Starting phenix.real_space_refine on Thu Feb 15 16:07:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6q_24208/02_2024/7n6q_24208_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6q_24208/02_2024/7n6q_24208.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6q_24208/02_2024/7n6q_24208_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6q_24208/02_2024/7n6q_24208_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6q_24208/02_2024/7n6q_24208_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6q_24208/02_2024/7n6q_24208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6q_24208/02_2024/7n6q_24208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6q_24208/02_2024/7n6q_24208_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6q_24208/02_2024/7n6q_24208_updated.pdb" } resolution = 3.87 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= -0.005 sd= 1.025 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 8672 2.51 5 N 1996 2.21 5 O 1984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 409": "OD1" <-> "OD2" Residue "B ARG 417": "NH1" <-> "NH2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 142": "OD1" <-> "OD2" Residue "C TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 409": "OD1" <-> "OD2" Residue "C ARG 417": "NH1" <-> "NH2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 142": "OD1" <-> "OD2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 409": "OD1" <-> "OD2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 419": "NH1" <-> "NH2" Residue "D TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 495": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12752 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "B" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "C" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "D" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'7T8': 1, 'CLR': 2, 'OLA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'7T8': 1, 'CLR': 2, 'OLA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'7T8': 1, 'CLR': 2, 'OLA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'7T8': 1, 'CLR': 2, 'OLA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.31, per 1000 atoms: 0.57 Number of scatterers: 12752 At special positions: 0 Unit cell: (150.773, 142.443, 79.135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 1984 8.00 N 1996 7.00 C 8672 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.53 Conformation dependent library (CDL) restraints added in 2.4 seconds 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 0 sheets defined 72.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 118 through 142 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 163 through 188 Proline residue: A 172 - end of helix Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 199 through 220 removed outlier: 3.621A pdb=" N LEU A 203 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU A 204 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS A 207 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 210 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU A 211 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 212 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 213 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU A 214 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 4.604A pdb=" N VAL A 218 " --> pdb=" O PRO A 215 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 220 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.767A pdb=" N VAL A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 removed outlier: 4.180A pdb=" N LEU A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.767A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 318 Processing helix chain 'A' and resid 320 through 323 No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 333 through 369 removed outlier: 4.624A pdb=" N LEU A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 4.483A pdb=" N TRP A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 387 through 393 Processing helix chain 'A' and resid 396 through 408 Processing helix chain 'A' and resid 410 through 413 No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 420 through 441 Processing helix chain 'A' and resid 448 through 462 Processing helix chain 'A' and resid 473 through 498 removed outlier: 3.583A pdb=" N ILE A 487 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 489 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 491 " --> pdb=" O GLN A 488 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 494 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 118 through 143 Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 163 through 188 Proline residue: B 172 - end of helix Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 200 through 206 removed outlier: 4.038A pdb=" N ALA B 205 " --> pdb=" O CYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 Proline residue: B 215 - end of helix removed outlier: 3.806A pdb=" N ALA B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 251 removed outlier: 3.816A pdb=" N VAL B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 276 removed outlier: 3.785A pdb=" N PHE B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 318 Processing helix chain 'B' and resid 320 through 323 No H-bonds generated for 'chain 'B' and resid 320 through 323' Processing helix chain 'B' and resid 333 through 369 removed outlier: 4.635A pdb=" N LEU B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Proline residue: B 346 - end of helix removed outlier: 4.509A pdb=" N TRP B 362 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 364 " --> pdb=" O HIS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 