Starting phenix.real_space_refine on Thu Feb 15 22:39:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyf_21458/02_2024/6vyf_21458.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyf_21458/02_2024/6vyf_21458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyf_21458/02_2024/6vyf_21458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyf_21458/02_2024/6vyf_21458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyf_21458/02_2024/6vyf_21458.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyf_21458/02_2024/6vyf_21458.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 8656 2.51 5 N 2312 2.21 5 O 2564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B ASP 124": "OD1" <-> "OD2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ASP 217": "OD1" <-> "OD2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ASP 458": "OD1" <-> "OD2" Residue "B ASP 469": "OD1" <-> "OD2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C ASP 124": "OD1" <-> "OD2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ASP 217": "OD1" <-> "OD2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 348": "OE1" <-> "OE2" Residue "C ASP 354": "OD1" <-> "OD2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C ASP 458": "OD1" <-> "OD2" Residue "C ASP 469": "OD1" <-> "OD2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "D ASP 124": "OD1" <-> "OD2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ASP 217": "OD1" <-> "OD2" Residue "D ASP 241": "OD1" <-> "OD2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 348": "OE1" <-> "OE2" Residue "D ASP 354": "OD1" <-> "OD2" Residue "D ASP 389": "OD1" <-> "OD2" Residue "D ASP 458": "OD1" <-> "OD2" Residue "D ASP 469": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13624 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3406 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3406 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 3 Chain: "C" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3406 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 3 Chain: "D" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3406 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 3 Time building chain proxies: 7.36, per 1000 atoms: 0.54 Number of scatterers: 13624 At special positions: 0 Unit cell: (126.145, 100.248, 117.791, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2564 8.00 N 2312 7.00 C 8656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.02 Conformation dependent library (CDL) restraints added in 2.4 seconds 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3248 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 47.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.563A pdb=" N ASN A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 68 removed outlier: 3.885A pdb=" N GLU A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 166 removed outlier: 4.279A pdb=" N ALA A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 166 " --> pdb=" O TYR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.885A pdb=" N ALA A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 226 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 227 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.635A pdb=" N THR A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 303 through 312 removed outlier: 3.723A pdb=" N TRP A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.769A pdb=" N ILE A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 348 through 352 removed outlier: 3.617A pdb=" N TRP A 351 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.647A pdb=" N GLY A 361 " --> pdb=" O ASN A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 removed outlier: 3.788A pdb=" N LYS A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 421 removed outlier: 3.533A pdb=" N SER A 401 " --> pdb=" O LYS A 397 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 removed outlier: 4.035A pdb=" N GLU A 425 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.537A pdb=" N VAL A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 470 through 486 removed outlier: 4.601A pdb=" N ALA A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.563A pdb=" N ASN B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 68 removed outlier: 3.885A pdb=" N GLU B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 166 removed outlier: 4.278A pdb=" N ALA B 157 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 229 removed outlier: 3.885A pdb=" N ALA B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 226 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 252 removed outlier: 3.635A pdb=" N THR B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 303 through 312 removed outlier: 3.722A pdb=" N TRP B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.769A pdb=" N ILE B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.617A