Starting phenix.real_space_refine (version: dev) on Fri May 13 08:49:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/05_2022/6hd1_0200_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/05_2022/6hd1_0200.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/05_2022/6hd1_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_0200/05_2022/6hd1_0200_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/05_2022/6hd1_0200_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/05_2022/6hd1_0200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/05_2022/6hd1_0200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/05_2022/6hd1_0200_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hd1_0200/05_2022/6hd1_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 Convert atoms to be neutral 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-4597/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: {'HEM': 1, 'NAP': 1, 'NAG': 1, 'FAD': 1, '44E': 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: {'HEM': 1, 'NAP': 1, 'NAG': 1, 'FAD': 1, '44E': 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: {'HEM': 1, 'NAP': 1, 'NAG': 1, 'FAD': 1, '44E': 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: 6.68, per 1000 atoms: 0.61 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: 4.68 Conformation dependent library (CDL) restraints added in 1.5 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: 1.09 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: 3.29 Time building geometry restraints manager: 5.01 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=" C10 FAD B 503 " pdb=" C4X FAD B 503 " ideal model delta sigma weight residual 2.301 1.432 0.869 2.00e-02 2.50e+03 1.89e+03 bond pdb=" C10 FAD A 503 " pdb=" C4X FAD A 503 " ideal model delta sigma weight residual 2.301 1.433 0.868 2.00e-02 2.50e+03 1.88e+03 bond pdb=" C10 FAD C 503 " pdb=" C4X FAD C 503 " ideal model delta sigma weight residual 2.301 1.433 0.868 2.00e-02 2.50e+03 1.88e+03 bond pdb=" C4X FAD C 503 " pdb=" N5 FAD C 503 " ideal model delta sigma weight residual 1.766 1.271 0.495 2.00e-02 2.50e+03 6.13e+02 bond pdb=" C4X FAD B 503 " pdb=" N5 FAD B 503 " ideal model delta sigma weight residual 1.766 1.271 0.495 2.00e-02 2.50e+03 6.13e+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=" N1 FAD B 503 " pdb=" C10 FAD B 503 " pdb=" N10 FAD B 503 " ideal model delta sigma weight residual 180.00 118.27 61.73 3.00e+00 1.11e-01 4.23e+02 angle pdb=" N1 FAD A 503 " pdb=" C10 FAD A 503 " pdb=" N10 FAD A 503 " ideal model delta sigma weight residual 180.00 118.32 61.68 3.00e+00 1.11e-01 4.23e+02 angle pdb=" N1 FAD C 503 " pdb=" C10 FAD C 503 " pdb=" N10 FAD C 503 " ideal model delta sigma weight residual 180.00 118.38 61.62 3.00e+00 1.11e-01 4.22e+02 angle pdb=" C4X FAD B 503 " pdb=" C10 FAD B 503 " pdb=" N1 FAD B 503 " ideal model delta sigma weight residual 74.31 125.05 -50.74 3.00e+00 1.11e-01 2.86e+02 angle pdb=" C4X FAD A 503 " pdb=" C10 FAD A 503 " pdb=" N1 FAD A 503 " ideal model delta sigma weight residual 74.31 125.04 -50.73 3.00e+00 1.11e-01 2.86e+02 ... (remaining 15493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 6414 35.83 - 71.67: 84 71.67 - 107.50: 39 107.50 - 143.33: 13 143.33 - 179.17: 17 Dihedral angle restraints: 6567 sinusoidal: 2742 harmonic: 3825 Sorted by residual: dihedral pdb="NC2 NAP B 501 " pdb="NC3 NAP B 501 " pdb="NC7 NAP B 501 " pdb="NO7 NAP B 501 " ideal model delta sinusoidal sigma weight residual 168.83 -10.34 179.17 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb="NC2 NAP A 501 " pdb="NC3 NAP A 501 " pdb="NC7 NAP A 501 " pdb="NO7 NAP A 501 " ideal model delta sinusoidal sigma weight residual 168.83 -10.32 179.14 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb="NC2 NAP C 501 " pdb="NC3 NAP C 501 " pdb="NC7 NAP C 501 " pdb="NO7 NAP C 501 " ideal model delta sinusoidal sigma weight residual 168.83 -10.25 179.08 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 6564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1230 0.060 - 0.119: 398 0.119 - 0.178: 88 0.178 - 0.238: 3 0.238 - 0.297: 3 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CB VAL C 310 " pdb=" CA VAL C 310 " pdb=" CG1 VAL C 310 " pdb=" CG2 VAL C 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB VAL A 310 " pdb=" CA VAL A 310 " pdb=" CG1 VAL A 310 " pdb=" CG2 VAL A 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB VAL B 310 " pdb=" CA VAL B 310 " pdb=" CG1 VAL B 310 " pdb=" CG2 VAL B 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1719 not shown) Planarity restraints: 1845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1B FAD C 503 " -0.221 2.00e-02 2.50e+03 5.77e-01 7.49e+03 pdb=" C2B FAD C 503 " 0.208 2.00e-02 2.50e+03 pdb=" C3B FAD C 503 " 0.623 2.00e-02 2.50e+03 pdb=" C4B FAD C 503 " -0.437 2.00e-02 2.50e+03 pdb=" C5B FAD C 503 " -0.037 2.00e-02 2.50e+03 pdb=" N9A FAD C 503 " 0.874 2.00e-02 2.50e+03 pdb=" O2B FAD C 503 " -0.882 2.00e-02 2.50e+03 pdb=" O3B FAD C 503 " 0.558 2.00e-02 2.50e+03 pdb=" O4B FAD C 503 " -0.686 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B FAD B 503 " -0.221 2.00e-02 2.50e+03 5.77e-01 7.49e+03 pdb=" C2B FAD B 503 " 0.208 2.00e-02 2.50e+03 pdb=" C3B FAD B 503 " 0.623 2.00e-02 2.50e+03 pdb=" C4B FAD B 503 " -0.437 2.00e-02 2.50e+03 pdb=" C5B FAD B 503 " -0.037 2.00e-02 2.50e+03 pdb=" N9A FAD B 503 " 0.874 2.00e-02 2.50e+03 pdb=" O2B FAD B 503 " -0.882 2.00e-02 2.50e+03 pdb=" O3B FAD B 503 " 0.558 2.00e-02 2.50e+03 pdb=" O4B FAD B 503 " -0.686 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B FAD A 503 " 0.221 2.00e-02 2.50e+03 5.77e-01 7.49e+03 pdb=" C2B FAD A 503 " -0.208 2.00e-02 2.50e+03 pdb=" C3B FAD A 503 " -0.623 2.00e-02 2.50e+03 pdb=" C4B FAD A 503 " 0.437 2.00e-02 2.50e+03 pdb=" C5B FAD A 503 " 0.037 2.00e-02 2.50e+03 pdb=" N9A FAD A 503 " -0.874 2.00e-02 2.50e+03 pdb=" O2B FAD A 503 " 0.882 2.00e-02 2.50e+03 pdb=" O3B FAD A 503 " -0.558 2.00e-02 2.50e+03 pdb=" O4B FAD A 503 " 0.686 2.00e-02 2.50e+03 ... (remaining 1842 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 3.120 nonbonded pdb=" O3' FAD C 503 " pdb=" O5' FAD C 503 " model vdw 2.271 3.040 ... (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 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. 