387 through 393 Processing helix chain 'B' and resid 396 through 408 Processing helix chain 'B' and resid 410 through 413 No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing helix chain 'B' and resid 420 through 441 Processing helix chain 'B' and resid 448 through 462 Processing helix chain 'B' and resid 473 through 498 removed outlier: 3.501A pdb=" N LEU B 483 " --> pdb=" O MET B 480 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 487 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 489 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 491 " --> pdb=" O GLN B 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B 492 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 494 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 495 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 118 through 142 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 163 through 188 Proline residue: C 172 - end of helix Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 199 through 220 removed outlier: 3.588A pdb=" N LEU C 203 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU C 204 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS C 207 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 210 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C 211 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS C 212 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA C 213 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU C 214 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Proline residue: C 215 - end of helix removed outlier: 4.562A pdb=" N VAL C 218 " --> pdb=" O PRO C 215 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 220 " --> pdb=" O HIS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.749A pdb=" N VAL C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 251 removed outlier: 4.173A pdb=" N LEU C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 276 removed outlier: 3.778A pdb=" N PHE C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 318 Processing helix chain 'C' and resid 320 through 323 No H-bonds generated for 'chain 'C' and resid 320 through 323' Processing helix chain 'C' and resid 333 through 369 removed outlier: 4.620A pdb=" N LEU C 345 " --> pdb=" O LEU C 341 " (cutoff:3.500A) Proline residue: C 346 - end of helix removed outlier: 4.506A pdb=" N TRP C 362 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 383 No H-bonds generated for 'chain 'C' and resid 381 through 383' Processing helix chain 'C' and resid 387 through 393 Processing helix chain 'C' and resid 396 through 408 Processing helix chain 'C' and resid 410 through 413 No H-bonds generated for 'chain 'C' and resid 410 through 413' Processing helix chain 'C' and resid 420 through 441 Processing helix chain 'C' and resid 448 through 462 Processing helix chain 'C' and resid 473 through 498 removed outlier: 3.577A pdb=" N ILE C 487 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 489 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 491 " --> pdb=" O GLN C 488 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN C 494 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 118 through 143 Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 163 through 188 Proline residue: D 172 - end of helix Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 200 through 206 removed outlier: 4.025A pdb=" N ALA D 205 " --> pdb=" O CYS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 220 Proline residue: D 215 - end of helix removed outlier: 3.814A pdb=" N ALA D 219 " --> pdb=" O PRO D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 251 removed outlier: 3.824A pdb=" N VAL D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 276 removed outlier: 3.780A pdb=" N PHE D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 318 Processing helix chain 'D' and resid 320 through 323 No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 333 through 369 removed outlier: 4.645A pdb=" N LEU D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Proline residue: D 346 - end of helix removed outlier: 4.529A pdb=" N TRP D 362 " --> pdb=" O PHE D 358 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU D 363 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN D 364 " --> pdb=" O HIS D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 383 No H-bonds generated for 'chain 'D' and resid 381 through 383' Processing helix chain 'D' and resid 387 through 393 Processing helix chain 'D' and resid 396 through 408 Processing helix chain 'D' and resid 410 through 413 No H-bonds generated for 'chain 'D' and resid 410 through 413' Processing helix chain 'D' and resid 420 through 441 Processing helix chain 'D' and resid 448 through 462 Processing helix chain 'D' and resid 473 through 498 removed outlier: 3.582A pdb=" N ILE D 487 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL D 489 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 491 " --> pdb=" O GLN D 488 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR D 492 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 494 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 495 " --> pdb=" O TYR D 492 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 1836 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: 3.46 Time building geometry restraints manager: 5.