Starting phenix.real_space_refine on Fri Mar 15 07:58:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/03_2024/6hd1_0200_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/03_2024/6hd1_0200.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/03_2024/6hd1_0200_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/03_2024/6hd1_0200_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/03_2024/6hd1_0200_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/03_2024/6hd1_0200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/03_2024/6hd1_0200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/03_2024/6hd1_0200_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/03_2024/6hd1_0200_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 3 7.16 5 P 18 5.49 5 S 51 5.16 5 C 7209 2.51 5 N 1800 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 377": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 448": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 448": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11007 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3487 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain: "A" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3487 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain: "B" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3487 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'44E': 1, 'FAD': 1, 'HEM': 1, 'NAG': 1, 'NAP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'44E': 1, 'FAD': 1, 'HEM': 1, 'NAG': 1, 'NAP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'44E': 1, 'FAD': 1, 'HEM': 1, 'NAG': 1, 'NAP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.53, per 1000 atoms: 0.59 Number of scatterers: 11007 At special positions: 0 Unit cell: (93.5935, 95.6505, 117.249, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 3 26.01 S 51 16.00 P 18 15.00 O 1926 8.00 N 1800 7.00 C 7209 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=3, symmetry=0 Links applied NAG-ASN " NAG A 504 " - " ASN A 323 " " NAG B 504 " - " ASN B 323 " " NAG C 504 " - " ASN C 323 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 2.0 seconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 6 sheets defined 58.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.559A pdb=" N SER C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.996A pdb=" N LYS C 72 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 removed outlier: 3.596A pdb=" N THR C 90 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 124 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 160 through 173 removed outlier: 3.643A pdb=" N ARG C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 171 " --> pdb=" O MET C 167 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 removed outlier: 4.004A pdb=" N LYS C 187 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 189 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU C 190 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Proline residue: C 193 - end of helix Processing helix chain 'C' and resid 200 through 222 removed outlier: 3.561A pdb=" N PHE C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 220 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG C 221 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 228 No H-bonds generated for 'chain 'C' and resid 225 through 228' Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 243 through 272 Proline residue: C 248 - end of helix removed outlier: 3.838A pdb=" N TYR C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Proline residue: C 261 - end of helix removed outlier: 3.595A pdb=" N LEU C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 288 Processing helix chain 'C' and resid 290 through 309 removed outlier: 3.602A pdb=" N VAL C 296 " --> pdb=" O GLN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 315 through 330 Processing helix chain 'C' and resid 339 through 345 Processing helix chain 'C' and resid 347 through 365 removed outlier: 3.501A pdb=" N PHE C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY C 363 " --> pdb=" O PHE C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 376 through 383 Processing helix chain 'C' and resid 385 through 405 removed outlier: 3.988A pdb=" N LEU C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 