Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 00:50:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/04_2023/6hd1_0200_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/04_2023/6hd1_0200.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/04_2023/6hd1_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_0200/04_2023/6hd1_0200_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/04_2023/6hd1_0200_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/04_2023/6hd1_0200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/04_2023/6hd1_0200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/04_2023/6hd1_0200_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/04_2023/6hd1_0200_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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 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 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 chiralities: 1 Time building chain proxies: 6.25, per 1000 atoms: 0.57 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: 4.79 Conformation dependent library (CDL) restraints added in 1.7 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: 1.11 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: 2.79 Time building geometry restraints manager: 5.14 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: 6345 35.61 - 71.21: 71 71.21 - 106.82: 22 106.82 - 142.42: 0 142.42 - 178.03: 3 Dihedral angle restraints: 6441 sinusoidal: 2616 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 6438 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: 1.170 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: 0.000 Extract box with map and model: 3.880 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 30.910 Find NCS groups from input model: 0.620 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.430 ------------------------------------------------------------------------------- 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 : 13.654 178.025 3987 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 % 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 *********************** 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 : 1.282 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 268 average time/residue: 0.2137 time to fit residues: 83.5934 Evaluate side-chains 120 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 C 383 GLN A 19 GLN A 117 ASN A 234 ASN A 383 GLN B 19 GLN B 117 ASN B 234 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 11325 Z= 0.221 Angle : 0.725 15.285 15498 Z= 0.322 Chirality : 0.043 0.162 1743 Planarity : 0.005 0.038 1839 Dihedral : 13.567 175.648 1572 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 2.99 % 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: -3.00 (0.21), residues: 1302 helix: -1.44 (0.16), residues: 828 sheet: -1.30 (0.51), residues: 102 loop : -3.13 (0.32), residues: 372 *********************** 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 195 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 1.226 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 185 average time/residue: 0.1759 time to fit residues: 51.9991 Evaluate side-chains 121 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0999 time to fit residues: 4.0559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 126 optimal weight: 0.0770 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN A 97 ASN B 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3097 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= 0.208 Angle : 0.681 15.366 15498 Z= 0.290 Chirality : 0.043 0.187 1743 Planarity : 0.004 0.032 1839 Dihedral : 13.047 171.927 1572 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 2.20 % 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: -1.73 (0.23), residues: 1302 helix: -0.25 (0.18), residues: 816 sheet: -1.24 (0.41), residues: 141 loop : -3.11 (0.33), residues: 345 *********************** 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 155 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.376 Fit side-chains outliers start: 25 outliers final: 6 residues processed: 150 average time/residue: 0.1756 time to fit residues: 41.9586 Evaluate side-chains 118 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0984 time to fit residues: 2.8405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8593 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 11325 Z= 0.320 Angle : 0.729 17.900 15498 Z= 0.304 Chirality : 0.044 0.194 1743 Planarity : 0.004 0.034 1839 Dihedral : 12.400 171.237 1572 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 2.29 % 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 (0.24), residues: 1302 helix: 0.39 (0.19), residues: 822 sheet: -1.04 (0.42), residues: 141 loop : -3.02 (0.34), residues: 339 *********************** 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 138 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.397 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 130 average time/residue: 0.1691 time to fit residues: 35.6735 Evaluate side-chains 119 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1150 time to fit residues: 4.7565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 ASN B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 11325 Z= 0.352 Angle : 0.737 17.686 15498 Z= 0.306 Chirality : 0.044 0.189 1743 Planarity : 0.004 0.033 1839 Dihedral : 11.694 170.540 1572 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 2.20 % 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: -0.56 (0.25), residues: 1302 helix: 0.78 (0.19), residues: 822 sheet: -0.99 (0.42), residues: 141 loop : -2.93 (0.33), residues: 339 *********************** 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 143 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.347 