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1748 1.30 - 1.43: 3997 1.43 - 1.56: 7222 1.56 - 1.69: 49 1.69 - 1.82: 156 Bond restraints: 13172 Sorted by residual: bond pdb=" C06 7T8 C 601 " pdb=" C42 7T8 C 601 " ideal model delta sigma weight residual 1.582 1.494 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C06 7T8 A 601 " pdb=" C42 7T8 A 601 " ideal model delta sigma weight residual 1.582 1.495 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C06 7T8 B 601 " pdb=" C42 7T8 B 601 " ideal model delta sigma weight residual 1.582 1.495 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C06 7T8 D 601 " pdb=" C42 7T8 D 601 " ideal model delta sigma weight residual 1.582 1.495 0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" N GLY D 373 " pdb=" CA GLY D 373 " ideal model delta sigma weight residual 1.445 1.479 -0.034 9.20e-03 1.18e+04 1.40e+01 ... (remaining 13167 not shown) Histogram of bond angle deviations from ideal: 97.40 - 104.92: 296 104.92 - 112.43: 6192 112.43 - 119.95: 6228 119.95 - 127.46: 5093 127.46 - 134.98: 155 Bond angle restraints: 17964 Sorted by residual: angle pdb=" C CYS A 319 " pdb=" N VAL A 320 " pdb=" CA VAL A 320 " ideal model delta sigma weight residual 120.33 124.75 -4.42 8.00e-01 1.56e+00 3.06e+01 angle pdb=" C CYS C 319 " pdb=" N VAL C 320 " pdb=" CA VAL C 320 " ideal model delta sigma weight residual 120.33 124.69 -4.36 8.00e-01 1.56e+00 2.97e+01 angle pdb=" C CYS B 319 " pdb=" N VAL B 320 " pdb=" CA VAL B 320 " ideal model delta sigma weight residual 120.33 124.68 -4.35 8.00e-01 1.56e+00 2.95e+01 angle pdb=" C CYS D 319 " pdb=" N VAL D 320 " pdb=" CA VAL D 320 " ideal model delta sigma weight residual 120.33 124.63 -4.30 8.00e-01 1.56e+00 2.88e+01 angle pdb=" CA ASP D 374 " pdb=" CB ASP D 374 " pdb=" CG ASP D 374 " ideal model delta sigma weight residual 112.60 117.21 -4.61 1.00e+00 1.00e+00 2.13e+01 ... (remaining 17959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.56: 7218 22.56 - 45.11: 549 45.11 - 67.67: 95 67.67 - 90.23: 2 90.23 - 112.79: 4 Dihedral angle restraints: 7868 sinusoidal: 3460 harmonic: 4408 Sorted by residual: dihedral pdb=" CA GLN B 408 " pdb=" C GLN B 408 " pdb=" N ASP B 409 " pdb=" CA ASP B 409 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLN A 408 " pdb=" C GLN A 408 " pdb=" N ASP A 409 " pdb=" CA ASP A 409 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA GLN C 408 " pdb=" C GLN C 408 " pdb=" N ASP C 409 " pdb=" CA ASP C 409 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 7865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1349 0.082 - 0.164: 605 0.164 - 0.246: 44 0.246 - 0.328: 10 0.328 - 0.410: 4 Chirality restraints: 2012 Sorted by residual: chirality pdb=" C15 7T8 A 601 " pdb=" C10 7T8 A 601 " pdb=" C14 7T8 A 601 " pdb=" C16 7T8 A 601 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C15 7T8 C 601 " pdb=" C10 7T8 C 601 " pdb=" C14 7T8 C 601 " pdb=" C16 7T8 C 601 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" C15 7T8 D 601 " pdb=" C10 7T8 D 601 " pdb=" C14 7T8 D 601 " pdb=" C16 7T8 D 601 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 2009 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 199 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C LEU A 199 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU A 199 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 200 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 199 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C LEU C 199 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU C 199 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY C 200 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 207 " 0.020 2.00e-02 2.50e+03 1.68e-02 4.23e+00 pdb=" CG HIS A 207 " -0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS A 207 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 207 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS A 207 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 HIS A 207 " 0.004 2.00e-02 2.50e+03 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2061 2.83 - 3.35: 13893 3.35 - 3.86: 19521 3.86 - 4.38: 24235 4.38 - 4.90: 40126 Nonbonded interactions: 99836 Sorted by model distance: nonbonded pdb=" NE2 GLN D 236 " pdb=" OH TYR D 436 " model vdw 2.311 2.520 nonbonded pdb=" NE2 GLN B 236 " pdb=" OH TYR B 436 " model vdw 2.321 2.520 nonbonded pdb=" O LEU C 336 " pdb=" OG SER C 339 " model vdw 2.366 2.440 nonbonded pdb=" O LEU A 336 " pdb=" OG SER A 339 " model vdw 2.368 2.440 nonbonded pdb=" OH TYR B 182 " pdb=" O PRO B 266 " model vdw 2.378 2.440 ... (remaining 99831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.760 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 37.940 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 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 : 0.014 0.088 13172 Z= 0.887 Angle : 1.803 7.691 17964 Z= 1.340 Chirality : 0.082 0.410 2012 Planarity : 0.004 0.029 2112 Dihedral : 15.967 112.785 5020 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.55 % Allowed : 8.05 % Favored : 90.40 % 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: -4.50 (0.17), residues: 1460 helix: -2.62 (0.12), residues: 1104 sheet: None (None), residues: 0 loop : -3.47 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 170 HIS 0.012 0.003 HIS A 207 PHE 0.028 0.003 PHE A 234 TYR 0.025 0.003 TYR D 182 ARG 0.004 0.001 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 323 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: A 187 LEU cc_start: 0.8064 (tp) cc_final: 0.7680 (mp) REVERT: A 207 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.8069 (t70) REVERT: A 317 ARG cc_start: 0.6010 (mmm160) cc_final: 0.5411 (mmm160) REVERT: A 331 PHE cc_start: 0.8427 (t80) cc_final: 0.8100 (t80) REVERT: A 350 MET cc_start: 0.5767 (mmm) cc_final: 0.5488 (mmm) REVERT: A 375 ARG cc_start: 0.7729 (mtt-85) cc_final: 0.7091 (mtt-85) REVERT: A 380 ASP cc_start: 0.8110 (p0) cc_final: 0.7829 (p0) REVERT: A 417 ARG cc_start: 0.6882 (pmt170) cc_final: 0.6534 (pmt170) REVERT: A 419 ARG cc_start: 