398 " --> pdb=" O CYS C 394 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 401 " --> pdb=" O HIS C 397 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG C 405 " --> pdb=" O TYR C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 437 removed outlier: 3.799A pdb=" N ILE C 425 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE C 426 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Proline residue: C 427 - end of helix removed outlier: 3.617A pdb=" N LEU C 431 " --> pdb=" O CYS C 428 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 432 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 434 " --> pdb=" O LEU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 449 removed outlier: 3.599A pdb=" N ASN C 444 " --> pdb=" O PRO C 440 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 39 removed outlier: 3.559A pdb=" N SER A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.996A pdb=" N LYS A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.596A pdb=" N THR A 90 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 124 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 160 through 173 removed outlier: 3.643A pdb=" N ARG A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 171 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 4.004A pdb=" N LYS A 187 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 189 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 190 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 200 through 222 removed outlier: 3.560A pdb=" N PHE A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 228 No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 243 through 272 Proline residue: A 248 - end of helix removed outlier: 3.838A pdb=" N TYR A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Proline residue: A 261 - end of helix removed outlier: 3.596A pdb=" N LEU A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 290 through 309 removed outlier: 3.604A pdb=" N VAL A 296 " --> pdb=" O GLN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 315 through 330 Processing helix chain 'A' and resid 339 through 345 Processing helix chain 'A' and resid 347 through 365 removed outlier: 3.502A pdb=" N PHE A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 385 through 405 removed outlier: 3.987A pdb=" N LEU A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 398 " --> pdb=" O CYS A 394 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 401 " --> pdb=" O HIS A 397 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.799A pdb=" N ILE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE A 426 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.617A pdb=" N LEU A 431 " --> pdb=" O CYS A 428 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 432 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.600A pdb=" N ASN A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 39 removed outlier: 3.559A pdb=" N SER B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.995A pdb=" N LYS B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.597A pdb=" N THR B 90 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 160 through 173 removed outlier: 3.644A pdb=" N ARG B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 171 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 removed outlier: 4.004A pdb=" N LYS B 187 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 189 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B 190 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 200 through 222 removed outlier: 3.561A pdb=" N PHE B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B 220 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 228 No H-bonds generated for 'chain 'B' and resid 225 through 228' Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 243 through 272 Proline residue: B 248 - end of helix removed outlier: 3.838A pdb=" N TYR B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Proline residue: B 261 - end of helix removed outlier: 3.595A pdb=" N LEU B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 290 through 309 removed outlier: 3.604A pdb=" N VAL B 296 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 315 through 330 Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.502A pdb=" N PHE