Starting phenix.real_space_refine on Mon Oct 14 01:07:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shq_40492/10_2024/8shq_40492.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shq_40492/10_2024/8shq_40492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shq_40492/10_2024/8shq_40492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shq_40492/10_2024/8shq_40492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shq_40492/10_2024/8shq_40492.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shq_40492/10_2024/8shq_40492.cif" } resolution = 2.9 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= 0.004 sd= 0.044 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: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 423 5.16 5 C 42490 2.51 5 N 11819 2.21 5 O 13163 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 68007 Number of models: 1 Model: "" Number of chains: 50 Chain: "P" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1507 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 9 Chain: "N" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1366 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain breaks: 1 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 35.68, per 1000 atoms: 0.52 Number of scatterers: 68007 At special positions: 0 Unit cell: (179.86, 176.686, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 423 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13163 8.00 N 11819 7.00 C 42490 6.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM67914 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67658 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.06 Conformation dependent library (CDL) restraints added in 7.9 seconds 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16450 Finding SS restraints... Secondary structure from input PDB file: 363 helices and 100 sheets defined 55.8% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.66 Creating SS restraints... Processing helix chain 'P' and resid 58 through 61 Processing helix chain 'P' and resid 62 through 87 removed outlier: 3.694A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU P 87 " --> pdb=" O GLU P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 140 removed outlier: 3.533A pdb=" N GLN P 139 " --> pdb=" O PHE P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 151 removed outlier: 4.418A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN P 151 " --> pdb=" O GLU P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 176 removed outlier: 3.883A pdb=" N LEU P 171 " --> pdb=" O GLY P 167 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE P 174 " --> pdb=" O PHE P 170 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS P 176 " --> pdb=" O ASP P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 209 removed outlier: 3.797A pdb=" N ALA P 207 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU P 208 " --> pdb=" O CYS P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 271 removed outlier: 3.763A pdb=" N PHE P 271 " --> pdb=" O PHE P 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 190 removed outlier: 3.682A pdb=" N LYS N 188 " --> pdb=" O ALA N 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.626A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.663A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.217A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.269A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.727A pdb=" N GLN A 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 258 through 280 removed outlier: 4.568A pdb=" N GLN A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 433 through 445 removed outlier: 4.154A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 480 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 Processing helix chain 'B' and resid 122 through 145 Processing helix chain 'B' and resid 151 through 169 removed outlier: 4.360A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.609A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 260 through 284 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.515A pdb=" N VAL B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 426 Processing helix chain 'B' and resid 431 through 454 Proline residue: B 447 - end of helix removed outlier: 3.619A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 28 through 50 removed outlier: 4.417A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.899A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.539A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 268 through 292 removed outlier: 3.971A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 441 Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.980A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.535A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 Processing helix chain 'D' and resid 512 through 531 removed outlier: 3.529A pdb=" N LYS D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.825A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 50 removed outlier: 4.251A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 107 through 125 removed outlier: 3.588A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 176 through 180 removed outlier: 4.020A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 196 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 270 through 295 removed outlier: 3.851A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 440 removed outlier: 3.882A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.568A pdb=" N GLN E 445 " --> pdb=" O PRO E 441 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.838A pdb=" N MET E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 484 Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'G' and resid 19 through 38 removed outlier: 3.696A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 62 through 69 removed outlier: 3.562A pdb=" N GLU G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 91 Processing helix chain 'G' and resid 94 through 114 removed outlier: 3.624A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.637A pdb=" N VAL G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 Processing helix chain 'G' and resid 163 through 167 removed outlier: 4.043A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 262 through 284 Processing helix chain 'G' and resid 297 through 307 removed outlier: 3.586A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 removed outlier: 3.616A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 471 removed outlier: 3.718A pdb=" N LEU G 462 " --> pdb=" O SER G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 35 Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.830A pdb=" N LEU H 40 " --> pdb=" O ARG H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.689A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.056A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 117 through 140 removed outlier: 3.720A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 164 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 171 through 186 removed outlier: 3.502A pdb=" N LEU H 186 " --> pdb=" O ALA H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 259 through 284 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 338 through 342 removed outlier: 3.568A pdb=" N LEU H 342 " --> pdb=" O ALA H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 402 Processing helix chain 'H' and resid 410 through 425 Processing helix chain 'H' and resid 429 through 442 removed outlier: 3.502A pdb=" N LEU H 433 " --> pdb=" O GLY H 429 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 454 Processing helix chain 'H' and resid 456 through 470 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 45 removed outlier: 4.316A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 Processing helix chain 'Q' and resid 80 through 97 Processing helix chain 'Q' and resid 100 through 122 Processing helix chain 'Q' and resid 124 through 143 Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 156 through 168 removed outlier: 3.750A pdb=" N VAL Q 160 " --> pdb=" O ASP Q 156 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 285 removed outlier: 4.837A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 Processing helix chain 'Q' and resid 317 through 329 Processing helix chain 'Q' and resid 340 through 344 removed outlier: 3.701A pdb=" N MET Q 344 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 429 removed outlier: 3.728A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.329A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 457 Processing helix chain 'Q' and resid 459 through 474 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.508A pdb=" N LEU Z 20 " --> pdb=" O ALA Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 59 through 66 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.584A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.840A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 3.990A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.661A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 189 No H-bonds generated for 'chain 'Z' and resid 187 through 189' Processing helix chain 'Z' and resid 200 through 204 removed outlier: 3.524A pdb=" N THR Z 204 " --> pdb=" O GLU Z 201 " (cutoff:3.500A) Processing helix chain 'Z' and