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 134 average time/residue: 0.1688 time to fit residues: 36.5332 Evaluate side-chains 120 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1027 time to fit residues: 3.6691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.4980 chunk 112 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 328 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3806 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= 0.165 Angle : 0.651 13.388 15498 Z= 0.274 Chirality : 0.042 0.193 1743 Planarity : 0.003 0.030 1839 Dihedral : 11.547 171.164 1572 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 1.58 % 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: -0.31 (0.25), residues: 1302 helix: 0.97 (0.19), residues: 822 sheet: -0.79 (0.43), residues: 141 loop : -2.87 (0.34), residues: 339 *********************** 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 148 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.339 Fit side-chains outliers start: 18 outliers final: 4 residues processed: 145 average time/residue: 0.1580 time to fit residues: 37.7884 Evaluate side-chains 123 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1255 time to fit residues: 2.4824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3926 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= 0.187 Angle : 0.664 13.231 15498 Z= 0.281 Chirality : 0.042 0.183 1743 Planarity : 0.003 0.030 1839 Dihedral : 11.396 170.881 1572 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1302 helix: 1.09 (0.19), residues: 819 sheet: -0.58 (0.44), residues: 141 loop : -2.71 (0.34), residues: 342 *********************** 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 132 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 1.161 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 132 average time/residue: 0.1734 time to fit residues: 37.0697 Evaluate side-chains 117 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1040 time to fit residues: 2.3423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 0.0050 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4057 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= 0.189 Angle : 0.661 13.324 15498 Z= 0.280 Chirality : 0.042 0.149 1743 Planarity : 0.003 0.033 1839 Dihedral : 11.304 171.239 1572 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1302 helix: 1.13 (0.19), residues: 822 sheet: -0.39 (0.44), residues: 141 loop : -2.60 (0.35), residues: 339 *********************** 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 131 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.242 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 129 average time/residue: 0.1705 time to fit residues: 35.9369 Evaluate side-chains 119 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0991 time to fit residues: 2.4167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 104 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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: 0.8556 moved from start: 0.4176 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= 0.175 Angle : 0.668 12.471 15498 Z= 0.283 Chirality : 0.041 0.208 1743 Planarity : 0.003 0.029 1839 Dihedral : 11.199 171.679 1572 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 0.26 % 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: 0.10 (0.25), residues: 1302 helix: 1.18 (0.19), residues: 822 sheet: -0.32 (0.44), residues: 141 loop : -2.54 (0.35), residues: 339 *********************** 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 133 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.185 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.1656 time to fit residues: 35.3685 Evaluate side-chains 118 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.346 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1080 time to fit residues: 2.0243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 11325 Z= 0.182 Angle : 0.670 12.175 15498 Z= 0.284 Chirality : 0.042 0.194 1743 Planarity : 0.003 0.029 1839 Dihedral : 11.113 172.214 1572 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.70 % 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: 0.16 (0.25), residues: 1302 helix: 1.26 (0.20), residues: 813 sheet: -0.23 (0.44), residues: 141 loop : -2.54 (0.34), residues: 348 ********************** 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 130 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.340 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 127 average time/residue: 0.1572 time to fit residues: 33.6947 Evaluate side-chains 116 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1076 time to fit residues: 2.3895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 12 optimal weight: 0.0010 chunk 18 optimal weight: 0.0870 chunk 89 optimal weight: 0.0020 chunk 5 optimal weight: 5.9990 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.077230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.058361 restraints weight = 31110.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.060552 restraints weight = 15545.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.061927 restraints weight = 10653.976| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4411 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= 0.161 Angle : 0.658 11.106 15498 Z= 0.281 Chirality : 0.041 0.168 1743 Planarity : 0.003 0.028 1839 Dihedral : 11.051 172.547 1572 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.26 % 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: 0.19 (0.25), residues: 1302 helix: 1.27 (0.20), residues: 810 sheet: -0.15 (0.44), residues: 141 loop : -2.52 (0.34), residues: 351 =============================================================================== Job complete usr+sys time: 1911.19 seconds wall clock time: 35 minutes 59.34 seconds (2159.34 seconds total)