5265 helix: 0.84 (0.10), residues: 2545 sheet: -0.05 (0.26), residues: 374 loop : -0.53 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 34 HIS 0.006 0.001 HIS c 98 PHE 0.014 0.001 PHE H 100 TYR 0.016 0.001 TYR e 129 ARG 0.005 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Evaluate side-chains 632 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 483 time to evaluate : 5.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: B 126 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: B 185 GLU cc_start: 0.7601 (tp30) cc_final: 0.7369 (mm-30) REVERT: B 199 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8446 (p) REVERT: C 61 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8512 (mmp) REVERT: C 234 MET cc_start: 0.7930 (ttt) cc_final: 0.7716 (tpp) REVERT: D 114 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7925 (tt) REVERT: D 254 MET cc_start: 0.7837 (tpt) cc_final: 0.7587 (tpt) REVERT: E 37 LYS cc_start: 0.7511 (mttt) cc_final: 0.6818 (tttp) REVERT: E 145 MET cc_start: 0.3204 (tpp) cc_final: 0.2680 (tpt) REVERT: E 161 GLU cc_start: 0.5989 (mt-10) cc_final: 0.4837 (mp0) REVERT: F 12 TRP cc_start: 0.7028 (m100) cc_final: 0.6730 (m100) REVERT: G 16 LYS cc_start: 0.8599 (mttt) cc_final: 0.8356 (tmtm) REVERT: G 59 LEU cc_start: 0.8386 (mp) cc_final: 0.8130 (tp) REVERT: G 62 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7919 (mt) REVERT: G 136 ASP cc_start: 0.7385 (t70) cc_final: 0.7112 (t0) REVERT: G 199 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: H 32 LYS cc_start: 0.8373 (mmmt) cc_final: 0.8159 (mmmt) REVERT: I 14 TYR cc_start: 0.8211 (t80) cc_final: 0.7952 (t80) REVERT: I 57 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7452 (mm-30) REVERT: I 110 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7369 (tppt) REVERT: K 45 TYR cc_start: 0.8842 (m-80) cc_final: 0.8550 (m-80) REVERT: a 35 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6053 (tpt-90) REVERT: a 350 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8304 (tp) REVERT: b 92 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7403 (mtp) REVERT: b 126 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7761 (tp30) REVERT: b 261 GLU cc_start: 0.6378 (tp30) cc_final: 0.6165 (tp30) REVERT: b 466 SER cc_start: 0.7462 (p) cc_final: 0.7260 (m) REVERT: c 9 MET cc_start: 0.8769 (mmm) cc_final: 0.8426 (tpp) REVERT: c 25 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8596 (p) REVERT: c 59 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: c 86 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8290 (tpp-160) REVERT: c 203 MET cc_start: 0.7826 (pp-130) cc_final: 0.7283 (pp-130) REVERT: c 234 MET cc_start: 0.7578 (tpt) cc_final: 0.6932 (tpt) REVERT: c 235 ILE cc_start: 0.7161 (mt) cc_final: 0.6913 (mt) REVERT: c 302 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8581 (mm) REVERT: c 341 ILE cc_start: 0.8301 (mt) cc_final: 0.8031 (pt) REVERT: d 257 TYR cc_start: 0.8001 (m-10) cc_final: 0.7743 (m-10) REVERT: f 36 GLU cc_start: 0.7251 (pt0) cc_final: 0.6996 (pt0) REVERT: g 57 ARG cc_start: 0.8275 (mtt90) cc_final: 0.7944 (mtm110) REVERT: g 133 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6908 (t80) REVERT: g 136 ASP cc_start: 0.7489 (t0) cc_final: 0.7141 (m-30) REVERT: g 233 ASP cc_start: 0.7703 (m-30) cc_final: 0.6813 (p0) REVERT: h 76 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8241 (mp) REVERT: h 122 CYS cc_start: 0.7873 (t) cc_final: 0.7451 (m) REVERT: k 53 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7704 (mtp85) REVERT: L 27 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6835 (mp10) outliers start: 149 outliers final: 58 residues processed: 593 average time/residue: 2.3920 time to fit residues: 1838.6828 Evaluate side-chains 520 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 444 time to evaluate : 5.