resid 252 through 264 removed outlier: 4.080A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 282 removed outlier: 3.648A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 307 Processing helix chain 'Z' and resid 317 through 329 removed outlier: 3.643A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 344 Processing helix chain 'Z' and resid 380 through 404 Processing helix chain 'Z' and resid 412 through 426 Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 430 through 431 No H-bonds generated for 'chain 'Z' and resid 430 through 431' Processing helix chain 'Z' and resid 432 through 445 removed outlier: 4.198A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.724A pdb=" N LYS Z 449 " --> pdb=" O LEU Z 445 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 474 Processing helix chain 'Z' and resid 489 through 493 Processing helix chain 'Z' and resid 498 through 517 Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.529A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 Processing helix chain 'a' and resid 89 through 109 removed outlier: 3.701A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 135 Processing helix chain 'a' and resid 144 through 157 removed outlier: 3.763A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.423A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE a 179 " --> pdb=" O ALA a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 removed outlier: 3.576A pdb=" N GLU a 207 " --> pdb=" O SER a 204 " (cutoff:3.500A) Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 281 removed outlier: 3.776A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR a 281 " --> pdb=" O LYS a 277 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 304 Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'a' and resid 381 through 405 Processing helix chain 'a' and resid 413 through 427 Processing helix chain 'a' and resid 428 through 430 No H-bonds generated for 'chain 'a' and resid 428 through 430' Processing helix chain 'a' and resid 433 through 445 removed outlier: 4.018A pdb=" N ALA a 437 " --> pdb=" O ARG a 433 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 removed outlier: 3.519A pdb=" N ALA a 456 " --> pdb=" O LEU a 452 " (cutoff:3.500A) Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 478 through 484 removed outlier: 3.663A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 78 through 95 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 145 Processing helix chain 'b' and resid 151 through 168 Processing helix chain 'b' and resid 169 through 174 removed outlier: 6.639A pdb=" N LEU b 172 " --> pdb=" O SER b 169 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 189 Processing helix chain 'b' and resid 195 through 197 No H-bonds generated for 'chain 'b' and resid 195 through 197' Processing helix chain 'b' and resid 208 through 212 Processing helix chain 'b' and resid 260 through 284 removed outlier: 3.575A pdb=" N VAL b 264 " --> pdb=" O SER b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 307 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 426 Processing helix chain 'b' and resid 430 through 454 removed outlier: 4.137A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.851A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 472 Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 Processing helix chain 'd' and resid 73 through 81 Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.653A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 152 Processing helix chain 'd' and resid 159 through 172 removed outlier: 3.614A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 178 removed outlier: 6.795A pdb=" N VAL d 176 " --> pdb=" O SER d 173 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 193 Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 217 through 221 Processing helix chain 'd' and resid 268 through 293 removed outlier: 3.930A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 310 through 320 Processing helix chain 'd' and resid 329 through 331 No H-bonds generated for 'chain 'd' and resid 329 through 331' Processing helix chain 'd' and resid 332 through 341 Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 352 through 356 Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 443 Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.541A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.631A pdb=" N SER d 463 " --> pdb=" O GLU d 459 " (cutoff:3.500A) Processing helix chain 'd' and resid 472 through 486 Processing helix chain 'd' and resid 504 through 507 Processing helix chain 'd' and resid 512 through 531 removed outlier: 5.062A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 50 removed outlier: 3.503A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) Processing helix chain 'e' and resid 73 through 81 Processing helix chain 'e' and resid 85 through 102 Processing helix chain 'e' and resid 107 through 126 removed outlier: 3.572A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 152 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 176 through 180 removed outlier: 3.870A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 181 through 196 Processing helix chain 'e' and resid 205 through 207 No H-bonds generated for 'chain 'e' and resid 205 through 207' Processing helix chain 'e' and resid 218 through 222 Processing helix chain 'e' and resid 270 through 295 removed outlier: 3.833A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 307 through 317 Processing helix chain 'e' and resid 326 through 338 Processing helix chain 'e' and resid 344 through 348 Processing helix chain 'e' and resid 349 through 353 Processing helix chain 'e' and resid 391 through 415 Processing helix chain 'e' and resid 423 through 439 removed outlier: 3.634A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.544A pdb=" N GLN e 445 " --> pdb=" O PRO e 441 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 Processing helix chain 'e' and resid 469 through 484 Processing helix chain 'e' and resid 500 through 505 Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 19 through 38 removed outlier: 3.664A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 39 through 41 No H-bonds generated for 'chain 'g' and resid 39 through 41' Processing helix chain 'g' and resid 62 through 69 removed outlier: 3.659A pdb=" N GLU g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 114 removed outlier: 3.566A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.633A pdb=" N VAL g 122 " --> pdb=" O HIS g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 161 Processing helix chain 'g' and resid 163 through 167 removed outlier: 3.970A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 Processing helix chain 'g' and resid 208 through 212 Processing helix chain 'g' and resid 262 through 284 Processing helix chain 'g' and resid 297 through 306 Processing helix chain 'g' and resid 316 through 328 Processing helix chain 'g' and resid 334 through 338 Processing helix chain 'g' and resid 339 through 343 Processing helix chain 'g' and resid 380 through 404 Processing helix chain 'g' and resid 412 through 427 Processing helix chain 'g' and resid 433 through 443 Processing helix chain 'g' and resid 445 through 456 Processing helix chain 'g' and resid 458 through 471 Processing helix chain 'g' and resid 490 through 494 Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 18 through 35 removed outlier: 3.557A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.659A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.261A pdb=" N THR h 98 " --> pdb=" O THR h 94 " (cutoff:3.500A) Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 117 through 140 removed outlier: 3.676A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 147 through 164 Processing helix chain 'h' and resid 168 through 170 No H-bonds generated for 'chain 'h' and resid 168 through 170' Processing helix chain 'h' and resid 171 through 186 removed outlier: 3.777A pdb=" N LEU h 186 " --> pdb=" O ALA h 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 191 through 193 No H-bonds generated for 'chain 'h' and resid 191 through 193' Processing helix chain 'h' and resid 204 through 208 Processing helix chain 'h' and resid 224 through 228 removed outlier: 3.556A pdb=" N MET h 227 " --> pdb=" O GLY h 224 " (cutoff:3.500A) Processing helix chain 'h' and resid 259 through 284 Processing helix chain 'h' and resid 296 through 306 Processing helix chain 'h' and resid 315 through 327 Processing helix chain 'h' and resid 338 through 342 removed outlier: 3.594A pdb=" N LEU h 342 " --> pdb=" O ALA h 339 " (cutoff:3.500A) Processing helix chain 'h' and resid 378 through 402 Processing helix chain 'h' and resid 410 through 425 Processing helix chain 'h' and resid 429 through 442 removed outlier: 3.597A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 454 Processing helix chain 'h' and resid 456 through 471 Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'q' and resid 10 through 15 Processing helix chain 'q' and resid 24 through 45 removed outlier: 4.676A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 Processing helix chain 'q' and resid 80 through 97 Processing helix chain 'q' and resid 100 through 122 Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 156 through 168 removed outlier: 