0.6814 (ptt180) cc_final: 0.5784 (ptm160) REVERT: A 477 MET cc_start: 0.7383 (tmm) cc_final: 0.6932 (tmm) REVERT: A 495 GLU cc_start: 0.8382 (tp30) cc_final: 0.7973 (tp30) REVERT: B 101 GLN cc_start: 0.7666 (mp-120) cc_final: 0.7113 (pp30) REVERT: B 170 TRP cc_start: 0.7444 (t60) cc_final: 0.6759 (t60) REVERT: B 276 PHE cc_start: 0.6800 (m-80) cc_final: 0.6524 (m-10) REVERT: B 296 TYR cc_start: 0.6938 (t80) cc_final: 0.6105 (t80) REVERT: B 382 TRP cc_start: 0.7844 (p90) cc_final: 0.7569 (p90) REVERT: B 394 TRP cc_start: 0.5589 (t-100) cc_final: 0.5000 (t60) REVERT: B 428 LEU cc_start: 0.8640 (mt) cc_final: 0.8304 (pp) REVERT: B 436 TYR cc_start: 0.8232 (t80) cc_final: 0.7094 (m-10) REVERT: C 183 GLN cc_start: 0.5338 (mm-40) cc_final: 0.5106 (mm-40) REVERT: C 207 HIS cc_start: 0.7101 (OUTLIER) cc_final: 0.6754 (t70) REVERT: C 323 PHE cc_start: 0.7944 (m-80) cc_final: 0.7614 (m-80) REVERT: C 331 PHE cc_start: 0.8310 (t80) cc_final: 0.7988 (t80) REVERT: C 375 ARG cc_start: 0.7153 (mtt-85) cc_final: 0.6332 (mtt-85) REVERT: C 395 ASN cc_start: 0.7060 (t0) cc_final: 0.6844 (t0) REVERT: C 417 ARG cc_start: 0.6612 (pmt170) cc_final: 0.6411 (pmt170) REVERT: C 419 ARG cc_start: 0.6498 (ptt180) cc_final: 0.5443 (ptm160) REVERT: C 477 MET cc_start: 0.7232 (tmm) cc_final: 0.6817 (tmm) REVERT: D 170 TRP cc_start: 0.7823 (t60) cc_final: 0.7092 (t60) REVERT: D 246 PHE cc_start: 0.8331 (t80) cc_final: 0.7482 (t80) REVERT: D 271 TYR cc_start: 0.6789 (t80) cc_final: 0.6199 (t80) REVERT: D 276 PHE cc_start: 0.6204 (m-80) cc_final: 0.5977 (m-80) REVERT: D 296 TYR cc_start: 0.7244 (t80) cc_final: 0.6396 (t80) REVERT: D 394 TRP cc_start: 0.6357 (t-100) cc_final: 0.5323 (t60) REVERT: D 428 LEU cc_start: 0.8657 (mt) cc_final: 0.8379 (pp) REVERT: D 436 TYR cc_start: 0.8245 (t80) cc_final: 0.7342 (m-10) REVERT: D 473 TRP cc_start: 0.7652 (t-100) cc_final: 0.7110 (t60) outliers start: 20 outliers final: 10 residues processed: 341 average time/residue: 0.2715 time to fit residues: 127.7216 Evaluate side-chains 235 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 223 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 238 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN A 325 ASN A 399 HIS A 434 HIS B 119 HIS B 236 GLN B 303 GLN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN C 325 ASN C 399 HIS C 434 HIS D 119 HIS D 236 GLN D 303 GLN D 434 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13172 Z= 0.215 Angle : 0.724 7.692 17964 Z= 0.348 Chirality : 0.053 0.555 2012 Planarity : 0.005 0.030 2112 Dihedral : 10.235 110.586 2340 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.10 % Allowed : 16.41 % Favored : 80.50 % 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: -1.80 (0.21), residues: 1460 helix: -0.67 (0.15), residues: 1116 sheet: None (None), residues: 0 loop : -2.53 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 381 HIS 0.009 0.001 HIS B 399 PHE 0.016 0.002 PHE B 174 TYR 0.017 0.002 TYR C 405 ARG 0.005 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 260 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8242 (pt0) REVERT: A 121 ARG cc_start: 0.6777 (mtp85) cc_final: 0.6425 (mtm-85) REVERT: A 187 LEU cc_start: 0.8206 (tp) cc_final: 0.7872 (mp) REVERT: A 238 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6341 (ttp-170) REVERT: A 350 MET cc_start: 0.5954 (mmm) cc_final: 0.5646 (mmm) REVERT: A 419 ARG cc_start: 0.6777 (ptt180) cc_final: 0.5675 (ptm160) REVERT: A 449 MET cc_start: 0.7446 (ttp) cc_final: 0.6411 (ptp) REVERT: A 477 MET cc_start: 0.7093 (tmm) cc_final: 0.6833 (tmm) REVERT: B 170 TRP cc_start: 0.7119 (t60) cc_final: 0.6894 (t60) REVERT: B 236 GLN cc_start: 0.5276 (OUTLIER) cc_final: 0.4755 (pt0) REVERT: B 296 TYR cc_start: 0.6956 (t80) cc_final: 0.6493 (t80) REVERT: B 394 TRP cc_start: 0.5428 (t-100) cc_final: 0.4808 (t60) REVERT: B 428 LEU cc_start: 0.8522 (mt) cc_final: 0.8150 (pp) REVERT: B 436 TYR cc_start: 0.8128 (t80) cc_final: 0.7005 (m-10) REVERT: B 449 MET cc_start: 0.6029 (ptm) cc_final: 0.5821 (ptm) REVERT: C 153 PHE cc_start: 0.5461 (m-10) cc_final: 0.5245 (m-10) REVERT: C 331 PHE cc_start: 0.8324 (t80) cc_final: 0.8101 (t80) REVERT: C 368 GLU cc_start: 0.7151 (tp30) cc_final: 0.6432 (tp30) REVERT: C 395 ASN cc_start: 0.7267 (t0) cc_final: 0.6902 (t0) REVERT: C 419 ARG cc_start: 0.6374 (ptt180) cc_final: 0.5247 (ptm160) REVERT: C 440 PHE cc_start: 0.7410 (t80) cc_final: 0.7063 (t80) REVERT: D 170 TRP cc_start: 0.7633 (t60) cc_final: 0.7396 (t60) REVERT: D 296 TYR cc_start: 0.7277 (t80) cc_final: 0.6924 (t80) REVERT: D 394 TRP cc_start: 0.6150 (t-100) cc_final: 0.5522 (t60) REVERT: D 428 LEU cc_start: 0.8694 (mt) cc_final: 0.8285 (pp) REVERT: D 436 TYR cc_start: 0.8217 (t80) cc_final: 0.7419 (m-10) outliers start: 40 outliers final: 22 residues processed: 281 average time/residue: 0.2270 time to fit residues: 92.5143 Evaluate side-chains 241 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 217 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain D residue 279 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 0.3980 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 133 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN B 236 GLN B 485 GLN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13172 Z= 0.328 Angle : 0.743 9.423 17964 Z= 0.358 Chirality : 0.055 0.576 2012 Planarity : 0.005 0.033 2112 Dihedral : 9.692 110.650 2318 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.41 % Allowed : 19.66 % Favored : 75.93 % 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: -1.00 (0.22), residues: 1460 helix: -0.17 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -1.89 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 