Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 23 18:07:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6j_15868/08_2023/8b6j_15868_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6j_15868/08_2023/8b6j_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_15868/08_2023/8b6j_15868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6j_15868/08_2023/8b6j_15868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6j_15868/08_2023/8b6j_15868_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6j_15868/08_2023/8b6j_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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 29.59, per 1000 atoms: 0.33 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: 59.05 Conformation dependent library (CDL) restraints added in 5.3 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: 7.99 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: 30.95 Time building geometry restraints manager: 61.94 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: 36782 34.80 - 69.60: 1071 69.60 - 104.41: 44 104.41 - 139.21: 4 139.21 - 174.01: 5 Dihedral angle restraints: 37906 sinusoidal: 17808 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 37903 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: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.040 Extract box with map and model: 28.310 Check model and map are aligned: 1.430 Set scattering table: 0.820 Process input model: 243.580 Find NCS groups from input model: 3.440 Set up NCS constraints: 0.700 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: 0.020 Load rotamer database and sin/cos tables:10.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 295.360 ------------------------------------------------------------------------------- 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 : 14.482 174.009 18220 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 % 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 *********************** 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 : 5.342 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 outliers start: 31 outliers final: 5 residues processed: 1432 average time/residue: 2.4073 time to fit residues: 4454.7168 Evaluate side-chains 705 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 700 time to evaluate : 5.372 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 2 average time/residue: 1.2221 time to fit residues: 10.6952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 449 optimal weight: 9.9990 chunk 403 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 271 optimal weight: 0.6980 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: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 389 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 ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN a 281 ASN a 485 HIS b 129 ASN b 135 GLN b 188 GLN b 247 ASN b 331 ASN b 432 HIS c 112 GLN ** c 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** L 27 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.190 48215 Z= 0.461 Angle : 0.883 13.935 64895 Z= 0.451 Chirality : 0.050 0.351 6590 Planarity : 0.007 0.122 8046 Dihedral : 15.867 176.073 7929 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.03 % Favored : 94.87 % Rotamer Outliers : 3.79 % 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: -0.56 (0.11), residues: 5265 helix: 0.12 (0.10), residues: 2557 sheet: 0.04 (0.27), residues: 376 loop : -0.89 (0.12), residues: 2332 *********************** 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 946 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 770 time to evaluate : 5.507 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 outliers start: 176 outliers final: 46 residues processed: 900 average time/residue: 2.3256 time to fit residues: 2735.6705 Evaluate side-chains 589 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 543 time to evaluate : 5.515 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 38 residues processed: 10 average time/residue: 1.1468 time to fit residues: 25.8477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 328 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 483 optimal weight: 2.9990 chunk 522 optimal weight: 2.9990 chunk 431 optimal weight: 7.9990 chunk 479 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN B 302 ASN B 423 ASN ** C 98 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 a 384 ASN b 129 ASN ** b 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 321 GLN ** d 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 31 ASN e 242 ASN g 258 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.6815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 48215 Z= 0.224 Angle : 0.553 8.673 64895 Z= 0.283 Chirality : 0.040 0.200 6590 Planarity : 0.004 0.047 8046 Dihedral : 14.587 174.380 7929 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 3.51 % 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: 0.04 (0.11), residues: 5265 helix: 0.70 (0.10), residues: 2537 sheet: -0.04 (0.26), residues: 374 loop : -0.62 (0.13), residues: 2354 *********************** 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 722 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 559 time to evaluate : 5.599 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 outliers start: 163 outliers final: 68 residues processed: 672 average time/residue: 2.3107 time to fit residues: 2035.7418 Evaluate side-chains 562 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 494 time to evaluate : 5.477 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 57 residues processed: 12 average time/residue: 1.0773 time to fit residues: 28.1006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 230 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 chunk 485 optimal weight: 1.9990 chunk 514 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 460 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 446 