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: 0.620 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: 3.770 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.100 Process input model: 31.870 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 0.030 0.869 11325 Z= 1.773 Angle : 1.893 61.728 15498 Z= 0.756 Chirality : 0.059 0.297 1722 Planarity : 0.024 0.577 1842 Dihedral : 19.385 179.167 4113 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.40 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 : 1.258 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 268 average time/residue: 0.2022 time to fit residues: 79.0269 Evaluate side-chains 120 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7620 ------------------------------------------------------------------------------- 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 B 19 GLN B 117 ASN B 234 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 11325 Z= 0.217 Angle : 1.090 22.326 15498 Z= 0.419 Chirality : 0.045 0.173 1722 Planarity : 0.005 0.038 1842 Dihedral : 24.279 179.376 1698 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 3.08 % 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: -3.01 (0.21), residues: 1302 helix: -1.46 (0.16), residues: 825 sheet: -1.27 (0.51), residues: 102 loop : -3.12 (0.32), residues: 375 *********************** 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 209 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 1.240 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 11 residues processed: 196 average time/residue: 0.1605 time to fit residues: 49.9367 Evaluate side-chains 124 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0958 time to fit residues: 3.6749 ------------------------------------------------------------------------------- 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: 0.9980 chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 11325 Z= 0.253 Angle : 1.049 20.955 15498 Z= 0.397 Chirality : 0.045 0.194 1722 Planarity : 0.004 0.032 1842 Dihedral : 23.874 178.733 1698 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.23), residues: 1302 helix: -0.35 (0.17), residues: 825 sheet: -1.27 (0.41), residues: 141 loop : -3.17 (0.33), residues: 336 *********************** 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 162 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.248 Fit side-chains outliers start: 31 outliers final: 13 residues processed: 155 average time/residue: 0.1677 time to fit residues: 41.3995 Evaluate side-chains 137 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0991 time to fit residues: 4.1223 ------------------------------------------------------------------------------- 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: 1.9990 chunk 88 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS C 117 ASN A 97 ASN A 383 GLN B 85 HIS B 97 ASN B 117 ASN B 383 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 11325 Z= 0.217 Angle : 1.017 20.811 15498 Z= 0.380 Chirality : 0.044 0.188 1722 Planarity : 0.003 0.032 1842 Dihedral : 23.472 179.633 1698 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 1.85 % 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: -1.14 (0.24), residues: 1302 helix: 0.23 (0.18), residues: 819 sheet: -1.06 (0.42), residues: 141 loop : -2.92 (0.33), residues: 342 *********************** 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 160 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.371 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 151 average time/residue: 0.1718 time to fit residues: 42.2459 Evaluate side-chains 137 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1078 time to fit residues: 4.0358 ------------------------------------------------------------------------------- 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: 2.9990 chunk 70 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 106 optimal weight: 0.0670 chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 31 optimal weight: 0.0570 overall best weight: 2.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 ASN A 85 HIS B 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 11325 Z= 0.363 Angle : 1.072 21.056 15498 Z= 0.405 Chirality : 0.047 0.220 1722 Planarity : 0.004 0.033 1842 Dihedral : 23.207 175.936 1698 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 2.02 % 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: -0.67 (0.24), residues: 1302 helix: 0.65 (0.19), residues: 822 sheet: -0.93 (0.43), residues: 141 loop : -2.90 (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 139 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.275 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 132 average time/residue: 0.1625 time to fit residues: 34.8959 Evaluate side-chains 113 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.281 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1012 time to fit residues: 3.7844 ------------------------------------------------------------------------------- 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: 0.9990 chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 11325 Z= 0.188 Angle : 1.003 20.727 15498 Z= 0.376 Chirality : 0.043 0.191 1722 