B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 363 " --> pdb=" O PHE B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 385 through 405 removed outlier: 3.987A pdb=" N LEU B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 398 " --> pdb=" O CYS B 394 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 401 " --> pdb=" O HIS B 397 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 405 " --> pdb=" O TYR B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.798A pdb=" N ILE B 425 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE B 426 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.616A pdb=" N LEU B 431 " --> pdb=" O CYS B 428 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 432 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS B 434 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 449 removed outlier: 3.599A pdb=" N ASN B 444 " --> pdb=" O PRO B 440 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 44 through 48 removed outlier: 6.366A pdb=" N ILE C 76 " --> pdb=" O CYS C 23 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE C 25 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 78 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE C 100 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE C 79 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C 102 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N HIS C 129 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP C 103 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL C 131 " --> pdb=" O ASP C 103 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 152 through 155 removed outlier: 6.248A pdb=" N THR C 176 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL C 155 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET C 178 " --> pdb=" O VAL C 155 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 44 through 48 removed outlier: 6.368A pdb=" N ILE A 76 " --> pdb=" O CYS A 23 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE A 25 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 78 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE A 100 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE A 79 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 102 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N HIS A 129 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP A 103 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 131 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 152 through 155 removed outlier: 6.249A pdb=" N THR A 176 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL A 155 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N MET A 178 " --> pdb=" O VAL A 155 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 44 through 48 removed outlier: 6.368A pdb=" N ILE B 76 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE B 25 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 78 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE B 100 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE B 79 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL B 102 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N HIS B 129 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP B 103 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 131 " --> pdb=" O ASP B 103 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 152 through 155 removed outlier: 6.249A pdb=" N THR B 176 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL B 155 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET B 178 " --> pdb=" O VAL B 155 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 402 hydrogen bonds defined for protein. 1098 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: 3.02 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 3426 1.36 - 1.54: 7678 1.54 - 1.72: 134 1.72 - 1.90: 78 1.90 - 2.07: 9 Bond restraints: 11325 Sorted by residual: bond pdb=" C1D NAP C 501 " pdb=" C2D NAP C 501 " ideal model delta sigma weight residual 1.533 1.296 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C1D NAP A 501 " pdb=" C2D NAP A 501 " ideal model delta sigma weight residual 1.533 1.297 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1D NAP B 501 " pdb=" C2D NAP B 501 " ideal model delta sigma weight residual 1.533 1.298 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1D