GLN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 ASN ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN a 176 GLN ** a 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 HIS b 302 ASN d 299 ASN g 273 ASN h 35 ASN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 ASN i 108 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.7679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 48215 Z= 0.306 Angle : 0.577 12.693 64895 Z= 0.293 Chirality : 0.040 0.148 6590 Planarity : 0.004 0.053 8046 Dihedral : 14.123 175.920 7929 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.39 % Favored : 95.59 % Rotamer Outliers : 3.01 % 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: 0.10 (0.11), residues: 5265 helix: 0.74 (0.10), residues: 2552 sheet: 0.01 (0.27), residues: 368 loop : -0.59 (0.13), residues: 2345 *********************** 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 671 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 531 time to evaluate : 5.473 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 outliers start: 140 outliers final: 75 residues processed: 634 average time/residue: 2.3441 time to fit residues: 1943.8349 Evaluate side-chains 547 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 472 time to evaluate : 5.496 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 61 residues processed: 15 average time/residue: 0.9685 time to fit residues: 31.9051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 428 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 382 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 438 optimal weight: 3.9990 chunk 355 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 461 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 B 446 GLN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 93 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.8345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 48215 Z= 0.287 Angle : 0.557 9.872 64895 Z= 0.286 Chirality : 0.040 0.163 6590 Planarity : 0.004 0.091 8046 Dihedral : 14.036 174.844 7929 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 3.42 % 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: 0.12 (0.11), residues: 5265 helix: 0.73 (0.10), residues: 2543 sheet: 0.16 (0.27), residues: 383 loop : -0.58 (0.13), residues: 2339 *********************** 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 646 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 487 time to evaluate : 5.521 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 outliers start: 159 outliers final: 83 residues processed: 606 average time/residue: 2.4353 time to fit residues: 1927.6106 Evaluate side-chains 515 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 432 time to evaluate : 5.504 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 69 residues processed: 15 average time/residue: 1.0586 time to fit residues: 33.3533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 173 optimal weight: 0.5980 chunk 463 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 301 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 514 optimal weight: 4.9990 chunk 427 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 243 ASN B 446 GLN ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 HIS b 302 ASN d 54 ASN e 91 GLN e 261 HIS ** 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.8747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 48215 Z= 0.339 Angle : 0.578 13.714 64895 Z= 0.293 Chirality : 0.040 0.193 6590 Planarity : 0.004 0.058 8046 Dihedral : 14.008 174.798 7929 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 2.91 % 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: 0.05 (0.11), residues: 5265 helix: 0.69 (0.10), residues: 2546 sheet: 0.16 (0.26), residues: 383 loop : -0.64 (0.13), residues: 2336 *********************** 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 592 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 457 time to evaluate : 6.117 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 outliers start: 135 outliers final: 82 residues processed: 561 average time/residue: 2.4948 time to fit residues: 1811.6282 Evaluate side-chains 513 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 431 time to evaluate : 5.512 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 70 residues processed: 14 average time/residue: 1.1027 time to fit residues: 32.5001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 293 optimal weight: 3.9990 chunk 375 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 433 optimal weight: 4.9990 chunk 287 optimal weight: 0.0370 chunk 512 optimal weight: 3.9990 chunk 320 optimal weight: 0.8980 chunk 312 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- 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 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 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** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.8880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 48215 Z= 0.211 Angle : 0.512 10.361 64895 Z= 0.262 Chirality : 0.038 0.150 6590 Planarity : 0.004 0.070 8046 Dihedral : 13.495 176.942 7929 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 2.50 % 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: 0.28 (0.12), residues: 5265 helix: 0.91 (0.11), residues: 2537 sheet: 0.18 (0.26), residues: 385 loop : -0.54 (0.13), residues: 2343 *********************** 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 573 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 457 time to evaluate : 5.576 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 outliers start: 116 outliers final: 78 residues processed: 543 average time/residue: 2.4648 time to fit residues: 1739.8816 Evaluate side-chains 505 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 427 time to evaluate : 5.660 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 66 residues processed: 12 average time/residue: 0.9912 time to fit residues: 