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain a residue 35 ARG Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 167 ILE Chi-restraints excluded: chain a residue 303 ASN Chi-restraints excluded: chain a residue 350 LEU Chi-restraints excluded: chain b residue 92 MET Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 235 THR Chi-restraints excluded: chain b residue 304 THR Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 420 THR Chi-restraints excluded: chain b residue 439 ILE Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 108 PHE Chi-restraints excluded: chain c residue 143 ASP Chi-restraints excluded: chain c residue 212 SER Chi-restraints excluded: chain c residue 292 CYS Chi-restraints excluded: chain c residue 302 LEU Chi-restraints excluded: chain c residue 312 GLN Chi-restraints excluded: chain c residue 320 GLU Chi-restraints excluded: chain c residue 325 THR Chi-restraints excluded: chain c residue 327 ARG Chi-restraints excluded: chain c residue 339 SER Chi-restraints excluded: chain d residue 282 LEU Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 188 THR Chi-restraints excluded: chain f residue 12 TRP Chi-restraints excluded: chain f residue 57 CYS Chi-restraints excluded: chain g residue 10 GLU Chi-restraints excluded: chain g residue 133 TYR Chi-restraints excluded: chain g residue 178 LEU Chi-restraints excluded: chain g residue 248 ARG Chi-restraints excluded: chain g residue 278 SER Chi-restraints excluded: chain g residue 281 ASP Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain h residue 129 SER Chi-restraints excluded: chain i residue 19 ILE Chi-restraints excluded: chain i residue 116 GLU Chi-restraints excluded: chain k residue 32 SER Chi-restraints excluded: chain l residue 16 SER Chi-restraints excluded: chain L residue 27 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 173 optimal weight: 1.9990 chunk 463 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 514 optimal weight: 3.9990 chunk 427 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN D 154 ASN ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 HIS b 302 ASN d 54 ASN g 11 GLN g 273 ASN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.8886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 48215 Z= 0.482 Angle : 0.677 16.213 64895 Z= 0.345 Chirality : 0.045 0.252 6590 Planarity : 0.006 0.114 8046 Dihedral : 16.177 170.006 8384 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.26 % Favored : 94.72 % Rotamer: Outliers : 3.46 % Allowed : 19.13 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 5265 helix: 0.42 (0.10), residues: 2541 sheet: -0.08 (0.26), residues: 381 loop : -0.87 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 34 HIS 0.010 0.002 HIS H 28 PHE 0.022 0.002 PHE a 246 TYR 0.022 0.002 TYR i 82 ARG 0.012 0.001 ARG g 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Evaluate side-chains 632 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 471 time to evaluate : 5.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7939 (mm-30) REVERT: A 328 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7239 (mp) REVERT: A 513 VAL cc_start: 0.8013 (t) cc_final: 0.7759 (t) REVERT: B 126 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: B 199 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8439 (p) REVERT: B 285 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6522 (pp20) REVERT: B 286 LYS cc_start: 0.7842 (tptt) cc_final: 0.7120 (tptt) REVERT: C 61 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8483 (mmt) REVERT: C 99 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7648 (tp) REVERT: C 234 MET cc_start: 0.8133 (ttt) cc_final: 0.7658 (tpt) REVERT: C 297 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8047 (mt) REVERT: C 393 MET cc_start: 0.8733 (mmt) cc_final: 0.8505 (mmm) REVERT: D 114 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8162 (tt) REVERT: D 254 MET cc_start: 0.7849 (tpt) cc_final: 0.7569 (tpt) REVERT: E 37 LYS cc_start: 0.7729 (mttt) cc_final: 0.7046 (tttp) REVERT: E 84 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6495 (pt0) REVERT: E 145 MET cc_start: 0.3133 (tpp) cc_final: 0.2547 (tpt) REVERT: E 161 GLU cc_start: 0.6075 (mt-10) cc_final: 0.5004 (mp0) REVERT: F 12 TRP cc_start: 0.7268 (m100) cc_final: 0.6851 (m100) REVERT: G 16 LYS cc_start: 0.8682 (mttt) cc_final: 0.8371 (tptp) REVERT: G 59 LEU cc_start: 0.8791 (mp) cc_final: 0.8476 (mt) REVERT: G 199 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: G 237 GLN cc_start: 0.7748 (mt0) cc_final: 0.7361 (mm-40) REVERT: H 116 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7438 (tpt90) REVERT: I 50 LYS cc_start: 0.6614 (mttt) cc_final: 0.6241 (mmpt) REVERT: I 110 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7460 (tppt) REVERT: K 45 TYR cc_start: 0.8938 (m-80) cc_final: 0.8689 (m-80) REVERT: a 35 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6049 (tpt-90) REVERT: a 53 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: a 443 ASN cc_start: 0.8096 (t0) cc_final: 0.7826 (t0) REVERT: b 92 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7540 (mtp) REVERT: b 126 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: c 25 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8598 (p) REVERT: c 59 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7521 (mm-30) REVERT: c 86 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8195 (tpp-160) REVERT: c 234 MET cc_start: 0.7588 (tpt) cc_final: 0.7077 (tpt) REVERT: c 245 CYS cc_start: 0.8465 (m) cc_final: 0.7874 (m) REVERT: c 341 ILE cc_start: 0.8433 (mt) cc_final: 0.8223 (pt) REVERT: d 257 TYR cc_start: 0.8044 (m-10) cc_final: 0.7787 (m-10) REVERT: g 136 ASP cc_start: 0.7499 (t0) cc_final: 0.7194 (m-30) REVERT: L 27 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7174 (mp10) outliers start: 161 outliers final: 77 residues processed: 593 average time/residue: 2.4827 time to fit residues: 1904.5506 Evaluate side-chains 528 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 432 time to evaluate : 5.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain a residue 35 ARG Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 167 ILE Chi-restraints excluded: chain a residue 170 ASN Chi-restraints excluded: chain a residue 303 ASN Chi-restraints excluded: chain b residue 92 MET Chi-restraints excluded: chain b residue 99 THR Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 151 PHE Chi-restraints excluded: chain b residue 178 VAL Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 304 THR Chi-restraints excluded: chain b residue 420 THR Chi-restraints excluded: chain b residue 439 ILE Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 77 THR Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 108 PHE Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain c residue 212 SER Chi-restraints excluded: chain c residue 235 ILE Chi-restraints excluded: chain c residue 292 CYS Chi-restraints excluded: chain c residue 312 GLN Chi-restraints excluded: chain c residue 315 ILE Chi-restraints excluded: chain c residue 320 GLU Chi-restraints excluded: chain c residue 325 THR Chi-restraints excluded: chain c residue 339 SER Chi-restraints excluded: chain c residue 389 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 282 LEU Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 188 THR Chi-restraints excluded: chain f residue 12 TRP Chi-restraints excluded: chain f residue 57 CYS Chi-restraints excluded: chain g residue 9 TRP Chi-restraints excluded: chain g residue 10 GLU Chi-restraints excluded: chain g residue 133 TYR Chi-restraints excluded: chain g residue 178 LEU Chi-restraints excluded: chain g residue 248 ARG Chi-restraints excluded: chain g residue 278 SER Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 124 ASP Chi-restraints excluded: chain h residue 129 SER Chi-restraints excluded: chain i residue 116 GLU Chi-restraints excluded: chain k residue 32 SER Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain l residue 16 SER Chi-restraints excluded: chain L residue 27 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 496 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 375 optimal weight: 0.6980 chunk 291 optimal weight: 0.9990 chunk 433 optimal weight: 3.9990 chunk 287 optimal weight: 0.0570 chunk 512 optimal weight: 1.9990 chunk 320 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 ASN ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 407 ASN a 492 HIS b 302 ASN d 54 ASN g 11 GLN g 273 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.8962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 48215 Z= 0.201 Angle : 0.523 11.105 64895 Z= 0.269 Chirality : 0.038 0.155 6590 Planarity : 0.004 0.078 8046 Dihedral : 15.260 172.457 8384 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.22 % Allowed : 20.42 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.12), residues: 5265 helix: 0.76 (0.10), residues: 2536 sheet: 0.02 (0.26), residues: 385 loop : -0.63 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 504 HIS 0.007 0.001 HIS a 492 PHE 0.022 0.001 PHE f 22 TYR 0.021 0.001 TYR i 89 ARG 0.008 0.000 ARG i 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Evaluate side-chains 572 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 469 time to evaluate : 5.