NAP C 501 " pdb=" O4D NAP C 501 " ideal model delta sigma weight residual 1.375 1.609 -0.234 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.608 -0.233 2.00e-02 2.50e+03 1.36e+02 ... (remaining 11320 not shown) Histogram of bond angle deviations from ideal: 86.69 - 105.08: 255 105.08 - 123.48: 14749 123.48 - 141.87: 488 141.87 - 160.27: 0 160.27 - 178.66: 6 Bond angle restraints: 15498 Sorted by residual: angle pdb=" O1N NAP A 501 " pdb=" PN NAP A 501 " pdb=" O2N NAP A 501 " ideal model delta sigma weight residual 122.51 109.02 13.49 3.00e+00 1.11e-01 2.02e+01 angle pdb=" O1N NAP B 501 " pdb=" PN NAP B 501 " pdb=" O2N NAP B 501 " ideal model delta sigma weight residual 122.51 109.04 13.47 3.00e+00 1.11e-01 2.02e+01 angle pdb=" O1N NAP C 501 " pdb=" PN NAP C 501 " pdb=" O2N NAP C 501 " ideal model delta sigma weight residual 122.51 109.06 13.45 3.00e+00 1.11e-01 2.01e+01 angle pdb=" O1A NAP A 501 " pdb=" PA NAP A 501 " pdb=" O2A NAP A 501 " ideal model delta sigma weight residual 121.77 109.99 11.78 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O1A NAP C 501 " pdb=" PA NAP C 501 " pdb=" O2A NAP C 501 " ideal model delta sigma weight residual 121.77 109.99 11.78 3.00e+00 1.11e-01 1.54e+01 ... (remaining 15493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 6561 35.61 - 71.21: 179 71.21 - 106.82: 34 106.82 - 142.42: 0 142.42 - 178.03: 3 Dihedral angle restraints: 6777 sinusoidal: 2952 harmonic: 3825 Sorted by residual: dihedral pdb=" C2C HEM A 502 " pdb=" C3C HEM A 502 " pdb=" CAC HEM A 502 " pdb=" CBC HEM A 502 " ideal model delta sinusoidal sigma weight residual 0.00 -79.75 79.75 2 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" C2C HEM B 502 " pdb=" C3C HEM B 502 " pdb=" CAC HEM B 502 " pdb=" CBC HEM B 502 " ideal model delta sinusoidal sigma weight residual -0.00 -79.74 79.74 2 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" C2C HEM C 502 " pdb=" C3C HEM C 502 " pdb=" CAC HEM C 502 " pdb=" CBC HEM C 502 " ideal model delta sinusoidal sigma weight residual -0.00 -79.68 79.68 2 1.00e+01 1.00e-02 4.65e+01 ... (remaining 6774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1427 0.075 - 0.151: 287 0.151 - 0.226: 23 0.226 - 0.301: 3 0.301 - 0.377: 3 Chirality restraints: 1743 Sorted by residual: chirality pdb=" C2B NAP C 501 " pdb=" C1B NAP C 501 " pdb=" C3B NAP C 501 " pdb=" O2B NAP C 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C2B NAP B 501 " pdb=" C1B NAP B 501 " pdb=" C3B NAP B 501 " pdb=" O2B NAP B 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" C2B NAP A 501 " pdb=" C1B NAP A 501 " pdb=" C3B NAP A 501 " pdb=" O2B NAP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 1740 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 286 " -0.017 2.00e-02 2.50e+03 1.53e-02 5.85e+00 pdb=" CG TRP C 286 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP C 286 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 286 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 286 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 286 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 286 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 286 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 286 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 286 " -0.017 2.00e-02 2.50e+03 1.53e-02 5.83e+00 pdb=" CG TRP B 286 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 286 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 286 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 286 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 286 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 286 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 286 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 286 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 286 " 0.017 2.00e-02 2.50e+03 1.51e-02 5.69e+00 pdb=" CG TRP A 286 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 286 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 286 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 286 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 286 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 286 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 286 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 286 " -0.002 