4.328A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 190 Processing helix chain 'q' and resid 198 through 200 No H-bonds generated for 'chain 'q' and resid 198 through 200' Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 261 through 286 removed outlier: 4.756A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR q 286 " --> pdb=" O ALA q 282 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 308 Processing helix chain 'q' and resid 317 through 329 Processing helix chain 'q' and resid 340 through 344 removed outlier: 3.548A pdb=" N MET q 344 " --> pdb=" O LEU q 341 " (cutoff:3.500A) Processing helix chain 'q' and resid 381 through 405 Processing helix chain 'q' and resid 413 through 429 removed outlier: 3.798A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 444 removed outlier: 4.182A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 457 Processing helix chain 'q' and resid 459 through 474 Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 2 through 8 removed outlier: 3.638A pdb=" N THR z 6 " --> pdb=" O ALA z 2 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 35 removed outlier: 3.667A pdb=" N LEU z 20 " --> pdb=" O ALA z 16 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 59 through 67 Processing helix chain 'z' and resid 71 through 88 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.585A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.838A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 3.768A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.535A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 189 No H-bonds generated for 'chain 'z' and resid 187 through 189' Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.817A pdb=" N THR z 204 " --> pdb=" O GLU z 201 " (cutoff:3.500A) Processing helix chain 'z' and resid 252 through 263 Processing helix chain 'z' and resid 264 through 282 removed outlier: 3.657A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 307 Processing helix chain 'z' and resid 317 through 329 removed outlier: 3.653A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 Processing helix chain 'z' and resid 380 through 404 removed outlier: 3.908A pdb=" N LEU z 384 " --> pdb=" O ASN z 380 " (cutoff:3.500A) Processing helix chain 'z' and resid 412 through 426 Processing helix chain 'z' and resid 427 through 429 No H-bonds generated for 'chain 'z' and resid 427 through 429' Processing helix chain 'z' and resid 430 through 432 No H-bonds generated for 'chain 'z' and resid 430 through 432' Processing helix chain 'z' and resid 433 through 445 Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.644A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 497 through 517 Processing sheet with id=AA1, first strand: chain 'P' and resid 162 through 164 removed outlier: 5.796A pdb=" N PHE P 162 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LYS P 218 " --> pdb=" O PHE P 162 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE P 164 " --> pdb=" O LYS P 218 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N CYS P 215 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET P 184 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL P 217 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N HIS P 186 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 200 through 203 removed outlier: 4.187A pdb=" N ALA N 200 " --> pdb=" O ALA N 213 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA N 213 " --> pdb=" O ALA N 200 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 242 through 244 Processing sheet with id=AA4, first strand: chain 'N' and resid 284 through 289 removed outlier: 3.877A pdb=" N SER N 298 " --> pdb=" O ARG N 306 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG N 306 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU N 307 " --> pdb=" O VAL N 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.392A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 52 through 55 removed outlier: 5.852A pdb=" N MET A 44 " --> pdb=" O VAL G 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA8, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.372A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.661A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.661A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.027A pdb=" N ASP G 255 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 252 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG B 255 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU H 254 " --> pdb=" O ILE Q 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AB4, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.355A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 61 through 64 removed outlier: 7.259A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB7, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.793A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.379A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER B 345 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LYS B 236 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS B 347 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS B 289 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE B 290 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AC1, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC2, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.383A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.475A pdb=" N CYS D 379 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA D 359 " --> pdb=" O CYS D 379 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.475A pdb=" N CYS D 379 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA D 359 " --> pdb=" O CYS D 379 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.651A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 28 through 29 removed outlier: 7.232A pdb=" N LEU H 48 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE E 533 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL H 50 " --> pdb=" O ILE E 533 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC8, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.499A pdb=" N LYS E 210 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE E 387 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU E 212 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N GLY E 389 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LYS E 214 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 228 through 230 removed outlier: 3.526A pdb=" N LEU E 358 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 248 through 250 removed outlier: 6.028A pdb=" N ALA E 249 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 57 through 60 removed outlier: 7.435A pdb=" N MET G 47 " --> pdb=" O GLU Z 520 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N MET Z 522 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET G 49 " --> pdb=" O MET Z 522 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD4, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.726A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD6, first strand: chain 'G' and resid 238 through 241 removed outlier: 3.526A pdb=" N THR G 292 " --> pdb=" O ILE G 312 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 407 through 409 Processing sheet with id=AD8, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AD9, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.274A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AE2, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.600A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AE4, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE5, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE6, first strand: chain 'Q' and resid 20 through 22 removed outlier: 4.874A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.932A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.478A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLY Q 379 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE Q 207 " --> pdb=" O GLY Q 379 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 220 through 223 removed outlier: 3.507A pdb=" N THR Q 358 " --> pdb=" O VAL Q 355 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AF2, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AF3, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AF4, first strand: chain 'Z' and resid 191 through 196 removed outlier: 3.547A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF6, first strand: chain 'Z' and resid 310 through 313 removed outlier: 9.060A pdb=" N VAL Z 311 " --> pdb=" O LYS Z 287 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE Z 289 " --> pdb=" O VAL Z 311 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU Z 313 " --> pdb=" O PHE Z 289 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL Z 291 " --> pdb=" O LEU Z 313 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.694A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 9 through 13 removed outlier: 4.290A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.185A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AG2, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AG3, first strand: chain 'a' and resid 196 through 201 removed outlier: 