27.5099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 317 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 325 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 403 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 209 ASN 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 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.9117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 48215 Z= 0.332 Angle : 0.570 14.034 64895 Z= 0.291 Chirality : 0.040 0.338 6590 Planarity : 0.004 0.075 8046 Dihedral : 13.667 176.476 7929 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 2.50 % 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: 0.78 (0.10), residues: 2541 sheet: 0.14 (0.26), residues: 381 loop : -0.65 (0.12), residues: 2343 *********************** 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 551 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 435 time to evaluate : 5.607 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 outliers start: 116 outliers final: 81 residues processed: 531 average time/residue: 2.3920 time to fit residues: 1665.1857 Evaluate side-chains 499 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 418 time to evaluate : 5.552 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 72 residues processed: 11 average time/residue: 1.1109 time to fit residues: 27.2153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 466 optimal weight: 0.9990 chunk 491 optimal weight: 0.0970 chunk 448 optimal weight: 20.0000 chunk 477 optimal weight: 2.9990 chunk 287 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 375 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 431 optimal weight: 1.9990 chunk 451 optimal weight: 2.9990 chunk 476 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 446 GLN C 312 GLN E 119 ASN H 42 ASN ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 HIS b 302 ASN d 54 ASN ** f 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 GLN g 14 ASN g 273 ASN h 96 ASN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.9189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 48215 Z= 0.197 Angle : 0.507 10.058 64895 Z= 0.260 Chirality : 0.038 0.190 6590 Planarity : 0.004 0.067 8046 Dihedral : 13.185 178.162 7929 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 2.00 % 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: 0.30 (0.12), residues: 5265 helix: 0.95 (0.11), residues: 2545 sheet: 0.13 (0.26), residues: 385 loop : -0.55 (0.13), residues: 2335 *********************** 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 534 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 441 time to evaluate : 5.850 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 outliers start: 93 outliers final: 72 residues processed: 522 average time/residue: 2.4726 time to fit residues: 1694.8705 Evaluate side-chains 489 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 417 time to evaluate : 5.608 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 68 residues processed: 6 average time/residue: 1.1106 time to fit residues: 18.0323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 313 optimal weight: 3.9990 chunk 505 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 351 optimal weight: 3.9990 chunk 530 optimal weight: 0.9980 chunk 487 optimal weight: 0.2980 chunk 422 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 326 optimal weight: 3.9990 chunk 258 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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** 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 ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.9277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 48215 Z= 0.202 Angle : 0.504 10.391 64895 Z= 0.258 Chirality : 0.038 0.202 6590 Planarity : 0.004 0.062 8046 Dihedral : 12.887 179.452 7929 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 1.74 % 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: 0.38 (0.12), residues: 5265 helix: 1.04 (0.11), residues: 2541 sheet: 0.21 (0.26), residues: 381 loop : -0.55 (0.13), residues: 2343 ********************** 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 514 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 433 time to evaluate : 5.547 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 outliers start: 81 outliers final: 67 residues processed: 506 average time/residue: 2.4900 time to fit residues: 1680.5114 Evaluate side-chains 487 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 420 time to evaluate : 5.862 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 64 residues processed: 4 average time/residue: 1.1298 time to fit residues: 14.8202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 335 optimal weight: 0.5980 chunk 449 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 389 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 422 optimal weight: 1.9990 chunk 176 optimal weight: 0.3980 chunk 434 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN H 42 ASN ** H 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 407 ASN a 492 HIS b 302 ASN d 54 ASN d 177 ASN ** f 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 273 ASN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117000 restraints weight = 193446.658| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.81 r_work: 0.3449 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.9336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 48215 Z= 0.174 Angle : 0.488 9.012 64895 Z= 0.250 Chirality : 0.037 0.174 6590 Planarity : 0.003 0.060 8046 Dihedral : 12.512 179.239 7929 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 1.59 % 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: 0.51 (0.12), residues: 5265 helix: 1.15 (0.11), residues: 2536 sheet: 0.29 (0.27), residues: 380 loop : -0.50 (0.13), residues: 2349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30111.54 seconds wall clock time: 519 minutes 43.92 seconds (31183.92 seconds total)