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 50 2.56 - 3.14: 8682 3.14 - 3.73: 16815 3.73 - 4.31: 24058 4.31 - 4.90: 38577 Nonbonded interactions: 88182 Sorted by model distance: nonbonded pdb=" NE2 HIS C 397 " pdb="FE HEM C 502 " model vdw 1.971 3.080 nonbonded pdb=" NE2 HIS B 397 " pdb="FE HEM B 502 " model vdw 1.972 3.080 nonbonded pdb=" NE2 HIS A 397 " pdb="FE HEM A 502 " model vdw 1.972 3.080 nonbonded pdb=" OD2 ASP A 148 " pdb=" N3 FAD B 503 " model vdw 2.246 2.520 nonbonded pdb=" O3' FAD C 503 " pdb=" O5' FAD C 503 " model vdw 2.271 2.440 ... (remaining 88177 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' } 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: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.450 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.990 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 : 0.015 0.241 11325 Z= 0.877 Angle : 1.215 13.490 15498 Z= 0.580 Chirality : 0.062 0.377 1743 Planarity : 0.008 0.059 1839 Dihedral : 16.632 178.025 4323 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.79 % Allowed : 4.22 % Favored : 94.99 % 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: -5.57 (0.16), residues: 1302 helix: -3.74 (0.10), residues: 816 sheet: -1.81 (0.46), residues: 102 loop : -3.53 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 286 HIS 0.012 0.002 HIS A 85 PHE 0.027 0.003 PHE C 359 TYR 0.024 0.002 TYR B 271 ARG 0.006 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 260 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: C 77 ILE cc_start: 0.9468 (mt) cc_final: 0.9260 (tp) REVERT: C 222 ASP cc_start: 0.8490 (m-30) cc_final: 0.8270 (m-30) REVERT: C 268 LEU cc_start: 0.9458 (tp) cc_final: 0.9212 (tp) REVERT: C 347 SER cc_start: 0.9420 (t) cc_final: 0.9062 (m) REVERT: C 366 SER cc_start: 0.9284 (m) cc_final: 0.9074 (p) REVERT: C 443 ASP cc_start: 0.9204 (t70) cc_final: 0.8972 (p0) REVERT: A 77 ILE cc_start: 0.9398 (mt) cc_final: 0.9183 (tp) REVERT: A 184 MET cc_start: 0.8214 (mmp) cc_final: 0.7967 (tmm) REVERT: A 202 PHE cc_start: 0.8417 (t80) cc_final: 0.8087 (t80) REVERT: A 222 ASP cc_start: 0.8487 (m-30) cc_final: 0.8094 (m-30) REVERT: A 259 TYR cc_start: 0.9125 (m-80) cc_final: 0.8841 (m-10) REVERT: A 282 TRP cc_start: 0.9279 (p-90) cc_final: 0.8935 (p-90) REVERT: A 347 SER cc_start: 0.9536 (t) cc_final: 0.9179 (m) REVERT: A 378 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8074 (mp0) REVERT: B 33 SER cc_start: 0.9468 (m) cc_final: 0.9185 (p) REVERT: B 92 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9028 (pp) REVERT: B 147 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8440 (pp) REVERT: B 168 ASP cc_start: 0.8122 (m-30) cc_final: 0.7786 (m-30) REVERT: B 184 MET cc_start: 0.8212 (mmp) cc_final: 0.7974 (tmm) REVERT: B 202 PHE cc_start: 0.8434 (t80) cc_final: 0.8202 (t80) REVERT: B 347 SER cc_start: 0.9455 (t) cc_final: 0.9084 (m) REVERT: B 447 THR cc_start: 0.9305 (m) cc_final: 0.9073 (p) outliers start: 9 outliers final: 0 residues processed: 268 average time/residue: 0.2081 time to fit residues: 81.4859 Evaluate side-chains 133 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 117 ASN C 234 ASN A 19 GLN A 117 ASN A 234 ASN B 19 GLN B 117 ASN B 234 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11325 Z= 0.202 Angle : 0.716 15.102 15498 Z= 0.316 Chirality : 0.043 0.161 1743 Planarity : 0.005 0.038 1839 Dihedral : 16.909 173.370 1912 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.17 % Allowed : 12.14 % Favored : 84.70 % 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: -3.02 (0.21), residues: 1302 helix: -1.49 (0.16), residues: 819 sheet: -1.28 (0.51), residues: 102 loop : -3.02 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 286 HIS 0.005 0.002 HIS A 397 PHE 0.027 0.001 PHE C 202 TYR 0.017 0.001 TYR A 67 ARG 0.004 0.000 ARG B 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.136 Fit side-chains REVERT: C 38 MET cc_start: 0.8958 (mtp) cc_final: 0.8577 (mtp) REVERT: C 77 ILE cc_start: 0.9335 (mt) cc_final: 0.9125 (tp) REVERT: C 150 SER cc_start: 0.9091 (p) cc_final: 0.8889 (p) REVERT: C 268 LEU cc_start: 0.9438 (tp) cc_final: 0.9219 (tt) REVERT: A 77 ILE cc_start: 0.9363 (mt) cc_final: 0.9152 (tp) REVERT: A 268 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9120 (tt) REVERT: A 378 