6.475A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.509A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.509A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.047A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 486 through 489 Processing sheet with id=AG8, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.424A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 61 through 64 removed outlier: 7.056A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AH2, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.594A pdb=" N HIS b 200 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU b 375 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE b 202 " --> pdb=" O LEU b 375 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY b 377 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LYS b 204 " --> pdb=" O GLY b 377 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.354A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU b 348 " --> pdb=" O GLU b 233 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU b 233 " --> pdb=" O LEU b 348 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH5, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH6, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.464A pdb=" N LYS d 209 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL d 390 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL d 211 " --> pdb=" O VAL d 390 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N GLY d 392 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LYS d 213 " --> pdb=" O GLY d 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.591A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.591A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AI1, first strand: chain 'e' and resid 26 through 29 removed outlier: 4.518A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AI3, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.350A pdb=" N LYS e 210 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE e 387 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU e 212 " --> pdb=" O ILE e 387 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N GLY e 389 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS e 214 " --> pdb=" O GLY e 389 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.465A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU e 299 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LYS e 247 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE e 301 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA e 249 " --> pdb=" O ILE e 301 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA e 300 " --> pdb=" O VAL e 322 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'g' and resid 57 through 60 removed outlier: 7.316A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI7, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI8, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.732A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AJ1, first strand: chain 'g' and resid 238 through 241 Processing sheet with id=AJ2, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AJ3, first strand: chain 'h' and resid 14 through 17 removed outlier: 6.479A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 141 through 142 Processing sheet with id=AJ5, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.449A pdb=" N GLY h 196 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU h 374 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS h 198 " --> pdb=" O LEU h 374 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLY h 376 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL h 200 " --> pdb=" O GLY h 376 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ7, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ8, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ9, first strand: chain 'q' and resid 20 through 23 removed outlier: 5.101A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.831A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.431A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY q 379 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE q 207 " --> pdb=" O GLY q 379 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AK4, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AK5, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK6, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK7, first strand: chain 'z' and resid 191 through 196 removed outlier: 3.564A pdb=" N SER z 205 " --> pdb=" O LEU z 375 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK9, first strand: chain 'z' and resid 310 through 313 removed outlier: 9.269A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'z' and resid 477 through 479 4070 hydrogen bonds defined for protein. 11619 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: 35.72 Time building geometry restraints manager: 16.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22830 1.34 - 1.46: 9480 1.46 - 1.58: 35680 1.58 - 1.70: 48 1.70 - 1.82: 745 Bond restraints: 68783 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" F2 AF3 a 603 " pdb="AL AF3 a 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.43e+01 bond pdb=" F2 AF3 D 603 " pdb="AL AF3 D 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" F2 AF3 A 603 " pdb="AL AF3 A 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.37e+01 ... (remaining 68778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 91904 2.12 - 4.24: 727 4.24 - 6.36: 222 6.36 - 8.48: 8 8.48 - 10.60: 1 Bond angle restraints: 92862 Sorted by residual: angle pdb=" C ASP a 47 " pdb=" N ASP a 48 " pdb=" CA ASP a 48 " ideal model delta sigma weight residual 122.61 127.92 -5.31 1.56e+00 4.11e-01 1.16e+01 angle pdb=" C GLU P 147 " pdb=" N MET P 148 " pdb=" CA MET P 148 " ideal model delta sigma weight residual 122.38 116.35 6.03 1.81e+00 3.05e-01 1.11e+01 angle pdb=" C VAL d 275 " pdb=" N LEU d 276 " pdb=" CA LEU d 276 " ideal model delta sigma weight residual 120.31 115.36 4.95 1.52e+00 4.33e-01 1.06e+01 angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 120.46 -7.28 2.37e+00 1.78e-01 9.43e+00 angle pdb=" C ALA Q 151 " pdb=" N LYS Q 152 " pdb=" CA LYS Q 152 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.21e+00 ... (remaining 92857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 41838 35.91 - 71.83: 585 71.83 - 107.74: 61 107.74 - 143.66: 7 143.66 - 179.57: 6 Dihedral angle restraints: 42497 sinusoidal: 17100 harmonic: 25397 Sorted by residual: dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 119.57 -179.57 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 116.13 -176.13 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 127.11 172.89 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 42494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 7582 0.033 - 0.067: 2299 0.067 - 0.100: 717 0.100 - 0.133: 433 0.133 - 0.167: 16 Chirality restraints: 11047 Sorted by residual: chirality pdb=" CA ASP a 48 " pdb=" N ASP a 48 " pdb=" C ASP a 48 " pdb=" CB ASP a 48 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CB ILE G 363 " pdb=" CA ILE G 363 " pdb=" CG1 ILE G 363 " pdb=" CG2 ILE G 363 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA GLN e 522 " pdb=" N GLN e 522 " pdb=" C GLN e 522 " pdb=" CB GLN e 522 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 11044 not shown) Planarity restraints: 11854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 5 " 0.056 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO G 6 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO G 6 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO G 6 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP a 47 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C ASP a 47 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP a 47 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP a 48 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO e 441 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.031 5.00e-02 4.00e+02 ... (remaining 11851 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 552 2.53 - 3.12: 51471 3.12 - 3.72: 107422 3.72 - 4.31: 149989 4.31 - 4.90: 257472 Nonbonded interactions: 566906 Sorted by model distance: nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.938 2.120 nonbonded pdb=" O1A ADP z 601 " pdb="MG MG z 602 " model vdw 1.982 2.170 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.983 2.120 nonbonded pdb="MG MG g 602 " pdb=" F1 AF3 g 603 " model vdw 1.984 2.120 nonbonded pdb=" OD1 ASP b 97 " pdb="MG MG b 602 " model vdw 1.985 2.170 ... (remaining 566901 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 2.150 Check model and map are aligned: 0.390 Set scattering table: 0.510 Process input model: 137.890 Find NCS groups from input model: 5.960 Set up NCS constraints: 0.460 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:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 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 0.161 68783 Z= 0.256 Angle : 0.514 10.599 92862 Z= 0.251 Chirality : 0.040 0.167 11047 Planarity : 0.003 0.083 11854 Dihedral : 14.165 179.570 26047 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.83 (0.09), residues: 8778 helix: 2.52 (0.08), residues: 4439 sheet: 0.32 (0.16), residues: 1163 loop : -0.32 (0.11), residues: 3176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.009 0.001 HIS z 161 PHE 0.019 0.001 PHE h 455 TYR 0.015 0.001 TYR