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7983 (mm-30) REVERT: A 224 ASN cc_start: 0.8184 (t0) cc_final: 0.7747 (t0) REVERT: B 57 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6780 (tmm160) REVERT: B 129 ASN cc_start: 0.7177 (p0) cc_final: 0.6910 (p0) REVERT: B 199 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8429 (p) REVERT: B 286 LYS cc_start: 0.7732 (tptt) cc_final: 0.7521 (tttp) REVERT: B 482 LYS cc_start: 0.7453 (ttmt) cc_final: 0.6859 (tptt) REVERT: C 61 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8468 (mmt) REVERT: C 234 MET cc_start: 0.7896 (ttt) cc_final: 0.7589 (tpt) REVERT: C 393 MET cc_start: 0.8692 (mmt) cc_final: 0.8464 (mmm) REVERT: E 37 LYS cc_start: 0.7661 (mttt) cc_final: 0.7030 (tttp) REVERT: E 84 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6439 (pt0) REVERT: E 145 MET cc_start: 0.3121 (tpp) cc_final: 0.2557 (tpt) REVERT: E 161 GLU cc_start: 0.6076 (mt-10) cc_final: 0.5036 (mp0) REVERT: E 245 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8126 (pp) REVERT: F 12 TRP cc_start: 0.7174 (m100) cc_final: 0.6776 (m100) REVERT: G 59 LEU cc_start: 0.8787 (mp) cc_final: 0.8454 (mt) REVERT: G 136 ASP cc_start: 0.7499 (t70) cc_final: 0.7260 (t0) REVERT: G 199 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: G 237 GLN cc_start: 0.7706 (mt0) cc_final: 0.7327 (mm-40) REVERT: I 110 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7419 (tppt) REVERT: K 53 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7359 (mtp-110) REVERT: a 443 ASN cc_start: 0.8090 (t0) cc_final: 0.7730 (t0) REVERT: b 92 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7542 (mtp) REVERT: b 126 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7672 (tp30) REVERT: c 25 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8578 (p) REVERT: c 59 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: c 86 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7656 (tpp-160) REVERT: c 234 MET cc_start: 0.7574 (tpt) cc_final: 0.6910 (tpt) REVERT: c 245 CYS cc_start: 0.8378 (m) cc_final: 0.7793 (m) REVERT: d 103 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7869 (mt) REVERT: d 257 TYR cc_start: 0.7903 (m-10) cc_final: 0.7648 (m-10) REVERT: g 136 ASP cc_start: 0.7462 (t0) cc_final: 0.7160 (m-30) REVERT: g 233 ASP cc_start: 0.7684 (m-30) cc_final: 0.6880 (p0) REVERT: L 27 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6948 (mp10) outliers start: 103 outliers final: 58 residues processed: 541 average time/residue: 2.5219 time to fit residues: 1755.6141 Evaluate side-chains 508 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 437 time to evaluate : 5.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 167 ILE Chi-restraints excluded: chain a residue 303 ASN Chi-restraints excluded: chain a residue 505 TYR Chi-restraints excluded: chain b residue 92 MET Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 296 ASN Chi-restraints excluded: chain b residue 304 THR Chi-restraints excluded: chain b residue 439 ILE Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 108 PHE Chi-restraints excluded: chain c residue 212 SER Chi-restraints excluded: chain c residue 235 ILE Chi-restraints excluded: chain c residue 312 GLN Chi-restraints excluded: chain c residue 320 GLU Chi-restraints excluded: chain c residue 325 THR Chi-restraints excluded: chain c residue 339 SER Chi-restraints excluded: chain c residue 389 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 282 LEU Chi-restraints excluded: chain e residue 181 ILE Chi-restraints excluded: chain e residue 188 THR Chi-restraints excluded: chain f residue 12 TRP Chi-restraints excluded: chain f residue 57 CYS Chi-restraints excluded: chain f residue 86 MET Chi-restraints excluded: chain g residue 10 GLU Chi-restraints excluded: chain g residue 133 TYR Chi-restraints excluded: chain g residue 178 LEU Chi-restraints excluded: chain g residue 278 SER Chi-restraints excluded: chain h residue 36 LEU Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain i residue 88 ILE Chi-restraints excluded: chain i residue 116 GLU Chi-restraints excluded: chain k residue 32 SER Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain L residue 27 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 317 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 325 optimal weight: 4.9990 chunk 349 optimal weight: 4.9990 chunk 253 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 403 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN C 312 GLN D 107 GLN ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 ASN ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 