381 HIS 0.009 0.001 HIS B 399 PHE 0.019 0.002 PHE A 323 TYR 0.019 0.002 TYR D 124 ARG 0.004 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 226 time to evaluate : 1.353 Fit side-chains REVERT: A 108 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6965 (tttp) REVERT: A 116 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8326 (pt0) REVERT: A 187 LEU cc_start: 0.8337 (tp) cc_final: 0.7974 (mp) REVERT: A 295 ASN cc_start: 0.8050 (t0) cc_final: 0.7796 (t0) REVERT: A 350 MET cc_start: 0.6004 (mmm) cc_final: 0.5665 (mmm) REVERT: A 368 GLU cc_start: 0.8328 (tp30) cc_final: 0.8101 (tp30) REVERT: A 419 ARG cc_start: 0.6666 (ptt180) cc_final: 0.5486 (ptm160) REVERT: A 449 MET cc_start: 0.7416 (ttp) cc_final: 0.6349 (ptp) REVERT: A 477 MET cc_start: 0.7148 (tmm) cc_final: 0.6592 (tmm) REVERT: B 170 TRP cc_start: 0.7245 (t60) cc_final: 0.6800 (t60) REVERT: B 296 TYR cc_start: 0.7470 (t80) cc_final: 0.6690 (t80) REVERT: B 402 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7041 (tt) REVERT: B 428 LEU cc_start: 0.8441 (mt) cc_final: 0.8109 (pp) REVERT: B 436 TYR cc_start: 0.8112 (t80) cc_final: 0.6907 (m-10) REVERT: B 449 MET cc_start: 0.6056 (ptm) cc_final: 0.5834 (ptm) REVERT: C 368 GLU cc_start: 0.7511 (tp30) cc_final: 0.6654 (tp30) REVERT: C 395 ASN cc_start: 0.7375 (t0) cc_final: 0.6992 (t0) REVERT: C 412 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.7102 (ttp-170) REVERT: C 419 ARG cc_start: 0.6342 (ptt180) cc_final: 0.5173 (ptm160) REVERT: C 440 PHE cc_start: 0.7437 (t80) cc_final: 0.7055 (t80) REVERT: C 449 MET cc_start: 0.7144 (ttp) cc_final: 0.6054 (ptp) REVERT: C 477 MET cc_start: 0.6799 (tmm) cc_final: 0.6345 (tmm) REVERT: D 296 TYR cc_start: 0.7793 (t80) cc_final: 0.7066 (t80) REVERT: D 382 TRP cc_start: 0.8024 (p90) cc_final: 0.7519 (p90) REVERT: D 428 LEU cc_start: 0.8659 (mt) cc_final: 0.8273 (pp) REVERT: D 436 TYR cc_start: 0.8218 (t80) cc_final: 0.7313 (m-10) REVERT: D 449 MET cc_start: 0.6621 (ptm) cc_final: 0.6409 (ptm) outliers start: 57 outliers final: 37 residues processed: 264 average time/residue: 0.2390 time to fit residues: 91.1209 Evaluate side-chains 249 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 210 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 HIS Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 chunk 135 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS B 236 GLN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 HIS D 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13172 Z= 0.258 Angle : 0.685 9.530 17964 Z= 0.326 Chirality : 0.053 0.573 2012 Planarity : 0.005 0.037 2112 Dihedral : 9.061 109.655 2314 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.49 % Allowed : 21.67 % Favored : 73.84 % 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: -0.68 (0.23), residues: 1460 helix: 0.08 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -1.87 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 170 HIS 0.010 0.001 HIS B 399 PHE 0.016 0.001 PHE B 440 TYR 0.017 0.002 TYR D 182 ARG 0.007 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 224 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8325 (pt0) REVERT: A 187 LEU cc_start: 0.8331 (tp) cc_final: 0.8066 (mp) REVERT: A 281 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7803 (mm) REVERT: A 350 MET cc_start: 0.6039 (mmm) cc_final: 0.5701 (mmm) REVERT: A 368 GLU cc_start: 0.8251 (tp30) cc_final: 0.7992 (tp30) REVERT: A 395 ASN cc_start: 0.7745 (t0) cc_final: 0.7349 (t0) REVERT: A 440 PHE cc_start: 0.8248 (t80) cc_final: 0.7954 (t80) REVERT: A 449 MET cc_start: 0.7427 (ttp) cc_final: 0.6300 (ptp) REVERT: A 477 MET cc_start: 0.7127 (tmm) cc_final: 0.6520 (tmm) REVERT: B 170 TRP cc_start: 0.7433 (t60) cc_final: 0.7085 (t60) REVERT: B 286 TYR cc_start: 0.6624 (m-80) cc_final: 0.6084 (m-80) REVERT: B 296 TYR cc_start: 0.7498 (t80) cc_final: 0.6586 (t80) REVERT: B 402 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6973 (tt) REVERT: B 428 LEU cc_start: 0.8391 (mt) cc_final: 0.8101 (pp) REVERT: B 436 TYR cc_start: 0.8071 (t80) cc_final: 0.6830 (m-10) REVERT: B 449 MET cc_start: 0.6047 (ptm) cc_final: 0.5793 (ptm) REVERT: C 108 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6757 (tttp) REVERT: C 368 GLU cc_start: 0.7470 (tp30) cc_final: 0.6817 (tp30) REVERT: C 419 ARG cc_start: 0.6120 (ptt180) cc_final: 0.4808 (ptm160) REVERT: C 440 PHE cc_start: 0.7458 (t80) cc_final: 0.7191 (t80) REVERT: C 449 MET cc_start: 0.7103 (ttp) cc_final: 0.5988 (ptp) REVERT: D 170 TRP cc_start: 0.7636 (t60) cc_final: 0.7325 (t60) REVERT: D 296 TYR cc_start: 0.7764 (t80) cc_final: 0.7263 (t80) REVERT: D 382 TRP cc_start: 0.7949 (p90) cc_final: 0.7459 (p90) REVERT: D 428 LEU cc_start: 0.8611 (mt) cc_final: 0.8243 (pp) REVERT: D 436 TYR cc_start: 0.8150 (t80) cc_final: 0.7136 (m-10) REVERT: D 437 ILE cc_start: 0.8641 (mm) cc_final: 0.8385 (mm) REVERT: D 449 MET cc_start: 0.6605 (ptm) cc_final: 0.6404 (ptm) outliers start: 58 outliers final: 38 residues processed: 264 average time/residue: 0.2250 time to fit residues: 87.8439 Evaluate side-chains 258 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 HIS Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13172 Z= 0.291 Angle : 0.706 9.026 17964 Z= 0.338 Chirality : 0.054 0.576 2012 Planarity : 0.005 0.037 2112 Dihedral : 9.158 109.536 2314 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.72 % Allowed : 23.14 % Favored : 72.14 % 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: -0.57 (0.23), residues: 1460 helix: 0.12 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 170 HIS 0.011 0.001 HIS B 399 PHE 0.021 0.002 PHE B 239 TYR 0.020 0.002 TYR D 124 ARG 0.005 