z 351 ARG 0.004 0.000 ARG Z 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 604 time to evaluate : 6.610 Fit side-chains revert: symmetry clash REVERT: P 84 MET cc_start: 0.6265 (ttp) cc_final: 0.5745 (mtm) REVERT: N 184 MET cc_start: 0.8670 (tmm) cc_final: 0.8406 (tmm) REVERT: N 288 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7539 (ttp-110) REVERT: N 308 TYR cc_start: 0.8225 (m-80) cc_final: 0.7684 (m-80) REVERT: A 47 ASP cc_start: 0.8067 (m-30) cc_final: 0.7651 (m-30) REVERT: G 152 MET cc_start: 0.9095 (mmm) cc_final: 0.8886 (mmm) REVERT: H 14 ASP cc_start: 0.8373 (t0) cc_final: 0.8078 (t0) REVERT: Z 86 ASP cc_start: 0.8144 (m-30) cc_final: 0.7908 (m-30) REVERT: a 473 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7805 (OUTLIER) REVERT: d 513 LEU cc_start: 0.9074 (tp) cc_final: 0.8834 (tm) REVERT: e 21 ASP cc_start: 0.8635 (m-30) cc_final: 0.8413 (m-30) REVERT: e 67 ASP cc_start: 0.8552 (m-30) cc_final: 0.8325 (m-30) REVERT: g 415 GLU cc_start: 0.8241 (mp0) cc_final: 0.8026 (mp0) REVERT: h 324 MET cc_start: 0.9219 (mmm) cc_final: 0.8837 (mmm) REVERT: h 440 LYS cc_start: 0.9130 (tttt) cc_final: 0.8925 (mtpp) REVERT: q 121 ILE cc_start: 0.8925 (pt) cc_final: 0.8718 (pt) REVERT: z 10 LYS cc_start: 0.9009 (pttm) cc_final: 0.8735 (pmtt) REVERT: z 17 GLN cc_start: 0.8769 (mp10) cc_final: 0.8550 (mp10) REVERT: z 389 ASP cc_start: 0.8496 (m-30) cc_final: 0.8155 (m-30) outliers start: 0 outliers final: 3 residues processed: 604 average time/residue: 1.6143 time to fit residues: 1252.5201 Evaluate side-chains 480 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 478 time to evaluate : 6.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain G residue 519 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 738 optimal weight: 9.9990 chunk 663 optimal weight: 2.9990 chunk 368 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 447 optimal weight: 3.9990 chunk 354 optimal weight: 0.9990 chunk 685 optimal weight: 9.9990 chunk 265 optimal weight: 0.0070 chunk 417 optimal weight: 6.9990 chunk 510 optimal weight: 0.9990 chunk 794 optimal weight: 9.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 164 ASN E 522 GLN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN Z 84 GLN a 217 ASN b 91 GLN d 25 GLN d 468 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 41 GLN z 84 GLN z 161 HIS z 380 ASN z 382 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 68783 Z= 0.203 Angle : 0.557 8.507 92862 Z= 0.277 Chirality : 0.042 0.162 11047 Planarity : 0.003 0.063 11854 Dihedral : 7.289 169.866 9546 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.39 % Favored : 96.59 % Rotamer: Outliers : 0.52 % Allowed : 6.09 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.83 (0.09), residues: 8778 helix: 2.54 (0.08), residues: 4481 sheet: 0.26 (0.16), residues: 1120 loop : -0.36 (0.11), residues: 3177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.010 0.001 HIS z 161 PHE 0.022 0.001 PHE P 158 TYR 0.013 0.001 TYR E 420 ARG 0.008 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 506 time to evaluate : 6.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 84 MET cc_start: 0.6248 (ttp) cc_final: 0.5848 (mtt) REVERT: P 198 MET cc_start: 0.8797 (ppp) cc_final: 0.8592 (ppp) REVERT: N 288 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7824 (ttm110) REVERT: N 290 TYR cc_start: 0.8545 (t80) cc_final: 0.8301 (t80) REVERT: N 294 ASP cc_start: 0.8446 (p0) cc_final: 0.8074 (p0) REVERT: N 306 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7286 (ptp-170) REVERT: N 308 TYR cc_start: 0.8390 (m-80) cc_final: 0.8129 (m-10) REVERT: A 47 ASP cc_start: 0.7896 (m-30) cc_final: 0.7345 (m-30) REVERT: A 106 GLU cc_start: 0.8478 (tp30) cc_final: 0.8215 (tp30) REVERT: E 4 MET cc_start: 0.6087 (tmm) cc_final: 0.5285 (mpp) REVERT: G 47 MET cc_start: 0.8685 (mtp) cc_final: 0.8306 (mtp) REVERT: G 152 MET cc_start: 0.9240 (mmm) cc_final: 0.9032 (mmm) REVERT: G 497 GLU cc_start: 0.8353 (pt0) cc_final: 0.8115 (pt0) REVERT: G 527 LYS cc_start: 0.9047 (tppt) cc_final: 0.8665 (tppt) REVERT: H 14 ASP cc_start: 0.8391 (t0) cc_final: 0.8153 (t0) REVERT: H 53 ARG cc_start: 0.8429 (mtt180) cc_final: 0.8182 (mtt180) REVERT: Z 86 ASP cc_start: 0.8148 (m-30) cc_final: 0.7901 (m-30) REVERT: Z 415 GLU cc_start: 0.8395 (mp0) cc_final: 0.8145 (mp0) REVERT: a 47 ASP cc_start: 0.8376 (p0) cc_final: 0.8103 (p0) REVERT: a 156 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8722 (mtp) REVERT: a 473 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7936 (tp30) REVERT: b 452 ASP cc_start: 0.8252 (m-30) cc_final: 0.7992 (m-30) REVERT: d 513 LEU cc_start: 0.9109 (tp) cc_final: 0.8890 (tm) REVERT: e 4 MET cc_start: 0.5933 (mpp) cc_final: 0.5676 (mpp) REVERT: e 21 ASP cc_start: 0.8656 (m-30) cc_final: 0.8415 (m-30) REVERT: g 415 GLU cc_start: 0.8247 (mp0) cc_final: 0.7983 (mp0) REVERT: g 527 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8354 (mmmm) REVERT: h 455 PHE cc_start: 0.8166 (m-80) cc_final: 0.7749 (m-80) REVERT: q 249 MET cc_start: 0.8425 (pmm) cc_final: 0.8202 (pmm) REVERT: z 10 LYS cc_start: 0.9059 (pttm) cc_final: 0.8748 (pmtt) REVERT: z 244 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8094 (t) REVERT: z 389 ASP cc_start: 0.8516 (m-30) cc_final: 0.8196 (m-30) REVERT: z 520 GLU cc_start: 0.8527 (tt0) cc_final: 0.8280 (tt0) REVERT: z 522 MET cc_start: 0.8450 (mtm) cc_final: 0.8104 (mtm) outliers start: 38 outliers final: 13 residues processed: 517 average time/residue: 1.4989 time to fit residues: 1013.6505 Evaluate side-chains 494 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 478 time to evaluate : 6.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 306 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 248 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 441 optimal weight: 0.7980 chunk 246 optimal weight: 5.9990 chunk 661 optimal weight: 7.9990 chunk 541 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 796 optimal weight: 9.9990 chunk 859 optimal weight: 1.9990 chunk 708 optimal weight: 8.9990 chunk 789 optimal weight: 0.3980 chunk 271 optimal weight: 7.9990 chunk 638 optimal weight: 10.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 275 GLN A 164 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 ASN z 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 68783 Z= 0.247 Angle : 0.552 10.795 92862 Z= 0.272 Chirality : 0.042 0.167 11047 Planarity : 0.003 0.058 11854 Dihedral : 7.039 177.936 9542 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.43 % Rotamer: Outliers : 0.73 % Allowed : 7.49 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.09), residues: 8778 helix: 2.54 (0.08), residues: 4480 sheet: 0.10 (0.16), residues: 1120 loop : -0.39 (0.11), residues: 3178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.011 0.001 HIS z 161 PHE 0.018 0.001 PHE E 16 TYR 0.028 0.001 TYR A 181 ARG 0.006 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 491 time to evaluate : 6.242 Fit side-chains revert: symmetry clash REVERT: P 84 MET cc_start: 0.6179 (ttp) cc_final: 0.5780 (mtt) REVERT: N 182 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7579 (tm-30) REVERT: N 290 TYR cc_start: 0.8527 (t80) cc_final: 0.8326 (t80) REVERT: N 294 ASP cc_start: 0.8425 (p0) cc_final: 0.7927 (p0) REVERT: N 306 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7525 (ptp-170) REVERT: N 308 TYR cc_start: 0.8624 (m-80) cc_final: 0.8225 (m-80) REVERT: A 47 ASP cc_start: 0.7912 (m-30) cc_final: 0.7700 (m-30) REVERT: B 245 ASP cc_start: 0.8775 (p0) cc_final: 0.8551 (p0) REVERT: E 4 MET cc_start: 0.6095 (tmm) cc_final: 0.5113 (mpp) REVERT: E 474 MET cc_start: 0.8483 (tmm) cc_final: 0.8213 (tmt) REVERT: G 15 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8741 (mptp) REVERT: G 47 MET cc_start: 0.8802 (mtp) cc_final: 0.8521 (mtp) REVERT: G 358 GLU cc_start: 0.7551 (pm20) cc_final: 0.7351 (pm20) REVERT: G 527 LYS cc_start: 0.8951 (tppt) cc_final: 0.8667 (tppt) REVERT: H 14 ASP cc_start: 0.8362 (t0) cc_final: 0.8099 (t0) REVERT: Z 86 ASP cc_start: 0.8184 (m-30) cc_final: 0.7938 (m-30) REVERT: Z 415 GLU cc_start: 0.8385 (mp0) cc_final: 0.8151 (mp0) REVERT: a 47 ASP cc_start: 0.8449 (p0) cc_final: 0.8141 (p0) REVERT: a 156 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8721 (mtp) REVERT: a 473 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7946 (tp30) REVERT: b 452 ASP cc_start: 0.8253 (m-30) cc_final: 0.7982 (m-30) REVERT: d 513 LEU cc_start: 0.9043 (tp) cc_final: 0.8781 (tm) REVERT: e 4 MET cc_start: 0.6242 (mpp) cc_final: 0.5735 (mpp) REVERT: e 21 ASP cc_start: 0.8622 (m-30) cc_final: 0.8412 (m-30) REVERT: g 415 GLU cc_start: 0.8365 (mp0) cc_final: 0.8067 (mp0) REVERT: g 527 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8363 (mmmm) REVERT: q 61 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8024 (mm-30) REVERT: q 249 MET cc_start: 0.8454 (pmm) cc_final: 0.8235 (pmm) REVERT: z 10 LYS cc_start: 0.9084 (pttm) cc_final: 0.8731 (pmtt) REVERT: z 389 ASP cc_start: 0.8527 (m-30) cc_final: 0.8202 (m-30) outliers start: 54 outliers final: 22 residues processed: 519 average time/residue: 1.5705 time to fit residues: 1058.7379 Evaluate side-chains 499 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 474 time to evaluate : 6.