407 ASN a 492 HIS b 302 ASN c 312 GLN d 54 ASN ** f 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 GLN g 273 ASN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.9155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 48215 Z= 0.302 Angle : 0.559 13.649 64895 Z= 0.285 Chirality : 0.040 0.186 6590 Planarity : 0.005 0.083 8046 Dihedral : 15.137 172.828 8384 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.26 % Allowed : 20.44 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 5265 helix: 0.78 (0.10), residues: 2533 sheet: 0.02 (0.26), residues: 381 loop : -0.66 (0.13), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 34 HIS 0.007 0.001 HIS a 492 PHE 0.022 0.001 PHE f 22 TYR 0.026 0.002 TYR i 89 ARG 0.011 0.001 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Evaluate side-chains 541 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 436 time to evaluate : 5.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7911 (mm-30) REVERT: B 126 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: B 199 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8423 (p) REVERT: B 482 LYS cc_start: 0.7473 (ttmt) cc_final: 0.6876 (tptt) REVERT: C 61 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8454 (mmt) REVERT: C 234 MET cc_start: 0.8006 (ttt) cc_final: 0.7636 (tpt) REVERT: C 393 MET cc_start: 0.8675 (mmt) cc_final: 0.8465 (mmm) REVERT: E 37 LYS cc_start: 0.7784 (mttt) cc_final: 0.7129 (tttp) REVERT: E 46 ASP cc_start: 0.7150 (t70) cc_final: 0.6529 (t0) REVERT: E 84 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6345 (pt0) REVERT: E 145 MET cc_start: 0.3173 (tpp) cc_final: 0.2610 (tpt) REVERT: E 161 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5075 (mp0) REVERT: E 245 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8080 (pp) REVERT: F 12 TRP cc_start: 0.7197 (m100) cc_final: 0.6810 (m100) REVERT: G 59 LEU cc_start: 0.8747 (mp) cc_final: 0.8496 (mt) REVERT: G 199 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7173 (m-30) REVERT: G 237 GLN cc_start: 0.7769 (mt0) cc_final: 0.7350 (mm-40) REVERT: K 37 TYR cc_start: 0.8322 (t80) cc_final: 0.8071 (t80) REVERT: K 53 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7381 (mtp-110) REVERT: b 92 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7546 (mtp) REVERT: b 126 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: c 25 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8571 (p) REVERT: c 59 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: c 86 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7824 (tpp-160) REVERT: c 234 MET cc_start: 0.7438 (tpt) cc_final: 0.6712 (tpt) REVERT: c 245 CYS cc_start: 0.8397 (m) cc_final: 0.7806 (m) REVERT: d 103 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7948 (mt) REVERT: d 257 TYR cc_start: 0.7787 (m-10) cc_final: 0.7543 (m-10) REVERT: d 259 MET cc_start: 0.8055 (mtp) cc_final: 0.7692 (mtt) REVERT: f 36 GLU cc_start: 0.7467 (pt0) cc_final: 0.7098 (pt0) REVERT: g 65 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8378 (tttt) REVERT: g 136 ASP cc_start: 0.7565 (t0) cc_final: 0.7227 (m-30) REVERT: L 27 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7032 (mp10) outliers start: 105 outliers final: 64 residues processed: 510 average time/residue: 2.5562 time to fit residues: 1693.4381 Evaluate side-chains 497 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 419 time to evaluate : 5.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 167 ILE Chi-restraints excluded: chain a residue 303 ASN Chi-restraints excluded: chain a residue 505 TYR Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 92 MET Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 296 ASN Chi-restraints excluded: chain b residue 304 THR Chi-restraints excluded: chain b residue 439 ILE Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 108 PHE Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain c residue 212 SER Chi-restraints excluded: chain c residue 235 ILE Chi-restraints excluded: chain c residue 320 GLU Chi-restraints excluded: chain c residue 325 THR Chi-restraints excluded: chain c residue 339 SER Chi-restraints excluded: chain c residue 389 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 282 LEU Chi-restraints excluded: chain e residue 181 ILE Chi-restraints excluded: chain e residue 188 THR Chi-restraints excluded: chain f residue 12 TRP Chi-restraints excluded: chain f residue 57 CYS Chi-restraints excluded: chain g residue 10 GLU Chi-restraints excluded: chain g residue 65 LYS Chi-restraints excluded: chain g residue 133 TYR Chi-restraints excluded: chain g residue 178 LEU Chi-restraints excluded: chain g residue 278 SER Chi-restraints excluded: chain g residue 281 ASP Chi-restraints excluded: chain g residue 321 LYS Chi-restraints excluded: chain h residue 36 LEU Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain i residue 116 GLU Chi-restraints excluded: chain k residue 32 SER Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain L residue 27 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 466 optimal weight: 2.9990 chunk 491 optimal weight: 0.9990 chunk 448 optimal weight: 10.0000 chunk 477 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 375 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 431 optimal weight: 2.9990 chunk 451 optimal weight: 3.9990 chunk 476 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN C 312 GLN ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 ASN ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 407 ASN a 492 HIS b 302 ASN c 45 GLN d 54 ASN ** f 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 273 ASN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.9237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 48215 Z= 0.213 Angle : 0.518 13.355 64895 Z= 0.264 Chirality : 0.038 0.152 6590 Planarity : 0.004 0.065 8046 Dihedral : 14.694 174.321 8384 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.94 % Allowed : 20.70 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.12), residues: 5265 helix: 0.88 (0.11), residues: 2539 sheet: 0.03 (0.26), residues: 383 loop : -0.60 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 12 HIS 0.007 0.001 HIS a 492 PHE 0.022 0.001 PHE f 22 TYR 0.023 0.001 TYR i 89 ARG 0.006 0.000 ARG k 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Evaluate side-chains 527 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 437 time to evaluate : 5.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6992 (tmm160) REVERT: B 126 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: B 199 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8414 (p) REVERT: B 482 LYS cc_start: 0.7434 (ttmt) cc_final: 0.6856 (tptt) REVERT: C 61 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8507 (mmt) REVERT: C 369 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.8003 (t) REVERT: D 209 MET cc_start: 0.9012 (ttp) cc_final: 0.8576 (ttp) REVERT: E 37 LYS cc_start: 0.7703 (mttt) cc_final: 0.6968 (tttp) REVERT: E 46 ASP cc_start: 0.7158 (t70) cc_final: 0.6536 (t0) REVERT: E 84 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6419 (pt0) REVERT: E 145 MET cc_start: 0.3162 (tpp) cc_final: 0.2617 (tpt) REVERT: E 161 GLU cc_start: 0.6140 (mt-10) cc_final: 0.5079 (mp0) REVERT: E 245 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8048 (pp) REVERT: F 12 TRP cc_start: 0.7073 (m100) cc_final: 0.6781 (m100) REVERT: G 59 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8494 (mt) REVERT: G 199 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7169 (m-30) REVERT: G 237 GLN cc_start: 0.7740 (mt0) cc_final: 0.7309 (mm-40) REVERT: K 37 TYR cc_start: 0.8289 (t80) cc_final: 0.8012 (t80) REVERT: K 53 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7346 (mtp-110) REVERT: a 112 ARG cc_start: 0.7898 (mtt-85) cc_final: 0.7608 (mtt90) REVERT: b 92 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7550 (mtp) REVERT: b 126 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: c 25 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8613 (p) REVERT: c 61 MET cc_start: 0.8861 (mmm) cc_final: 0.8630 (mmm) REVERT: c 234 MET cc_start: 0.7330 (tpt) cc_final: 0.6664 (tpt) REVERT: c 245 CYS cc_start: 0.8380 (m) cc_final: 0.7817 (m) REVERT: d 103 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7910 (mt) REVERT: d 257 TYR cc_start: 0.7755 (m-10) cc_final: 0.7539 (m-10) REVERT: d 259 MET cc_start: 0.8156 (mtp) cc_final: 0.7734 (mtt) REVERT: f 36 GLU cc_start: 0.7441 (pt0) cc_final: 0.7099 (pt0) REVERT: g 57 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7873 (mtm110) REVERT: g 65 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8307 (tttt) REVERT: g 136 ASP cc_start: 0.7478 (t0) cc_final: 0.7137 (m-30) REVERT: k 5 THR cc_start: 0.8985 (m) cc_final: 0.8687 (t) REVERT: L 27 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7047 (mp10) outliers start: 90 outliers final: 55 residues processed: 502 average time/residue: 2.5534 time to fit residues: 1672.0419 Evaluate side-chains 492 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 423 time to evaluate : 5.