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8180 (mt-10) REVERT: A 391 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9417 (tm) REVERT: B 33 SER cc_start: 0.9449 (m) cc_final: 0.9229 (p) REVERT: B 92 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9051 (pp) REVERT: B 147 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8449 (pp) REVERT: B 202 PHE cc_start: 0.8266 (t80) cc_final: 0.7934 (t80) outliers start: 36 outliers final: 12 residues processed: 201 average time/residue: 0.1566 time to fit residues: 50.3685 Evaluate side-chains 129 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS C 97 ASN A 85 HIS A 97 ASN B 85 HIS B 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11325 Z= 0.285 Angle : 0.732 17.788 15498 Z= 0.308 Chirality : 0.045 0.200 1743 Planarity : 0.004 0.033 1839 Dihedral : 14.971 173.461 1912 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.69 % Allowed : 14.16 % Favored : 82.15 % 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: -1.62 (0.23), residues: 1302 helix: -0.15 (0.18), residues: 822 sheet: -1.25 (0.48), residues: 120 loop : -3.06 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 286 HIS 0.005 0.001 HIS C 85 PHE 0.023 0.002 PHE A 202 TYR 0.013 0.001 TYR B 259 ARG 0.002 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 1.239 Fit side-chains REVERT: C 77 ILE cc_start: 0.9337 (mt) cc_final: 0.9102 (tp) REVERT: C 268 LEU cc_start: 0.9435 (tp) cc_final: 0.9013 (tt) REVERT: A 77 ILE cc_start: 0.9342 (mt) cc_final: 0.9127 (tp) REVERT: A 268 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9132 (tt) REVERT: B 33 SER cc_start: 0.9506 (m) cc_final: 0.9305 (p) REVERT: B 147 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8469 (pp) outliers start: 42 outliers final: 22 residues processed: 161 average time/residue: 0.1576 time to fit residues: 41.2874 Evaluate side-chains 144 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.0470 chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 ASN A 117 ASN B 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11325 Z= 0.164 Angle : 0.632 12.920 15498 Z= 0.270 Chirality : 0.042 0.175 1743 Planarity : 0.003 0.032 1839 Dihedral : 14.169 171.233 1910 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.02 % Allowed : 17.24 % Favored : 80.74 % 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: -0.96 (0.24), residues: 1302 helix: 0.39 (0.18), residues: 816 sheet: -0.89 (0.42), residues: 141 loop : -2.94 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 286 HIS 0.004 0.001 HIS A 397 PHE 0.023 0.001 PHE B 202 TYR 0.013 0.001 TYR C 348 ARG 0.002 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.268 Fit side-chains REVERT: C 38 MET cc_start: 0.8930 (mtp) cc_final: 0.8604 (mtp) REVERT: C 77 ILE cc_start: 0.9304 (mt) cc_final: 0.9076 (tp) REVERT: C 268 LEU cc_start: 0.9368 (tp) cc_final: 0.8970 (tt) REVERT: A 77 ILE cc_start: 0.9326 (mt) cc_final: 0.9112 (tp) REVERT: A 281 ASP cc_start: 0.7538 (m-30) cc_final: 0.7241 (m-30) REVERT: B 33 SER cc_start: 0.9490 (m) cc_final: 0.9287 (p) REVERT: B 147 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8390 (pp) outliers start: 23 outliers final: 15 residues processed: 164 average time/residue: 0.1605 time to fit residues: 42.4224 Evaluate side-chains 140 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 0.0670 chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 ASN A 117 ASN B 97 ASN B 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11325 Z= 0.273 Angle : 0.686 16.438 15498 Z= 0.287 Chirality : 0.043 0.142 1743 Planarity : 0.003 0.032 1839 Dihedral : 13.681 170.824 1910 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.52 % Allowed : 17.41 % Favored : 79.07 % 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: -0.58 (0.25), residues: 1302 helix: 0.75 (0.19), residues: 819 sheet: -0.84 (0.49), residues: 120 loop : -2.86 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 286 HIS 0.003 0.001 HIS C 397 PHE 0.022 0.001 PHE B 202 TYR 0.012 0.001 TYR B 348 ARG 0.002 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.156 Fit side-chains REVERT: C 38 MET cc_start: 0.8936 (mtp) cc_final: 0.8704 (mtp) REVERT: C 77 ILE cc_start: 0.9322 (mt) cc_final: 0.9094 (tp) REVERT: C 380 ARG cc_start: 0.8871 (ttp-170) cc_final: 0.8533 (ttt90) REVERT: A 77 ILE