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 306 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 244 MET Chi-restraints excluded: chain b residue 248 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 185 MET Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 786 optimal weight: 0.9980 chunk 598 optimal weight: 1.9990 chunk 413 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 379 optimal weight: 8.9990 chunk 534 optimal weight: 8.9990 chunk 798 optimal weight: 6.9990 chunk 845 optimal weight: 8.9990 chunk 417 optimal weight: 8.9990 chunk 757 optimal weight: 0.9990 chunk 227 optimal weight: 0.2980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN D 502 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 68783 Z= 0.170 Angle : 0.527 11.928 92862 Z= 0.258 Chirality : 0.041 0.156 11047 Planarity : 0.003 0.056 11854 Dihedral : 6.869 175.282 9542 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.16 % Favored : 96.82 % Rotamer: Outliers : 0.72 % Allowed : 8.61 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.84 (0.09), residues: 8778 helix: 2.61 (0.08), residues: 4475 sheet: 0.11 (0.16), residues: 1114 loop : -0.39 (0.11), residues: 3189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.012 0.001 HIS z 161 PHE 0.016 0.001 PHE E 16 TYR 0.016 0.001 TYR D 24 ARG 0.008 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 508 time to evaluate : 6.451 Fit side-chains revert: symmetry clash REVERT: N 188 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8962 (tppt) REVERT: N 210 ILE cc_start: 0.8948 (pt) cc_final: 0.8591 (pp) REVERT: N 289 TYR cc_start: 0.7383 (m-80) cc_final: 0.6661 (m-80) REVERT: N 306 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7513 (pmm-80) REVERT: N 308 TYR cc_start: 0.8581 (m-80) cc_final: 0.8377 (m-10) REVERT: E 4 MET cc_start: 0.5960 (tmm) cc_final: 0.5424 (ptp) REVERT: E 185 MET cc_start: 0.9079 (mmt) cc_final: 0.8733 (mmm) REVERT: E 448 MET cc_start: 0.8960 (mtt) cc_final: 0.8737 (mmm) REVERT: E 474 MET cc_start: 0.8439 (tmm) cc_final: 0.8133 (tmt) REVERT: G 47 MET cc_start: 0.8761 (mtp) cc_final: 0.8464 (mtp) REVERT: G 358 GLU cc_start: 0.7609 (pm20) cc_final: 0.7390 (pm20) REVERT: G 527 LYS cc_start: 0.8908 (tppt) cc_final: 0.8611 (tppt) REVERT: H 14 ASP cc_start: 0.8311 (t0) cc_final: 0.8075 (t0) REVERT: Z 86 ASP cc_start: 0.8172 (m-30) cc_final: 0.7923 (m-30) REVERT: Z 415 GLU cc_start: 0.8421 (mp0) cc_final: 0.8182 (mp0) REVERT: a 47 ASP cc_start: 0.8527 (p0) cc_final: 0.8204 (p0) REVERT: a 156 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8556 (mtm) REVERT: a 416 GLU cc_start: 0.8314 (mp0) cc_final: 0.7782 (mp0) REVERT: a 473 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7942 (tp30) REVERT: b 452 ASP cc_start: 0.8236 (m-30) cc_final: 0.7973 (m-30) REVERT: d 513 LEU cc_start: 0.9005 (tp) cc_final: 0.8744 (tm) REVERT: e 4 MET cc_start: 0.6282 (mpp) cc_final: 0.5802 (mpp) REVERT: g 415 GLU cc_start: 0.8381 (mp0) cc_final: 0.8096 (mp0) REVERT: h 455 PHE cc_start: 0.8174 (m-10) cc_final: 0.7970 (m-10) REVERT: q 61 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8050 (mm-30) REVERT: q 249 MET cc_start: 0.8480 (pmm) cc_final: 0.8248 (pmm) REVERT: z 10 LYS cc_start: 0.8969 (pttm) cc_final: 0.8699 (pmtt) REVERT: z 244 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8043 (t) REVERT: z 389 ASP cc_start: 0.8514 (m-30) cc_final: 0.8196 (m-30) outliers start: 53 outliers final: 19 residues processed: 533 average time/residue: 1.5348 time to fit residues: 1071.0181 Evaluate side-chains 499 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 477 time to evaluate : 6.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 306 ARG Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 704 optimal weight: 6.9990 chunk 480 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 629 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 chunk 721 optimal weight: 8.9990 chunk 584 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 431 optimal weight: 9.9990 chunk 759 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 151 GLN N 231 GLN A 164 ASN ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 217 ASN a 435 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 41 GLN z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 68783 Z= 0.284 Angle : 0.563 12.404 92862 Z= 0.277 Chirality : 0.042 0.170 11047 Planarity : 0.003 0.056 11854 Dihedral : 6.814 171.572 9542 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 0.91 % Allowed : 9.61 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.77 (0.09), residues: 8778 helix: 2.56 (0.08), residues: 4480 sheet: -0.03 (0.15), residues: 1146 loop : -0.40 (0.11), residues: 3152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 304 HIS 0.012 0.001 HIS z 161 PHE 0.018 0.001 PHE E 16 TYR 0.028 0.001 TYR A 181 ARG 0.007 0.000 ARG N 311 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 478 time to evaluate : 6.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7593 (tm-30) REVERT: N 210 ILE cc_start: 0.8964 (pt) cc_final: 0.8593 (pp) REVERT: N 288 ARG cc_start: 0.8063 (ttm170) cc_final: 0.7764 (ttm170) REVERT: N 306 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7364 (pmm-80) REVERT: A 47 ASP cc_start: 0.7903 (m-30) cc_final: 0.7691 (p0) REVERT: E 474 MET cc_start: 0.8466 (tmm) cc_final: 0.8164 (tmt) REVERT: G 15 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8755 (mptp) REVERT: G 47 MET cc_start: 0.8862 (mtp) cc_final: 0.8529 (mtp) REVERT: G 527 LYS cc_start: 0.8893 (tppt) cc_final: 0.8616 (tppt) REVERT: H 14 ASP cc_start: 0.8360 (t0) cc_final: 0.8110 (t0) REVERT: Z 86 ASP cc_start: 0.8219 (m-30) cc_final: 0.7955 (m-30) REVERT: Z 244 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8365 (t) REVERT: Z 415 GLU cc_start: 0.8488 (mp0) cc_final: 0.8226 (mp0) REVERT: a 47 ASP cc_start: 0.8544 (p0) cc_final: 0.8276 (p0) REVERT: a 156 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8572 (mtm) REVERT: a 416 GLU cc_start: 0.8333 (mp0) cc_final: 0.7797 (mp0) REVERT: a 473 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7948 (tp30) REVERT: b 452 ASP cc_start: 0.8276 (m-30) cc_final: 0.8031 (m-30) REVERT: d 513 LEU cc_start: 0.9031 (tp) cc_final: 0.8748 (tm) REVERT: e 4 MET cc_start: 0.6298 (mpp) cc_final: 0.5762 (mpp) REVERT: e 80 MET cc_start: 0.8996 (mmt) cc_final: 0.8539 (mtt) REVERT: g 415 GLU cc_start: 0.8404 (mp0) cc_final: 0.8115 (mp0) REVERT: g 527 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8379 (mmmm) REVERT: h 316 GLU cc_start: 0.8000 (tp30) cc_final: 0.7740 (tp30) REVERT: q 61 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8163 (mm-30) REVERT: q 249 MET cc_start: 0.8479 (pmm) cc_final: 0.8219 (pmm) REVERT: z 10 LYS cc_start: 0.8962 (pttm) cc_final: 0.8670 (pmtt) REVERT: z 244 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8111 (t) REVERT: z 389 ASP cc_start: 0.8562 (m-30) cc_final: 0.8221 (m-30) outliers start: 67 outliers final: 28 residues processed: 516 average time/residue: 1.5036 time to fit residues: 1014.1027 Evaluate side-chains 503 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 470 time to evaluate : 6.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 306 ARG Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 196 MET Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 522 GLN Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 284 optimal weight: 2.9990 chunk 761 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 496 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 chunk 846 optimal weight: 9.9990 chunk 702 optimal weight: 2.9990 chunk 391 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 280 optimal weight: 7.9990 chunk 444 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN G 111 HIS ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 68783 Z= 0.270 Angle : 0.564 12.710 92862 Z= 0.276 Chirality : 0.042 0.165 11047 Planarity : 0.003 0.056 11854 Dihedral : 6.751 170.935 9542 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 0.98 % Allowed : 10.23 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.75 (0.09), residues: 8778 helix: 2.54 (0.08), residues: 4486 sheet: -0.03 (0.16), residues: 1130 loop : -0.42 (0.11), residues: 3162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 304 HIS 0.017 0.001 HIS z 161 PHE 0.028 0.001 PHE N 296 TYR 0.018 0.001 TYR D 24 ARG 0.009 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 483 time to evaluate : 6.