Planarity : 0.003 0.030 1842 Dihedral : 22.750 177.570 1698 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1302 helix: 1.02 (0.20), residues: 798 sheet: -0.64 (0.43), residues: 141 loop : -2.60 (0.33), residues: 363 *********************** 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 150 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.363 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 147 average time/residue: 0.1663 time to fit residues: 39.5681 Evaluate side-chains 111 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1324 time to fit residues: 2.8721 ------------------------------------------------------------------------------- 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: 1.9990 chunk 71 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 0.2980 chunk 124 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 269 GLN A 117 ASN B 328 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 11325 Z= 0.181 Angle : 1.002 20.697 15498 Z= 0.374 Chirality : 0.044 0.222 1722 Planarity : 0.003 0.029 1842 Dihedral : 22.419 179.394 1698 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1302 helix: 1.04 (0.19), residues: 816 sheet: -0.34 (0.44), residues: 141 loop : -2.71 (0.34), residues: 345 *********************** 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 141 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.312 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 134 average time/residue: 0.1775 time to fit residues: 37.6091 Evaluate side-chains 124 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1011 time to fit residues: 3.4107 ------------------------------------------------------------------------------- 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: 1.9990 chunk 74 optimal weight: 0.0010 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4254 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= 0.195 Angle : 0.999 20.895 15498 Z= 0.373 Chirality : 0.043 0.211 1722 Planarity : 0.003 0.029 1842 Dihedral : 21.993 179.144 1698 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1302 helix: 1.12 (0.19), residues: 819 sheet: -0.21 (0.45), residues: 141 loop : -2.62 (0.34), residues: 342 *********************** 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 133 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.212 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 130 average time/residue: 0.1521 time to fit residues: 32.2432 Evaluate side-chains 111 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1058 time to fit residues: 2.6627 ------------------------------------------------------------------------------- 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: 0.1980 chunk 115 optimal weight: 0.0170 chunk 119 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN C 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4397 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= 0.169 Angle : 0.999 20.840 15498 Z= 0.374 Chirality : 0.043 0.196 1722 Planarity : 0.003 0.028 1842 Dihedral : 21.585 179.734 1698 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: 0.08 (0.25), residues: 1302 helix: 1.13 (0.19), residues: 819 sheet: -0.08 (0.45), residues: 141 loop : -2.55 (0.34), residues: 342 *********************** 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 132 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 1.350 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 129 average time/residue: 0.1548 time to fit residues: 33.4466 Evaluate side-chains 120 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1006 time to fit residues: 2.1639 ------------------------------------------------------------------------------- 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: 0.9990 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 0.0980 chunk 128 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 0.0010 chunk 109 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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: 0.8520 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11325 Z= 0.171 Angle : 1.000 20.848 15498 Z= 0.374 Chirality : 0.043 0.185 1722 Planarity : 0.003 0.027 1842 Dihedral : 21.208 179.340 1698 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.00 % 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: 1.17 (0.19), residues: 819 sheet: 0.02 (0.46), residues: 141 loop : -2.50 (0.34), residues: 342 ********************** 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 126 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.390 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1560 time to fit residues: 32.7930 Evaluate side-chains 115 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5951 ------------------------------------------------------------------------------- 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: 0.7980 chunk 94 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.077083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.058732 restraints weight = 30907.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.060956 restraints weight = 14786.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.062311 restraints weight = 9841.213| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 11325 Z= 0.203 Angle : 1.007 20.959 15498 Z= 0.377 Chirality : 0.044 0.189 1722 Planarity : 0.003 0.027 1842 Dihedral : 20.938 177.855 1698 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1302 helix: 1.20 (0.20), residues: 822 sheet: 0.03 (0.46), residues: 141 loop : -2.39 (0.35), residues: 339 =============================================================================== Job complete usr+sys time: 1861.50 seconds wall clock time: 35 minutes 0.22 seconds (2100.22 seconds total)