cc_start: 0.9322 (mt) cc_final: 0.9028 (tp) REVERT: B 147 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8455 (pp) outliers start: 40 outliers final: 27 residues processed: 152 average time/residue: 0.1613 time to fit residues: 39.1111 Evaluate side-chains 142 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN C 117 ASN A 117 ASN B 117 ASN B 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11325 Z= 0.180 Angle : 0.636 12.996 15498 Z= 0.270 Chirality : 0.042 0.198 1743 Planarity : 0.003 0.030 1839 Dihedral : 13.465 169.560 1910 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.64 % Allowed : 19.00 % Favored : 78.36 % 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: -0.24 (0.25), residues: 1302 helix: 1.00 (0.19), residues: 819 sheet: -0.55 (0.44), residues: 141 loop : -2.86 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 286 HIS 0.003 0.000 HIS B 397 PHE 0.023 0.001 PHE B 202 TYR 0.012 0.001 TYR C 348 ARG 0.002 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 1.232 Fit side-chains REVERT: C 38 MET cc_start: 0.8895 (mtp) cc_final: 0.8594 (mtp) REVERT: C 77 ILE cc_start: 0.9269 (mt) cc_final: 0.9031 (tp) REVERT: C 380 ARG cc_start: 0.8867 (ttp-170) cc_final: 0.8545 (ttt90) REVERT: A 77 ILE cc_start: 0.9295 (mt) cc_final: 0.9011 (tp) REVERT: A 147 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8469 (pp) REVERT: A 380 ARG cc_start: 0.8782 (ttp-170) cc_final: 0.8410 (ttt90) REVERT: B 147 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8332 (pp) REVERT: B 378 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8215 (mp0) REVERT: B 380 ARG cc_start: 0.8864 (ttp-170) cc_final: 0.8495 (ttt90) outliers start: 30 outliers final: 22 residues processed: 152 average time/residue: 0.1758 time to fit residues: 42.0573 Evaluate side-chains 140 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11325 Z= 0.177 Angle : 0.642 12.934 15498 Z= 0.274 Chirality : 0.042 0.149 1743 Planarity : 0.003 0.029 1839 Dihedral : 13.309 168.592 1910 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.90 % Allowed : 18.82 % Favored : 78.28 % 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: -0.09 (0.25), residues: 1302 helix: 1.09 (0.19), residues: 822 sheet: -0.42 (0.44), residues: 141 loop : -2.78 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 286 HIS 0.003 0.000 HIS B 397 PHE 0.023 0.001 PHE B 202 TYR 0.012 0.001 TYR C 348 ARG 0.002 0.000 ARG C 245 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 1.248 Fit side-chains REVERT: C 38 MET cc_start: 0.8869 (mtp) cc_final: 0.8567 (mtp) REVERT: C 77 ILE cc_start: 0.9248 (mt) cc_final: 0.9008 (tp) REVERT: C 380 ARG cc_start: 0.8866 (ttp-170) cc_final: 0.8542 (ttt90) REVERT: A 77 ILE cc_start: 0.9275 (mt) cc_final: 0.8980 (tp) REVERT: A 380 ARG cc_start: 0.8828 (ttp-170) cc_final: 0.8505 (ttt90) REVERT: B 147 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8338 (pp) REVERT: B 380 ARG cc_start: 0.8867 (ttp-170) cc_final: 0.8506 (ttt90) outliers start: 33 outliers final: 27 residues processed: 150 average time/residue: 0.1777 time to fit residues: 41.8380 Evaluate side-chains 149 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11325 Z= 0.177 Angle : 0.653 13.679 15498 Z= 0.277 Chirality : 0.042 0.171 1743 Planarity : 0.003 0.029 1839 Dihedral : 13.163 168.192 1910 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.25 % Allowed : 19.17 % Favored : 77.57 % 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: 0.04 (0.25), residues: 1302 helix: 1.15 (0.19), residues: 822 sheet: -0.28 (0.45), residues: 141 loop : -2.69 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 286 HIS 0.003 0.000 HIS C 397 PHE 0.024 0.001 PHE B 202 TYR 0.011 0.001 TYR C 348 ARG 0.001 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 1.219 Fit side-chains REVERT: C 38 MET cc_start: 0.8883 (mtp) cc_final: 0.8566 (mtp) REVERT: C 77 ILE cc_start: 0.9259 (mt) cc_final: 0.9020 (tp) REVERT: C 380 ARG cc_start: 0.8858 (ttp-170) cc_final: 0.8514 (ttt90) REVERT: A 380 ARG cc_start: 0.8830 (ttp-170) cc_final: 0.8491 (ttt90) REVERT: B 38 MET cc_start: 0.8849 (mtp) cc_final: 0.8447 (mtp) REVERT: B 147 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8345 (pp) REVERT: B 380 ARG cc_start: 0.8852 (ttp-170) cc_final: 0.8507 (ttt90) outliers start: 37 outliers final: 