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7579 (tm-30) REVERT: N 210 ILE cc_start: 0.8974 (pt) cc_final: 0.8602 (pp) REVERT: N 306 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7326 (pmm-80) REVERT: N 308 TYR cc_start: 0.8686 (m-80) cc_final: 0.8186 (m-80) REVERT: B 245 ASP cc_start: 0.8794 (p0) cc_final: 0.8587 (p0) REVERT: E 4 MET cc_start: 0.6057 (tmm) cc_final: 0.5025 (mpp) REVERT: E 448 MET cc_start: 0.8971 (mtt) cc_final: 0.8697 (mmm) REVERT: G 15 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8760 (mptp) REVERT: G 47 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8509 (mtp) REVERT: G 527 LYS cc_start: 0.8869 (tppt) cc_final: 0.8633 (tppt) REVERT: H 14 ASP cc_start: 0.8389 (t0) cc_final: 0.8110 (t0) REVERT: H 455 PHE cc_start: 0.8049 (m-10) cc_final: 0.7836 (m-10) REVERT: Q 61 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: Z 86 ASP cc_start: 0.8217 (m-30) cc_final: 0.7948 (m-30) REVERT: Z 244 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8346 (t) REVERT: Z 415 GLU cc_start: 0.8468 (mp0) cc_final: 0.8208 (mp0) REVERT: a 156 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8496 (mtm) REVERT: a 416 GLU cc_start: 0.8337 (mp0) cc_final: 0.7796 (mp0) REVERT: a 473 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7967 (tp30) REVERT: b 87 MET cc_start: 0.9155 (ttp) cc_final: 0.8928 (ttp) REVERT: b 244 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8454 (mtm) REVERT: b 452 ASP cc_start: 0.8272 (m-30) cc_final: 0.8027 (m-30) REVERT: d 513 LEU cc_start: 0.9020 (tp) cc_final: 0.8740 (tm) REVERT: e 4 MET cc_start: 0.6339 (mpp) cc_final: 0.5771 (mpp) REVERT: e 80 MET cc_start: 0.8982 (mmt) cc_final: 0.8539 (mtt) REVERT: e 526 MET cc_start: 0.9176 (ttt) cc_final: 0.8814 (ttt) REVERT: g 415 GLU cc_start: 0.8420 (mp0) cc_final: 0.8138 (mp0) REVERT: h 7 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8521 (pp) REVERT: q 61 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8148 (mm-30) REVERT: q 249 MET cc_start: 0.8477 (pmm) cc_final: 0.8210 (pmm) REVERT: z 10 LYS cc_start: 0.8932 (pttm) cc_final: 0.8659 (pmtt) REVERT: z 244 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8038 (t) REVERT: z 389 ASP cc_start: 0.8562 (m-30) cc_final: 0.8218 (m-30) outliers start: 72 outliers final: 25 residues processed: 526 average time/residue: 1.5520 time to fit residues: 1064.9049 Evaluate side-chains 498 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 464 time to evaluate : 6.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 306 ARG Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Z residue 196 MET Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 244 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 522 GLN Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 816 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 482 optimal weight: 2.9990 chunk 618 optimal weight: 0.4980 chunk 479 optimal weight: 5.9990 chunk 712 optimal weight: 4.9990 chunk 472 optimal weight: 4.9990 chunk 843 optimal weight: 3.9990 chunk 527 optimal weight: 0.3980 chunk 514 optimal weight: 0.9990 chunk 389 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN G 111 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 68783 Z= 0.155 Angle : 0.536 13.649 92862 Z= 0.261 Chirality : 0.041 0.177 11047 Planarity : 0.003 0.055 11854 Dihedral : 6.533 166.568 9542 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 0.64 % Allowed : 10.82 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.09), residues: 8778 helix: 2.63 (0.08), residues: 4481 sheet: 0.08 (0.16), residues: 1104 loop : -0.39 (0.11), residues: 3193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.015 0.001 HIS z 161 PHE 0.015 0.001 PHE E 16 TYR 0.027 0.001 TYR A 181 ARG 0.009 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 504 time to evaluate : 6.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 188 LYS cc_start: 0.9342 (tppt) cc_final: 0.9130 (tppp) REVERT: N 210 ILE cc_start: 0.8904 (pt) cc_final: 0.8545 (pp) REVERT: N 289 TYR cc_start: 0.7479 (m-80) cc_final: 0.6724 (m-80) REVERT: N 306 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7561 (pmm-80) REVERT: N 308 TYR cc_start: 0.8712 (m-80) cc_final: 0.8335 (m-80) REVERT: D 28 ASP cc_start: 0.8451 (t0) cc_final: 0.8060 (t70) REVERT: E 4 MET cc_start: 0.5922 (tmm) cc_final: 0.4869 (mpp) REVERT: E 48 MET cc_start: 0.9156 (tpp) cc_final: 0.8931 (mmm) REVERT: G 15 LYS cc_start: 0.9001 (mptm) cc_final: 0.8752 (mptp) REVERT: G 47 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8519 (mtp) REVERT: H 14 ASP cc_start: 0.8314 (t0) cc_final: 0.8076 (t0) REVERT: Q 61 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: Z 36 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9177 (p) REVERT: Z 86 ASP cc_start: 0.8158 (m-30) cc_final: 0.7905 (m-30) REVERT: Z 244 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8244 (t) REVERT: Z 415 GLU cc_start: 0.8459 (mp0) cc_final: 0.8194 (mp0) REVERT: a 156 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8459 (mtm) REVERT: a 344 MET cc_start: 0.8289 (mmm) cc_final: 0.7851 (mmm) REVERT: a 473 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7938 (tp30) REVERT: b 244 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8461 (mtm) REVERT: b 452 ASP cc_start: 0.8206 (m-30) cc_final: 0.7957 (m-30) REVERT: d 513 LEU cc_start: 0.8979 (tp) cc_final: 0.8713 (tm) REVERT: e 4 MET cc_start: 0.6415 (mpp) cc_final: 0.5851 (mpp) REVERT: e 80 MET cc_start: 0.8925 (mmt) cc_final: 0.8494 (mtt) REVERT: e 526 MET cc_start: 0.9129 (ttt) cc_final: 0.8834 (ttt) REVERT: g 415 GLU cc_start: 0.8439 (mp0) cc_final: 0.8210 (mp0) REVERT: g 527 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8272 (mmmm) REVERT: h 7 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8546 (pp) REVERT: h 185 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8252 (mtp) REVERT: h 455 PHE cc_start: 0.8093 (m-10) cc_final: 0.7786 (m-10) REVERT: q 61 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8130 (mm-30) REVERT: q 249 MET cc_start: 0.8481 (pmm) cc_final: 0.8214 (pmm) REVERT: z 10 LYS cc_start: 0.8926 (pttm) cc_final: 0.8650 (pmtt) REVERT: z 244 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8002 (t) REVERT: z 389 ASP cc_start: 0.8537 (m-30) cc_final: 0.8181 (m-30) outliers start: 47 outliers final: 21 residues processed: 531 average time/residue: 1.5347 time to fit residues: 1066.9456 Evaluate side-chains 514 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 483 time to evaluate : 6.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 306 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 244 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 522 GLN Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 185 MET Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 521 optimal weight: 0.8980 chunk 336 optimal weight: 0.9990 chunk 503 optimal weight: 10.0000 chunk 254 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 536 optimal weight: 1.9990 chunk 574 optimal weight: 7.9990 chunk 416 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 662 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 ASN A 164 ASN G 111 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 68783 Z= 0.158 Angle : 0.540 15.053 92862 Z= 0.261 Chirality : 0.041 0.169 11047 Planarity : 0.003 0.057 11854 Dihedral : 6.413 163.779 9542 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 0.65 % Allowed : 11.25 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.88 (0.09), residues: 8778 helix: 2.67 (0.08), residues: 4474 sheet: 0.04 (0.16), residues: 1129 loop : -0.38 (0.11), residues: 3175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 222 HIS 0.016 0.001 HIS z 161 PHE 0.032 0.001 PHE N 296 TYR 0.020 0.001 TYR z 498 ARG 0.008 0.000 ARG N 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 502 time to evaluate : 6.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 188 LYS cc_start: 0.9360 (tppt) cc_final: 0.9126 (tppp) REVERT: N 210 ILE cc_start: 0.8882 (pt) cc_final: 0.8545 (pp) REVERT: N 289 TYR cc_start: 0.7577 (m-80) cc_final: 0.6834 (m-80) REVERT: N 294 ASP cc_start: 0.8266 (p0) cc_final: 0.8005 (p0) REVERT: D 28 ASP cc_start: 0.8455 (t0) cc_final: 0.8100 (t70) REVERT: E 4 MET cc_start: 0.6030 (tmm) cc_final: 0.4942 (mpp) REVERT: E 48 MET cc_start: 0.9154 (tpp) cc_final: 0.8927 (mmm) REVERT: E 185 MET cc_start: 0.9065 (mmt) cc_final: 0.8715 (mmm) REVERT: E 474 MET cc_start: 0.8597 (tmm) cc_final: 0.8225 (tmt) REVERT: G 15 LYS cc_start: 0.9016 (mptm) cc_final: 0.8743 (mptp) REVERT: G 47 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8511 (mtp) REVERT: H 14 ASP cc_start: 0.8312 (t0) cc_final: 0.8068 (t0) REVERT: Q 61 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: Z 86 ASP cc_start: 0.8161 (m-30) cc_final: 0.7911 (m-30) REVERT: Z 244 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8231 (t) REVERT: Z 415 GLU cc_start: 0.8477 (mp0) cc_final: 0.8227 (mp0) REVERT: a 156 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8452 (mtm) REVERT: a 473 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7935 (tp30) REVERT: b 452 ASP cc_start: 0.8193 (m-30) cc_final: 0.7948 (m-30) REVERT: d 458 MET cc_start: 0.8953 (mmp) cc_final: 0.8751 (mmm) REVERT: d 513 LEU cc_start: 0.8996 (tp) cc_final: 0.8719 (tm) REVERT: e 4 MET cc_start: 0.6452 (mpp) cc_final: 0.5887 (mpp) REVERT: e 80 MET cc_start: 0.8905 (mmt) cc_final: 0.8499 (mtt) REVERT: e 526 MET cc_start: 0.9145 (ttt) cc_final: 0.8826 (ttt) REVERT: g 415 GLU cc_start: 0.8449 (mp0) cc_final: 0.8244 (mp0) REVERT: g 527 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8248 (mmmm) REVERT: h 7 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8572 (pp) REVERT: h 185 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8122 (mtp) REVERT: h 221 SER cc_start: 0.9143 (m) cc_final: 0.8840 (p) REVERT: h 455 PHE cc_start: 0.8073 (m-10) cc_final: 0.7858 (m-10) REVERT: q 61 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8115 (mm-30) REVERT: q 249 MET cc_start: 0.8466 (pmm) cc_final: 0.8191 (pmm) REVERT: z 10 LYS cc_start: 0.8945 (pttm) cc_final: 0.8600 (pmtt) REVERT: z 244 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.8010 (t) REVERT: z 389 ASP cc_start: 0.8504 (m-30) cc_final: 0.8147 (m-30) outliers start: 48 outliers final: 24 residues processed: 529 average time/residue: 1.5082 time to fit residues: 1053.3371 Evaluate side-chains 514 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 483 time to evaluate : 6.