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 220 time to evaluate : 1.447 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8284 (pt0) REVERT: A 187 LEU cc_start: 0.8391 (tp) cc_final: 0.8142 (mp) REVERT: A 368 GLU cc_start: 0.8313 (tp30) cc_final: 0.7625 (tp30) REVERT: A 394 TRP cc_start: 0.6585 (OUTLIER) cc_final: 0.6310 (t-100) REVERT: A 440 PHE cc_start: 0.8241 (t80) cc_final: 0.7993 (t80) REVERT: A 449 MET cc_start: 0.7450 (ttp) cc_final: 0.6356 (ptp) REVERT: B 236 GLN cc_start: 0.5402 (OUTLIER) cc_final: 0.5048 (pt0) REVERT: B 296 TYR cc_start: 0.7544 (t80) cc_final: 0.6589 (t80) REVERT: B 402 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7058 (tt) REVERT: B 428 LEU cc_start: 0.8388 (mt) cc_final: 0.8133 (pp) REVERT: B 436 TYR cc_start: 0.8110 (t80) cc_final: 0.6818 (m-10) REVERT: B 449 MET cc_start: 0.6031 (ptm) cc_final: 0.5793 (ptm) REVERT: C 108 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6820 (tttp) REVERT: C 368 GLU cc_start: 0.7551 (tp30) cc_final: 0.7238 (tp30) REVERT: C 394 TRP cc_start: 0.5734 (OUTLIER) cc_final: 0.5245 (t-100) REVERT: C 440 PHE cc_start: 0.7498 (t80) cc_final: 0.7248 (t80) REVERT: C 449 MET cc_start: 0.7180 (ttp) cc_final: 0.6072 (ptp) REVERT: D 296 TYR cc_start: 0.7800 (t80) cc_final: 0.7291 (t80) REVERT: D 428 LEU cc_start: 0.8595 (mt) cc_final: 0.8248 (pp) REVERT: D 436 TYR cc_start: 0.8172 (t80) cc_final: 0.7131 (m-10) REVERT: D 437 ILE cc_start: 0.8790 (mm) cc_final: 0.8501 (mm) REVERT: D 449 MET cc_start: 0.6640 (ptm) cc_final: 0.6403 (ptm) outliers start: 61 outliers final: 44 residues processed: 263 average time/residue: 0.2178 time to fit residues: 86.3438 Evaluate side-chains 259 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 210 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 394 TRP Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 276 PHE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 HIS Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 66 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN B 303 GLN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN D 303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13172 Z= 0.240 Angle : 0.675 8.910 17964 Z= 0.320 Chirality : 0.052 0.576 2012 Planarity : 0.005 0.042 2112 Dihedral : 9.112 110.961 2314 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.88 % Allowed : 23.68 % Favored : 71.44 % 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: -0.39 (0.23), residues: 1460 helix: 0.29 (0.16), residues: 1112 sheet: None (None), residues: 0 loop : -1.81 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 170 HIS 0.010 0.001 HIS B 399 PHE 0.021 0.001 PHE A 444 TYR 0.017 0.001 TYR D 124 ARG 0.004 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 222 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8270 (pt0) REVERT: A 368 GLU cc_start: 0.8257 (tp30) cc_final: 0.7606 (tp30) REVERT: A 382 TRP cc_start: 0.8133 (p90) cc_final: 0.7831 (p90) REVERT: A 395 ASN cc_start: 0.7732 (t0) cc_final: 0.7292 (t0) REVERT: A 449 MET cc_start: 0.7311 (ttp) cc_final: 0.6341 (ptp) REVERT: A 477 MET cc_start: 0.6935 (tmm) cc_final: 0.6492 (tmm) REVERT: B 296 TYR cc_start: 0.7558 (t80) cc_final: 0.6562 (t80) REVERT: B 428 LEU cc_start: 0.8382 (mt) cc_final: 0.8118 (pp) REVERT: B 436 TYR cc_start: 0.8077 (t80) cc_final: 0.6830 (m-10) REVERT: B 449 MET cc_start: 0.6051 (ptm) cc_final: 0.5812 (ptm) REVERT: C 108 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6775 (tttp) REVERT: C 221 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7074 (mp0) REVERT: C 380 ASP cc_start: 0.8266 (p0) cc_final: 0.7931 (p0) REVERT: C 394 TRP cc_start: 0.5662 (OUTLIER) cc_final: 0.5250 (t-100) REVERT: C 440 PHE cc_start: 0.7433 (t80) cc_final: 0.7225 (t80) REVERT: C 449 MET cc_start: 0.7087 (ttp) cc_final: 0.6047 (ptp) REVERT: D 101 GLN cc_start: 0.8206 (pp30) cc_final: 0.7934 (pp30) REVERT: D 136 ILE cc_start: 0.7670 (mm) cc_final: 0.7436 (mt) REVERT: D 272 LEU cc_start: 0.8318 (pp) cc_final: 0.8015 (tp) REVERT: D 428 LEU cc_start: 0.8582 (mt) cc_final: 0.8241 (pp) REVERT: D 436 TYR cc_start: 0.8163 (t80) cc_final: 0.7087 (m-10) REVERT: D 437 ILE cc_start: 0.8671 (mm) cc_final: 0.8437 (mm) REVERT: D 449 MET cc_start: 0.6647 (ptm) cc_final: 0.6402 (ptm) outliers start: 63 outliers final: 48 residues processed: 267 average time/residue: 0.2098 time to fit residues: 84.1678 Evaluate side-chains 261 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 211 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 394 TRP Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 PHE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 120 optimal weight: 30.0000 chunk 79 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN B 236 GLN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN D 408 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13172 Z= 0.213 Angle : 0.662 11.037 17964 Z= 0.313 Chirality : 0.052 0.577 2012 Planarity : 0.004 0.041 2112 Dihedral : 8.904 111.198 2314 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.03 % Allowed : 24.07 % Favored : 70.90 % 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: -0.23 (0.23), residues: 1460 helix: 0.42 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -1.80 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 170 HIS 0.012 0.001 HIS B 399 PHE 0.024 0.001 PHE B 331 TYR 0.015 0.001 TYR D 124 ARG 0.004 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 225 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8281 (pt0) REVERT: A 221 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7761 (mp0) REVERT: A 350 MET cc_start: 0.5909 (mmm) cc_final: 0.5617 (mmm) REVERT: A 368 GLU cc_start: 0.8209 (tp30) cc_final: 0.7539 (tp30) REVERT: A 380 ASP cc_start: 0.8391 (p0) cc_final: 0.8059 (p0) REVERT: A 382 TRP cc_start: 0.8048 (p90) cc_final: 0.7730 (p90) REVERT: A 395 ASN cc_start: 0.7747 (t0) cc_final: 0.7322 (t0) REVERT: A 449 MET cc_start: 0.7288 (ttp) cc_final: 0.6325 (ptp) REVERT: A 477 MET cc_start: 0.6960 (tmm) cc_final: 0.6489 (tmm) REVERT: B 160 PHE cc_start: 0.7968 (m-80) cc_final: 0.7736 (m-80) REVERT: B 296 TYR cc_start: 0.7508 (t80) cc_final: 0.6465 (t80) REVERT: B 428 LEU cc_start: 0.8359 (mt) cc_final: 0.8071 (pp) REVERT: B 436 TYR cc_start: 0.8073 (t80) cc_final: 0.6863 (m-10) REVERT: B 449 MET cc_start: 0.6050 (ptm) cc_final: 0.5796 (ptm) REVERT: C 221 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7243 (mp0) REVERT: C 368 GLU cc_start: 0.7387 (tp30) cc_final: 0.6784 (tp30) REVERT: C 380 ASP cc_start: 0.8297 (p0) cc_final: 0.7934 (p0) REVERT: C 394 TRP cc_start: 0.5634 (OUTLIER) cc_final: 0.5267 (t-100) REVERT: C 449 MET cc_start: 0.7029 (ttp) cc_final: 0.5997 (ptp) REVERT: D 136 ILE cc_start: 0.7612 (mm) cc_final: 0.7390 (mt) REVERT: D 272 LEU cc_start: 0.8307 (pp) cc_final: 0.8088 (tp) REVERT: D 428 LEU cc_start: 0.8572 (mt) cc_final: 0.8226 (pp) REVERT: D 436 TYR cc_start: 0.8106 (t80) cc_final: 0.7060 (m-10) REVERT: D 437 ILE cc_start: 0.8669 (mm) cc_final: 0.8402 (mm) REVERT: D 449 MET cc_start: 0.6612 (ptm) cc_final: 0.6359 (ptm) outliers start: 65 outliers final: 47 residues processed: 270 average time/residue: 0.2160 time to fit residues: 87.6727 Evaluate side-chains 267 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 219 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 394 TRP Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 PHE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 493 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN B 236 GLN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13172 Z= 0.193 Angle : 0.650 9.729 17964 Z= 0.305 Chirality : 0.051 0.578 2012 Planarity : 0.004 0.040 2112 Dihedral : 8.689 110.658 2314 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.18 % Allowed : 25.08 % Favored : 70.74 % 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: -0.22 (0.23), residues: 1460 helix: 0.46 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 170 HIS 0.014 0.001 HIS D 399 PHE 0.017 0.001 PHE C 440 TYR 0.020 0.001 TYR B 407 ARG 0.003 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 225 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8252 (pt0) REVERT: A 221 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7805 (mp0) REVERT: A 350 MET cc_start: 0.5888 (mmm) cc_final: 0.5626 (mmm) REVERT: A 380 ASP cc_start: 0.8343 (p0) cc_final: 0.8029 (p0) REVERT: A 395 ASN cc_start: 0.7709 (t0) cc_final: 0.7272 (t0) REVERT: A 449 MET cc_start: 0.7278 (ttp) cc_final: 0.6289 (ptp) REVERT: A 477 MET cc_start: 0.6962 (tmm) cc_final: 0.6507 (tmm) REVERT: B 102 LYS cc_start: 0.7256 (tttt) cc_final: 0.7031 (tttm) REVERT: B 160 PHE cc_start: 0.7977 (m-80) cc_final: 0.7735 (m-80) REVERT: B 296 TYR cc_start: 0.7461 (t80) cc_final: 0.6466 (t80) REVERT: B 428 LEU cc_start: 0.8372 (mt) cc_final: 0.8086 (pp) REVERT: B 436 TYR cc_start: 0.8070 (t80) cc_final: 0.6867 (m-10) REVERT: B 449 MET cc_start: 0.6084 (ptm) cc_final: 0.5815 (ptm) REVERT: B 463 MET cc_start: 0.0494 (ttm) cc_final: 0.0142 (tpt) REVERT: C 221 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7251 (mp0) REVERT: C 380 ASP cc_start: 0.8263 (p0) cc_final: 0.7870 (p0) REVERT: C 449 MET cc_start: 0.6989 (ttp) cc_final: 0.5920 (ptp) REVERT: D 136 ILE cc_start: 0.7640 (mm) cc_final: 0.7419 (mt) REVERT: D 428 LEU cc_start: 0.8482 (mt) cc_final: 0.8183 (pp) REVERT: D 436 TYR cc_start: 0.8083 (t80) cc_final: 0.7043 (m-10) REVERT: D 437 ILE cc_start: 0.8658 (mm) cc_final: 0.8392 (mm) REVERT: D 449 MET cc_start: 0.6659 (ptm) cc_final: 0.6395 (ptm) outliers start: 54 outliers final: 43 residues processed: 262 average time/residue: 0.2092 time to fit residues: 82.5072 Evaluate side-chains 261 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 218 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 PHE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 0.0670 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 30.0000 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13172 Z= 0.214 Angle : 0.657 9.178 17964 Z= 0.310 Chirality : 0.052 0.578 2012 Planarity : 0.004 0.040 2112 Dihedral : 8.582 110.954 2314 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.72 % Allowed : 24.61 % Favored : 70.67 % 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: -0.14 (0.23), residues: 1460 helix: 0.52 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.97 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 188 HIS 0.012 0.001 HIS D 399 PHE 0.032 0.001 PHE B 239 TYR 0.019 0.001 TYR B 407 ARG 0.003 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 229 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8190 (pt0) REVERT: A 221 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7803 (mp0) REVERT: A 247 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7564 (mt) REVERT: A 281 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 368 GLU cc_start: 0.8107 (tp30) cc_final: 0.7421 (tp30) REVERT: A 380 ASP cc_start: 0.8355 (p0) cc_final: 0.8018 (p0) REVERT: A 395 ASN cc_start: 0.7658 (t0) cc_final: 0.7167 (t0) REVERT: A 449 MET cc_start: 0.7285 (ttp) cc_final: 0.6293 (ptp) REVERT: A 477 MET cc_start: 0.7007 (tmm) cc_final: 0.6542 (tmm) REVERT: B 102 LYS cc_start: 0.7204 (tttt) cc_final: 0.6943 (tttm) REVERT: B 160 PHE cc_start: 0.7979 (m-80) cc_final: 0.7729 (m-80) REVERT: B 188 TRP cc_start: 0.7935 (OUTLIER) cc_final: 0.7102 (m-90) REVERT: B 236 GLN cc_start: 0.5221 (OUTLIER) cc_final: 