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 140 GLN Chi-restraints excluded: chain a residue 303 ASN Chi-restraints excluded: chain a residue 505 TYR Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 92 MET Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 296 ASN Chi-restraints excluded: chain b residue 304 THR Chi-restraints excluded: chain b residue 439 ILE Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 108 PHE Chi-restraints excluded: chain c residue 212 SER Chi-restraints excluded: chain c residue 320 GLU Chi-restraints excluded: chain c residue 325 THR Chi-restraints excluded: chain c residue 339 SER Chi-restraints excluded: chain c residue 389 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 282 LEU Chi-restraints excluded: chain e residue 181 ILE Chi-restraints excluded: chain e residue 188 THR Chi-restraints excluded: chain f residue 12 TRP Chi-restraints excluded: chain f residue 57 CYS Chi-restraints excluded: chain g residue 10 GLU Chi-restraints excluded: chain g residue 65 LYS Chi-restraints excluded: chain g residue 133 TYR Chi-restraints excluded: chain g residue 178 LEU Chi-restraints excluded: chain g residue 281 ASP Chi-restraints excluded: chain h residue 36 LEU Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain i residue 116 GLU Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain L residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 313 optimal weight: 5.9990 chunk 505 optimal weight: 2.9990 chunk 308 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 351 optimal weight: 2.9990 chunk 530 optimal weight: 1.9990 chunk 487 optimal weight: 0.8980 chunk 422 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 ASN ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 407 ASN a 492 HIS b 302 ASN d 54 ASN ** f 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 GLN g 273 ASN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.9301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 48215 Z= 0.252 Angle : 0.529 11.872 64895 Z= 0.270 Chirality : 0.039 0.151 6590 Planarity : 0.004 0.074 8046 Dihedral : 14.649 174.557 8384 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.83 % Allowed : 20.98 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.11), residues: 5265 helix: 0.88 (0.11), residues: 2541 sheet: 0.04 (0.26), residues: 381 loop : -0.61 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 12 HIS 0.007 0.001 HIS a 492 PHE 0.026 0.001 PHE f 22 TYR 0.022 0.001 TYR i 89 ARG 0.008 0.000 ARG k 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Evaluate side-chains 515 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 430 time to evaluate : 5.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7069 (tmm160) REVERT: B 126 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7284 (tp30) REVERT: B 199 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8412 (p) REVERT: B 201 GLU cc_start: 0.7053 (tp30) cc_final: 0.6725 (mm-30) REVERT: B 482 LYS cc_start: 0.7455 (ttmt) cc_final: 0.6876 (tptt) REVERT: C 61 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8504 (mmt) REVERT: C 369 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.7995 (t) REVERT: D 209 MET cc_start: 0.9029 (ttp) cc_final: 0.8634 (ttp) REVERT: E 37 LYS cc_start: 0.7728 (mttt) cc_final: 0.6983 (tttp) REVERT: E 46 ASP cc_start: 0.7228 (t70) cc_final: 0.6616 (t0) REVERT: E 84 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6441 (pt0) REVERT: E 145 MET cc_start: 0.3160 (tpp) cc_final: 0.2627 (tpt) REVERT: E 161 GLU cc_start: 0.6147 (mt-10) cc_final: 0.5052 (mp0) REVERT: E 211 TYR cc_start: 0.3032 (OUTLIER) cc_final: 0.2422 (m-80) REVERT: E 245 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8051 (pp) REVERT: F 12 TRP cc_start: 0.7102 (m100) cc_final: 0.6810 (m100) REVERT: G 59 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8539 (mt) REVERT: G 199 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7169 (m-30) REVERT: G 237 GLN cc_start: 0.7744 (mt0) cc_final: 0.7311 (mm-40) REVERT: K 37 TYR cc_start: 0.8299 (t80) cc_final: 0.8022 (t80) REVERT: K 53 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7342 (mtp-110) REVERT: a 112 ARG cc_start: 0.7888 (mtt-85) cc_final: 0.7612 (mtt90) REVERT: b 92 