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 522 GLN Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 185 MET Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 767 optimal weight: 1.9990 chunk 807 optimal weight: 8.9990 chunk 737 optimal weight: 0.8980 chunk 785 optimal weight: 0.6980 chunk 473 optimal weight: 0.1980 chunk 342 optimal weight: 0.4980 chunk 617 optimal weight: 0.6980 chunk 241 optimal weight: 0.6980 chunk 710 optimal weight: 2.9990 chunk 743 optimal weight: 10.0000 chunk 783 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN G 111 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 217 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 30 GLN h 331 GLN z 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 68783 Z= 0.133 Angle : 0.532 15.828 92862 Z= 0.257 Chirality : 0.040 0.180 11047 Planarity : 0.003 0.057 11854 Dihedral : 6.245 156.199 9542 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.05 % Rotamer: Outliers : 0.48 % Allowed : 11.73 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.94 (0.09), residues: 8778 helix: 2.72 (0.08), residues: 4470 sheet: 0.06 (0.16), residues: 1137 loop : -0.35 (0.11), residues: 3171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.017 0.001 HIS z 161 PHE 0.012 0.001 PHE E 16 TYR 0.026 0.001 TYR A 181 ARG 0.008 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 516 time to evaluate : 7.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 210 ILE cc_start: 0.8856 (pt) cc_final: 0.8555 (pp) REVERT: N 289 TYR cc_start: 0.7756 (m-80) cc_final: 0.7103 (m-80) REVERT: N 294 ASP cc_start: 0.8090 (p0) cc_final: 0.7855 (p0) REVERT: N 296 PHE cc_start: 0.8544 (p90) cc_final: 0.8325 (p90) REVERT: N 311 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8447 (mtm-85) REVERT: D 28 ASP cc_start: 0.8442 (t0) cc_final: 0.8112 (t70) REVERT: D 186 MET cc_start: 0.8530 (ttm) cc_final: 0.8119 (ttm) REVERT: E 4 MET cc_start: 0.6016 (tmm) cc_final: 0.4931 (mpp) REVERT: E 48 MET cc_start: 0.9131 (tpp) cc_final: 0.8930 (mmm) REVERT: G 15 LYS cc_start: 0.9019 (mptm) cc_final: 0.8740 (mptp) REVERT: G 47 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8480 (mtp) REVERT: Q 61 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: Z 36 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9172 (p) REVERT: Z 415 GLU cc_start: 0.8470 (mp0) cc_final: 0.8220 (mp0) REVERT: a 156 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8412 (mtm) REVERT: a 344 MET cc_start: 0.8268 (mmm) cc_final: 0.7849 (mmm) REVERT: a 473 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7931 (tp30) REVERT: b 452 ASP cc_start: 0.8151 (m-30) cc_final: 0.7908 (m-30) REVERT: d 513 LEU cc_start: 0.8961 (tp) cc_final: 0.8696 (tm) REVERT: e 4 MET cc_start: 0.6478 (mpp) cc_final: 0.5914 (mpp) REVERT: e 80 MET cc_start: 0.8895 (mmt) cc_final: 0.8328 (mtt) REVERT: e 426 GLU cc_start: 0.8508 (mp0) cc_final: 0.8250 (mp0) REVERT: e 448 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8060 (mmt) REVERT: e 526 MET cc_start: 0.9102 (ttt) cc_final: 0.8805 (ttt) REVERT: g 527 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8268 (mmmm) REVERT: h 185 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8090 (mtp) REVERT: q 61 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8082 (mm-30) REVERT: q 208 LEU cc_start: 0.8327 (mt) cc_final: 0.8101 (mt) REVERT: q 249 MET cc_start: 0.8422 (pmm) cc_final: 0.8156 (pmm) REVERT: z 10 LYS cc_start: 0.8936 (pttm) cc_final: 0.8597 (pmtt) REVERT: z 244 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.7955 (t) REVERT: z 389 ASP cc_start: 0.8478 (m-30) cc_final: 0.8132 (m-30) outliers start: 35 outliers final: 17 residues processed: 538 average time/residue: 1.5297 time to fit residues: 1080.2899 Evaluate side-chains 516 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 492 time to evaluate : 6.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 448 MET Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 185 MET Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 516 optimal weight: 4.9990 chunk 831 optimal weight: 3.9990 chunk 507 optimal weight: 2.9990 chunk 394 optimal weight: 0.8980 chunk 577 optimal weight: 0.0270 chunk 871 optimal weight: 5.9990 chunk 802 optimal weight: 6.9990 chunk 694 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 536 optimal weight: 2.9990 chunk 425 optimal weight: 0.0980 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN G 111 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 41 GLN z 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 68783 Z= 0.162 Angle : 0.544 17.585 92862 Z= 0.262 Chirality : 0.041 0.222 11047 Planarity : 0.003 0.057 11854 Dihedral : 6.194 152.857 9542 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.98 % Rotamer: Outliers : 0.45 % Allowed : 12.03 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.94 (0.09), residues: 8778 helix: 2.71 (0.08), residues: 4480 sheet: 0.07 (0.16), residues: 1136 loop : -0.34 (0.11), residues: 3162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 222 HIS 0.016 0.001 HIS z 161 PHE 0.025 0.001 PHE h 455 TYR 0.028 0.001 TYR z 498 ARG 0.008 0.000 ARG E 478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 496 time to evaluate : 6.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 210 ILE cc_start: 0.8900 (pt) cc_final: 0.8603 (pp) REVERT: N 289 TYR cc_start: 0.7806 (m-80) cc_final: 0.7144 (m-80) REVERT: N 294 ASP cc_start: 0.8052 (p0) cc_final: 0.7806 (p0) REVERT: N 311 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8408 (mtm-85) REVERT: D 28 ASP cc_start: 0.8436 (t0) cc_final: 0.8111 (t70) REVERT: D 186 MET cc_start: 0.8539 (ttm) cc_final: 0.8153 (ttm) REVERT: E 4 MET cc_start: 0.5910 (tmm) cc_final: 0.4876 (mpp) REVERT: E 48 MET cc_start: 0.9137 (tpp) cc_final: 0.8930 (mmm) REVERT: G 15 LYS cc_start: 0.9049 (mptm) cc_final: 0.8768 (mptp) REVERT: G 17 GLU cc_start: 0.7808 (mp0) cc_final: 0.7589 (mp0) REVERT: Q 61 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: Z 415 GLU cc_start: 0.8469 (mp0) cc_final: 0.8212 (mp0) REVERT: a 156 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8426 (mtm) REVERT: a 344 MET cc_start: 0.8264 (mmm) cc_final: 0.7837 (mmm) REVERT: a 473 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7932 (tp30) REVERT: b 248 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8790 (mmtp) REVERT: b 452 ASP cc_start: 0.8132 (m-30) cc_final: 0.7796 (m-30) REVERT: d 513 LEU cc_start: 0.8982 (tp) cc_final: 0.8703 (tm) REVERT: e 4 MET cc_start: 0.6474 (mpp) cc_final: 0.5908 (mpp) REVERT: e 80 MET cc_start: 0.8893 (mmt) cc_final: 0.8331 (mtt) REVERT: e 426 GLU cc_start: 0.8517 (mp0) cc_final: 0.8256 (mp0) REVERT: e 526 MET cc_start: 0.9139 (ttt) cc_final: 0.8811 (ttt) REVERT: g 527 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8268 (mmmm) REVERT: h 185 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8094 (mtp) REVERT: h 316 GLU cc_start: 0.7891 (tp30) cc_final: 0.7638 (tp30) REVERT: q 61 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8124 (mm-30) REVERT: q 208 LEU cc_start: 0.8385 (mt) cc_final: 0.8160 (mt) REVERT: q 249 MET cc_start: 0.8415 (pmm) cc_final: 0.8145 (pmm) REVERT: z 10 LYS cc_start: 0.8938 (pttm) cc_final: 0.8597 (pmtt) REVERT: z 244 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8003 (t) REVERT: z 389 ASP cc_start: 0.8484 (m-30) cc_final: 0.8150 (m-30) outliers start: 33 outliers final: 16 residues processed: 516 average time/residue: 1.5729 time to fit residues: 1060.4145 Evaluate side-chains 503 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 482 time to evaluate : 6.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 248 LYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 185 MET Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 551 optimal weight: 6.9990 chunk 739 optimal weight: 4.9990 chunk 212 optimal weight: 0.2980 chunk 640 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 695 optimal weight: 10.0000 chunk 290 optimal weight: 0.5980 chunk 713 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN G 111 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN z 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.074065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.058681 restraints weight = 235481.910| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.49 r_work: 0.2619 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 68783 Z= 0.140 Angle : 0.541 18.854 92862 Z= 0.260 Chirality : 0.041 0.195 11047 Planarity : 0.003 0.057 11854 Dihedral : 6.091 145.925 9542 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.05 % Rotamer: Outliers : 0.39 % Allowed : 12.05 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.96 (0.09), residues: 8778 helix: 2.74 (0.08), residues: 4472 sheet: 0.06 (0.16), residues: 1138 loop : -0.35 (0.11), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.017 0.001 HIS z 161 PHE 0.026 0.001 PHE N 296 TYR 0.029 0.001 TYR z 498 ARG 0.008 0.000 ARG H 425 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17340.43 seconds wall clock time: 303 minutes 58.58 seconds (18238.58 seconds total)