30 residues processed: 148 average time/residue: 0.1885 time to fit residues: 44.0926 Evaluate side-chains 156 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 0.0170 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11325 Z= 0.189 Angle : 0.671 13.093 15498 Z= 0.284 Chirality : 0.042 0.185 1743 Planarity : 0.003 0.028 1839 Dihedral : 13.072 168.016 1910 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.73 % Allowed : 19.79 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1302 helix: 1.17 (0.19), residues: 822 sheet: -0.19 (0.45), residues: 141 loop : -2.63 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 286 HIS 0.002 0.000 HIS C 397 PHE 0.028 0.001 PHE C 202 TYR 0.011 0.001 TYR C 348 ARG 0.001 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 1.217 Fit side-chains REVERT: C 38 MET cc_start: 0.8863 (mtp) cc_final: 0.8531 (mtp) REVERT: C 77 ILE cc_start: 0.9246 (mt) cc_final: 0.8992 (tp) REVERT: C 380 ARG cc_start: 0.8863 (ttp-170) cc_final: 0.8515 (ttt90) REVERT: A 244 ASN cc_start: 0.9491 (t0) cc_final: 0.9201 (t0) REVERT: A 380 ARG cc_start: 0.8836 (ttp-170) cc_final: 0.8467 (ttt90) REVERT: B 38 MET cc_start: 0.8847 (mtp) cc_final: 0.8432 (mtp) REVERT: B 328 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8111 (tp-100) REVERT: B 380 ARG cc_start: 0.8844 (ttp-170) cc_final: 0.8510 (ttt90) outliers start: 31 outliers final: 28 residues processed: 149 average time/residue: 0.1747 time to fit residues: 40.9415 Evaluate side-chains 155 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.0010 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 118 optimal weight: 0.0970 chunk 102 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 ASN B 328 GLN B 383 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11325 Z= 0.169 Angle : 0.677 12.241 15498 Z= 0.288 Chirality : 0.042 0.236 1743 Planarity : 0.003 0.029 1839 Dihedral : 12.986 167.627 1908 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.64 % Allowed : 19.96 % Favored : 77.40 % 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: 0.15 (0.25), residues: 1302 helix: 1.18 (0.19), residues: 822 sheet: -0.06 (0.45), residues: 141 loop : -2.56 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 286 HIS 0.003 0.000 HIS C 397 PHE 0.028 0.001 PHE A 202 TYR 0.011 0.001 TYR C 348 ARG 0.002 0.000 ARG B 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 1.286 Fit side-chains REVERT: C 77 ILE cc_start: 0.9260 (mt) cc_final: 0.8970 (tp) REVERT: C 223 VAL cc_start: 0.9227 (m) cc_final: 0.8990 (p) REVERT: C 380 ARG cc_start: 0.8850 (ttp-170) cc_final: 0.8497 (ttt90) REVERT: A 244 ASN cc_start: 0.9489 (t0) cc_final: 0.9238 (t0) REVERT: A 284 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7999 (t0) REVERT: A 380 ARG cc_start: 0.8825 (ttp-170) cc_final: 0.8458 (ttt90) REVERT: B 38 MET cc_start: 0.8857 (mtp) cc_final: 0.8468 (mtp) REVERT: B 173 LEU cc_start: 0.9331 (mp) cc_final: 0.9036 (mp) REVERT: B 380 ARG cc_start: 0.8833 (ttp-170) cc_final: 0.8504 (ttt90) outliers start: 30 outliers final: 26 residues processed: 149 average time/residue: 0.1659 time to fit residues: 38.9704 Evaluate side-chains 151 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 0.0010 chunk 5 optimal weight: 9.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.077533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.058161 restraints weight = 31179.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.060386 restraints weight = 15120.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.061776 restraints weight = 10216.898| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11325 Z= 0.177 Angle : 0.681 12.430 15498 Z= 0.289 Chirality : 0.042 0.214 1743 Planarity : 0.003 0.030 1839 Dihedral : 12.881 167.458 1908 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.37 % Allowed : 20.23 % Favored : 77.40 % 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: 0.21 (0.25), residues: 1302 helix: 1.21 (0.19), residues: 822 sheet: 0.03 (0.45), residues: 141 loop : -2.52 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 286 HIS 0.002 0.000 HIS C 397 PHE 0.027 0.001 PHE A 202 TYR 0.011 0.001 TYR C 348 ARG 0.001 0.000 ARG C 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1969.14 seconds wall clock time: 38 minutes 21.02 seconds (2301.02 seconds total)