0.4949 (pt0) REVERT: B 296 TYR cc_start: 0.7462 (t80) cc_final: 0.6456 (t80) REVERT: B 428 LEU cc_start: 0.8361 (mt) cc_final: 0.8078 (pp) REVERT: B 436 TYR cc_start: 0.8069 (t80) cc_final: 0.6839 (m-10) REVERT: B 449 MET cc_start: 0.6048 (ptm) cc_final: 0.5772 (ptm) REVERT: B 463 MET cc_start: 0.0539 (ttm) cc_final: 0.0129 (tpt) REVERT: C 221 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7255 (mp0) REVERT: C 368 GLU cc_start: 0.7212 (tp30) cc_final: 0.6905 (tp30) REVERT: C 380 ASP cc_start: 0.8272 (p0) cc_final: 0.7856 (p0) REVERT: C 394 TRP cc_start: 0.5627 (OUTLIER) cc_final: 0.5296 (t-100) REVERT: C 449 MET cc_start: 0.6991 (ttp) cc_final: 0.5896 (ptp) REVERT: D 136 ILE cc_start: 0.7682 (mm) cc_final: 0.7472 (mt) REVERT: D 428 LEU cc_start: 0.8439 (mt) cc_final: 0.8146 (pp) REVERT: D 436 TYR cc_start: 0.8085 (t80) cc_final: 0.7041 (m-10) REVERT: D 437 ILE cc_start: 0.8647 (mm) cc_final: 0.8385 (mm) REVERT: D 449 MET cc_start: 0.6650 (ptm) cc_final: 0.6377 (ptm) outliers start: 61 outliers final: 49 residues processed: 273 average time/residue: 0.2175 time to fit residues: 89.0301 Evaluate side-chains 276 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 222 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 188 TRP Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 394 TRP Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 PHE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13172 Z= 0.235 Angle : 0.667 9.093 17964 Z= 0.315 Chirality : 0.052 0.578 2012 Planarity : 0.004 0.040 2112 Dihedral : 8.536 111.437 2314 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.72 % Allowed : 24.77 % Favored : 70.51 % 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: -0.01 (0.23), residues: 1460 helix: 0.59 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -1.80 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 170 HIS 0.012 0.001 HIS D 399 PHE 0.018 0.001 PHE C 440 TYR 0.019 0.001 TYR B 407 ARG 0.003 0.000 ARG C 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 224 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8171 (pt0) REVERT: A 221 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7801 (mp0) REVERT: A 247 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7528 (mt) REVERT: A 281 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7777 (mm) REVERT: A 368 GLU cc_start: 0.8144 (tp30) cc_final: 0.7480 (tp30) REVERT: A 380 ASP cc_start: 0.8389 (p0) cc_final: 0.8047 (p0) REVERT: A 395 ASN cc_start: 0.7619 (t0) cc_final: 0.7101 (t0) REVERT: A 449 MET cc_start: 0.7289 (ttp) cc_final: 0.6295 (ptp) REVERT: A 477 MET cc_start: 0.6987 (tmm) cc_final: 0.6508 (tmm) REVERT: B 102 LYS cc_start: 0.7232 (tttt) cc_final: 0.6960 (tttm) REVERT: B 160 PHE cc_start: 0.7986 (m-80) cc_final: 0.7757 (m-80) REVERT: B 188 TRP cc_start: 0.7823 (OUTLIER) cc_final: 0.6693 (m-90) REVERT: B 236 GLN cc_start: 0.5137 (OUTLIER) cc_final: 0.4854 (pt0) REVERT: B 296 TYR cc_start: 0.7456 (t80) cc_final: 0.6479 (t80) REVERT: B 428 LEU cc_start: 0.8335 (mt) cc_final: 0.8054 (pp) REVERT: B 436 TYR cc_start: 0.8065 (t80) cc_final: 0.6830 (m-10) REVERT: B 449 MET cc_start: 0.6046 (ptm) cc_final: 0.5787 (ptm) REVERT: B 463 MET cc_start: 0.0388 (ttm) cc_final: -0.0052 (tpt) REVERT: C 221 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7257 (mp0) REVERT: C 368 GLU cc_start: 0.7205 (tp30) cc_final: 0.6919 (tp30) REVERT: C 394 TRP cc_start: 0.5643 (OUTLIER) cc_final: 0.5301 (t-100) REVERT: C 449 MET cc_start: 0.6973 (ttp) cc_final: 0.5831 (ptp) REVERT: D 136 ILE cc_start: 0.7686 (mm) cc_final: 0.7478 (mt) REVERT: D 188 TRP cc_start: 0.7289 (OUTLIER) cc_final: 0.7066 (m-90) REVERT: D 428 LEU cc_start: 0.8433 (mt) cc_final: 0.8121 (pp) REVERT: D 436 TYR cc_start: 0.8093 (t80) cc_final: 0.7033 (m-10) REVERT: D 449 MET cc_start: 0.6655 (ptm) cc_final: 0.6414 (ptm) outliers start: 61 outliers final: 54 residues processed: 266 average time/residue: 0.2153 time to fit residues: 85.8635 Evaluate side-chains 280 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 220 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 188 TRP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 HIS Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 394 TRP Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 188 TRP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 276 PHE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 HIS Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 32 optimal weight: 0.0060 chunk 117 optimal weight: 0.0570 chunk 49 optimal weight: 0.7980 chunk 120 optimal weight: 30.0000 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.3512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.174765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.147322 restraints weight = 17588.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.144589 restraints weight = 22322.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141682 restraints weight = 13437.575| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13172 Z= 0.179 Angle : 0.639 8.871 17964 Z= 0.300 Chirality : 0.051 0.579 2012 Planarity : 0.004 0.039 2112 Dihedral : 8.314 114.897 2314 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.18 % Allowed : 25.39 % Favored : 70.43 % 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: 0.16 (0.23), residues: 1460 helix: 0.73 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -1.83 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 170 HIS 0.013 0.001 HIS D 399 PHE 0.013 0.001 PHE C 440 TYR 0.015 0.001 TYR B 405 ARG 0.004 0.000 ARG B 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2739.33 seconds wall clock time: 50 minutes 32.16 seconds (3032.16 seconds total)