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7551 (mtp) REVERT: b 126 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7657 (tp30) REVERT: c 25 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8621 (p) REVERT: c 59 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7425 (mm-30) REVERT: c 61 MET cc_start: 0.8881 (mmm) cc_final: 0.8627 (mmm) REVERT: c 203 MET cc_start: 0.7895 (pp-130) cc_final: 0.7400 (pp-130) REVERT: c 234 MET cc_start: 0.7407 (tpt) cc_final: 0.6741 (tpt) REVERT: c 245 CYS cc_start: 0.8436 (m) cc_final: 0.7849 (m) REVERT: d 103 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7910 (mt) REVERT: d 257 TYR cc_start: 0.7757 (m-10) cc_final: 0.7541 (m-10) REVERT: d 259 MET cc_start: 0.8154 (mtp) cc_final: 0.7877 (mtt) REVERT: f 36 GLU cc_start: 0.7453 (pt0) cc_final: 0.7112 (pt0) REVERT: g 57 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7884 (mtm110) REVERT: g 136 ASP cc_start: 0.7491 (t0) cc_final: 0.7140 (m-30) REVERT: k 5 THR cc_start: 0.8965 (m) cc_final: 0.8702 (t) REVERT: k 53 ARG cc_start: 0.8004 (ptp-110) cc_final: 0.7335 (mtp-110) REVERT: L 27 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7005 (mp10) outliers start: 85 outliers final: 60 residues processed: 489 average time/residue: 2.4773 time to fit residues: 1563.1356 Evaluate side-chains 501 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 426 time to evaluate : 5.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 211 TYR Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 222 ASN Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 140 GLN Chi-restraints excluded: chain a residue 303 ASN Chi-restraints excluded: chain a residue 505 TYR Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 92 MET Chi-restraints excluded: chain b residue 126 GLU Chi-restraints excluded: chain b residue 296 ASN Chi-restraints excluded: chain b residue 304 THR Chi-restraints excluded: chain b residue 439 ILE Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 108 PHE Chi-restraints excluded: chain c residue 212 SER Chi-restraints excluded: chain c residue 235 ILE Chi-restraints excluded: chain c residue 320 GLU Chi-restraints excluded: chain c residue 325 THR Chi-restraints excluded: chain c residue 339 SER Chi-restraints excluded: chain c residue 389 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 282 LEU Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 181 ILE Chi-restraints excluded: chain e residue 188 THR Chi-restraints excluded: chain f residue 12 TRP Chi-restraints excluded: chain f residue 57 CYS Chi-restraints excluded: chain g residue 10 GLU Chi-restraints excluded: chain g residue 133 TYR Chi-restraints excluded: chain g residue 178 LEU Chi-restraints excluded: chain g residue 281 ASP Chi-restraints excluded: chain g residue 321 LYS Chi-restraints excluded: chain h residue 36 LEU Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain i residue 88 ILE Chi-restraints excluded: chain i residue 116 GLU Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain L residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 335 optimal weight: 0.9980 chunk 449 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 389 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 422 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 434 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 ASN ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 407 ASN a 492 HIS b 302 ASN d 54 ASN ** f 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 273 ASN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113426 restraints weight = 192611.358| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.76 r_work: 0.3364 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.9296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 48215 Z= 0.316 Angle : 0.611 59.197 64895 Z= 0.333 Chirality : 0.040 0.229 6590 Planarity : 0.004 0.070 8046 Dihedral : 14.659 174.584 8384 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.87 % Allowed : 20.94 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.11), residues: 5265 helix: 0.87 (0.10), residues: 2541 sheet: 0.04 (0.26), residues: 381 loop : -0.61 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 12 HIS 0.006 0.001 HIS a 492 PHE 0.020 0.001 PHE f 22 TYR 0.019 0.001 TYR i 89 ARG 0.008 0.000 ARG k 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30549.38 seconds wall clock time: 527 minutes 19.24 seconds (31639.24 seconds total)