pdb=" N TRP B 351 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.647A pdb=" N GLY B 361 " --> pdb=" O ASN B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 removed outlier: 3.788A pdb=" N LYS B 380 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 421 removed outlier: 3.533A pdb=" N SER B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 removed outlier: 4.035A pdb=" N GLU B 425 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.538A pdb=" N VAL B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 470 through 486 removed outlier: 4.601A pdb=" N ALA B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.563A pdb=" N ASN C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 68 removed outlier: 3.885A pdb=" N GLU C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 166 removed outlier: 4.279A pdb=" N ALA C 157 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU C 158 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 166 " --> pdb=" O TYR C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 229 removed outlier: 3.885A pdb=" N ALA C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE C 226 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 227 " --> pdb=" O ASN C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.635A pdb=" N THR C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 303 through 312 removed outlier: 3.723A pdb=" N TRP C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.768A pdb=" N ILE C 325 " --> pdb=" O PHE C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 342 Processing helix chain 'C' and resid 348 through 352 removed outlier: 3.617A pdb=" N TRP C 351 " --> pdb=" O GLU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 366 removed outlier: 3.647A pdb=" N GLY C 361 " --> pdb=" O ASN C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 383 removed outlier: 3.787A pdb=" N LYS C 380 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 421 removed outlier: 3.533A pdb=" N SER C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 426 removed outlier: 4.036A pdb=" N GLU C 425 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 456 removed outlier: 3.537A pdb=" N VAL C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 470 through 486 removed outlier: 4.601A pdb=" N ALA C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.562A pdb=" N ASN D 38 " --> pdb=" O ASN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 68 removed outlier: 3.885A pdb=" N GLU D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 166 removed outlier: 4.278A pdb=" N ALA D 157 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 166 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 229 removed outlier: 3.884A pdb=" N ALA D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE D 226 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 227 " --> pdb=" O ASN D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 252 removed outlier: 3.635A pdb=" N THR D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 Processing helix chain 'D' and resid 303 through 312 removed outlier: 3.723A pdb=" N TRP D 311 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS D 312 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.769A pdb=" N ILE D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 342 Processing helix chain 'D' and resid 348 through 352 removed outlier: 3.617A pdb=" N TRP D 351 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 366 removed outlier: 3.647A pdb=" N GLY D 361 " --> pdb=" O ASN D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 383 removed outlier: 3.787A pdb=" N LYS D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 382 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 421 removed outlier: 3.533A pdb=" N SER D 401 " --> pdb=" O LYS D 397 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 414 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 426 removed outlier: 4.036A pdb=" N GLU D 425 " --> pdb=" O LYS D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 456 removed outlier: 3.538A pdb=" N VAL D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 461 No H-bonds generated for 'chain 'D' and resid 459 through 461' Processing helix chain 'D' and resid 470 through 486 removed outlier: 4.600A pdb=" N ALA D 476 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.968A pdb=" N GLY A 272 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR A 261 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS A 260 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY A 432 " --> pdb=" O CYS A 260 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A 262 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASP A 434 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE A 264 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE A 429 " --> pdb=" O ILE A 464 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.968A pdb=" N GLY B 272 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR B 261 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS B 260 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY B 432 " --> pdb=" O CYS B 260 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 262 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ASP B 434 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE B 264 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE B 429 " --> pdb=" O ILE B 464 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 101 Processing sheet with id=AA6, first strand: chain 'B' and resid 177 through 178 Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.967A pdb=" N GLY C 272 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR C 261 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS C 260 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY C 432 " --> pdb=" O CYS C 260 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 262 " --> pdb=" O GLY C 432 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ASP C 434 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE C 264 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE C 429 " --> pdb=" O ILE C 464 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 101 Processing sheet with id=AA9, first strand: chain 'C' and resid 177 through 178 Processing sheet with id=AB1, first strand: chain 'D' and resid 82 through 83 removed outlier: 3.968A pdb=" N GLY D 272 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR D 261 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS D 260 " --> pdb=" O SER D 430 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY D 432 " --> pdb=" O CYS D 260 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE D 262 " --> pdb=" O GLY D 432 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASP D 434 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE D 264 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE D 429 " --> pdb=" O ILE D 464 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 96 through 101 Processing sheet with id=AB3, first strand: chain 'D' and resid 177 through 178 536 hydrogen bonds defined for protein. 1536 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: 4.17 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4424 1.34 - 1.46: 3140 1.46 - 1.58: 6204 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 13896 Sorted by residual: bond pdb=" C HIS A 68 " pdb=" N PRO A 69 " ideal model delta sigma weight residual 1.334 1.321 0.012 8.40e-03 1.42e+04 2.11e+00 bond pdb=" C HIS C 68 " pdb=" N PRO C 69 " ideal model delta sigma weight residual 1.334 1.322 0.012 8.40e-03 1.42e+04 1.93e+00 bond pdb=" C HIS B 68 " pdb=" N PRO B 69 " ideal model delta sigma weight residual 1.334 1.322 0.012 8.40e-03 1.42e+04 1.90e+00 bond pdb=" C HIS D 68 " pdb=" N PRO D 69 " ideal model delta sigma weight residual 1.334 1.322 0.011 8.40e-03 1.42e+04 1.86e+00 bond pdb=" CA GLN B 319 " pdb=" C GLN B 319 " ideal model delta sigma weight residual 1.530 1.517 0.013 1.17e-02 7.31e+03 1.29e+00 ... (remaining 13891 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.31: 288 106.31 - 113.24: 7585 113.24 - 120.18: 5023 120.18 - 127.11: 5719 127.11 - 134.05: 129 Bond angle restraints: 18744 Sorted by residual: angle pdb=" CB MET B 222 " pdb=" CG MET B 222 " pdb=" SD MET B 222 " ideal model delta sigma weight residual 112.70 123.20 -10.50 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB MET C 222 " pdb=" CG MET C 222 " pdb=" SD MET C 222 " ideal model delta sigma weight residual 112.70 123.17 -10.47 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB MET A 222 " pdb=" CG MET A 222 " pdb=" SD MET A 222 " ideal model delta sigma weight residual 112.70 123.16 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB MET D 222 " pdb=" CG MET D 222 " pdb=" SD MET D 222 " ideal model delta sigma weight residual 112.70 123.16 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N ASN C 315 " pdb=" CA ASN C 315 " pdb=" C ASN C 315 " ideal model delta sigma weight residual 110.61 106.52 4.09 1.25e+00 6.40e-01 1.07e+01 ... (remaining 18739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.77: 7116 13.77 - 27.53: 900 27.53 - 41.30: 288 41.30 - 55.06: 52 55.06 - 68.83: 20 Dihedral angle restraints: 8376 sinusoidal: 3352 harmonic: 5024 Sorted by residual: dihedral pdb=" CA PHE B 108 " pdb=" C PHE B 108 " pdb=" N ARG B 109 " pdb=" CA ARG B 109 " ideal model delta harmonic sigma weight residual 180.00 -146.55 -33.45 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA PHE C 108 " pdb=" C PHE C 108 " pdb=" N ARG C 109 " pdb=" CA ARG C 109 " ideal model delta harmonic sigma weight residual 180.00 -146.55 -33.45 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA PHE A 108 " pdb=" C PHE A 108 " pdb=" N ARG A 109 " pdb=" CA ARG A 109 " ideal model delta harmonic sigma weight residual 180.00 -146.58 -33.42 0 5.00e+00 4.00e-02 4.47e+01 ... (remaining 8373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1282 0.035 - 0.070: 563 0.070 - 0.105: 144 0.105 - 0.141: 67 0.141 - 0.176: 4 Chirality restraints: 2060 Sorted by residual: chirality pdb=" CA ILE B 291 " pdb=" N ILE B 291 " pdb=" C ILE B 291 " pdb=" CB ILE B 291 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ILE C 291 " pdb=" N ILE C 291 " pdb=" C ILE C 291 " pdb=" CB ILE C 291 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ILE D 291 " pdb=" N ILE D 291 " pdb=" C ILE D 291 " pdb=" CB ILE D 291 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 2057 not shown) Planarity restraints: 2396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 184 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO C 185 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 185 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 185 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 184 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO A 185 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 185 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 185 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 184 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO D 185 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 185 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 185 " 0.022 5.00e-02 4.00e+02 ... (remaining 2393 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2386 2.76 - 3.29: 12880 3.29 - 3.83: 20541 3.83 - 4.36: 25628 4.36 - 4.90: 43787 Nonbonded interactions: 105222 Sorted by model distance: nonbonded pdb=" O GLU A 322 " pdb=" OG SER A 326 " model vdw 2.223 2.440 nonbonded pdb=" O GLU C 322 " pdb=" OG SER C 326 " model vdw 2.223 2.440 nonbonded pdb=" O GLU D 322 " pdb=" OG SER D 326 " model vdw 2.224 2.440 nonbonded pdb=" O GLU B 322 " pdb=" OG SER B 326 " model vdw 2.224 2.440 nonbonded pdb=" O PRO B 74 " pdb=" ND1 HIS B 75 " model vdw 2.226 2.520 ... (remaining 105217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 4.400 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 36.850 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.005 0.033 13896 Z= 0.353 Angle : 0.678 10.495 18744 Z= 0.404 Chirality : 0.044 0.176 2060 Planarity : 0.004 0.040 2396 Dihedral : 13.956 68.828 5128 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.27 % Allowed : 7.46 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.53 (0.18), residues: 1696 helix: -2.08 (0.16), residues: 728 sheet: -0.89 (0.33), residues: 228 loop : -3.04 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 311 HIS 0.006 0.002 HIS A 75 PHE 0.016 0.001 PHE B 108 TYR 0.016 0.002 TYR D 162 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 1.623 Fit side-chains REVERT: A 124 ASP cc_start: 0.7549 (p0) cc_final: 0.7334 (p0) REVERT: A 180 PHE cc_start: 0.8068 (t80) cc_final: 0.7790 (t80) REVERT: A 222 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7177 (tpp) REVERT: A 318 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7821 (mtp85) REVERT: B 25 ILE cc_start: 0.7692 (mm) cc_final: 0.7469 (mm) REVERT: B 180 PHE cc_start: 0.8103 (t80) cc_final: 0.7757 (t80) REVERT: B 222 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6976 (tpp) REVERT: B 310 ASP cc_start: 0.8513 (t70) cc_final: 0.8177 (t0) REVERT: C 180 PHE cc_start: 0.8109 (t80) cc_final: 0.7861 (t80) REVERT: C 222 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7189 (tpp) REVERT: D 180 PHE cc_start: 0.8111 (t80) cc_final: 0.7777 (t80) REVERT: D 222 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7182 (tpp) REVERT: D 318 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7780 (mtp85) outliers start: 4 outliers final: 0 residues processed: 193 average time/residue: 0.3160 time to fit residues: 84.1738 Evaluate side-chains 143 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN A 449 GLN A 485 GLN B 340 ASN B 366 ASN B 485 GLN C 366 ASN C 449 GLN C 485 GLN D 340 ASN D 366 ASN D 449 GLN D 485 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 13896 Z= 0.195 Angle : 0.504 6.052 18744 Z= 0.275 Chirality : 0.042 0.148 2060 Planarity : 0.004 0.036 2396 Dihedral : 5.586 45.967 1864 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.68 % Allowed : 12.50 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.19 (0.19), residues: 1696 helix: -0.48 (0.19), residues: 736 sheet: -0.54 (0.34), residues: 228 loop : -2.81 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 311 HIS 0.004 0.001 HIS D 75 PHE 0.015 0.001 PHE C 108 TYR 0.013 0.001 TYR B 162 ARG 0.001 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.688 Fit side-chains REVERT: A 180 PHE cc_start: 0.8005 (t80) cc_final: 0.7769 (t80) REVERT: B 25 ILE cc_start: 0.7718 (mm) cc_final: 0.7517 (mm) REVERT: B 124 ASP cc_start: 0.7883 (p0) cc_final: 0.7652 (p0) REVERT: B 180 PHE cc_start: 0.8107 (t80) cc_final: 0.7759 (t80) REVERT: C 124 ASP cc_start: 0.7629 (p0) cc_final: 0.7411 (p0) REVERT: C 180 PHE cc_start: 0.8039 (t80) cc_final: 0.7820 (t80) REVERT: D 124 ASP cc_start: 0.7408 (p0) cc_final: 0.7146 (p0) REVERT: D 180 PHE cc_start: 0.8024 (t80) cc_final: 0.7760 (t80) outliers start: 25 outliers final: 20 residues processed: 167 average time/residue: 0.3269 time to fit residues: 75.4022 Evaluate side-chains 163 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 0.0370 chunk 43 optimal weight: 10.0000 chunk 156 optimal weight: 0.0980 chunk 169 optimal weight: 0.0870 chunk 139 optimal weight: 20.0000 chunk 155 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13896 Z= 0.132 Angle : 0.458 5.132 18744 Z= 0.248 Chirality : 0.041 0.136 2060 Planarity : 0.003 0.030 2396 Dihedral : 4.643 27.002 1852 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.35 % Allowed : 13.44 % Favored : 84.21 % 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: -1.52 (0.20), residues: 1696 helix: 0.38 (0.20), residues: 728 sheet: -0.39 (0.34), residues: 228 loop : -2.73 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 311 HIS 0.004 0.001 HIS C 65 PHE 0.013 0.001 PHE B 108 TYR 0.011 0.001 TYR C 162 ARG 0.001 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 1.668 Fit side-chains REVERT: A 124 ASP cc_start: 0.7276 (p0) cc_final: 0.7025 (p0) REVERT: A 180 PHE cc_start: 0.8008 (t80) cc_final: 0.7786 (t80) REVERT: B 25 ILE cc_start: 0.7748 (mm) cc_final: 0.7498 (mm) REVERT: B 124 ASP cc_start: 0.7782 (p0) cc_final: 0.7572 (p0) REVERT: B 164 MET cc_start: 0.6801 (tpt) cc_final: 0.6313 (tpt) REVERT: B 180 PHE cc_start: 0.8036 (t80) cc_final: 0.7736 (t80) REVERT: C 109 ARG cc_start: 0.7404 (ptt90) cc_final: 0.6914 (ptt90) REVERT: C 124 ASP cc_start: 0.7689 (p0) cc_final: 0.7470 (p0) REVERT: C 180 PHE cc_start: 0.8039 (t80) cc_final: 0.7793 (t80) REVERT: D 124 ASP cc_start: 0.7518 (p0) cc_final: 0.7260 (p0) REVERT: D 180 PHE cc_start: 0.8014 (t80) cc_final: 0.7745 (t80) outliers start: 35 outliers final: 23 residues processed: 173 average time/residue: 0.2763 time to fit residues: 68.6223 Evaluate side-chains 159 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 81 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN B 290 ASN C 290 ASN D 290 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 13896 Z= 0.149 Angle : 0.452 5.096 18744 Z= 0.244 Chirality : 0.041 0.140 2060 Planarity : 0.003 0.027 2396 Dihedral : 4.534 25.856 1852 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.56 % Allowed : 15.05 % Favored : 81.38 % 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: -1.25 (0.20), residues: 1696 helix: 0.75 (0.20), residues: 728 sheet: -0.17 (0.37), residues: 188 loop : -2.66 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 311 HIS 0.004 0.001 HIS B 75 PHE 0.013 0.001 PHE B 108 TYR 0.011 0.001 TYR C 162 ARG 0.002 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 140 time to evaluate : 1.532 Fit side-chains REVERT: A 124 ASP cc_start: 0.7409 (p0) cc_final: 0.7163 (p0) REVERT: B 25 ILE cc_start: 0.7738 (mm) cc_final: 0.7499 (mm) REVERT: B 164 MET cc_start: 0.6784 (tpt) cc_final: 0.6268 (tpt) REVERT: B 180 PHE cc_start: 0.8047 (t80) cc_final: 0.7710 (t80) REVERT: C 109 ARG cc_start: 0.7404 (ptt90) cc_final: 0.6921 (ptt90) REVERT: C 180 PHE cc_start: 0.8001 (t80) cc_final: 0.7798 (t80) REVERT: D 124 ASP cc_start: 0.7603 (p0) cc_final: 0.7354 (p0) REVERT: D 180 PHE cc_start: 0.7986 (t80) cc_final: 0.7749 (t80) outliers start: 53 outliers final: 39 residues processed: 175 average time/residue: 0.2635 time to fit residues: 67.0230 Evaluate side-chains 167 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 GLN C 449 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13896 Z= 0.400 Angle : 0.601 6.133 18744 Z= 0.320 Chirality : 0.046 0.166 2060 Planarity : 0.004 0.029 2396 Dihedral : 5.327 32.010 1852 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 4.17 % Allowed : 15.12 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.47 (0.20), residues: 1696 helix: 0.20 (0.19), residues: 756 sheet: -0.38 (0.34), residues: 228 loop : -2.51 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 351 HIS 0.007 0.002 HIS C 75 PHE 0.016 0.002 PHE B 108 TYR 0.014 0.002 TYR C 162 ARG 0.004 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 137 time to evaluate : 1.820 Fit side-chains REVERT: A 124 ASP cc_start: 0.7336 (p0) cc_final: 0.7127 (p0) REVERT: A 318 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7777 (mtp85) REVERT: B 25 ILE cc_start: 0.7683 (mm) cc_final: 0.7428 (mm) REVERT: B 180 PHE cc_start: 0.8138 (t80) cc_final: 0.7873 (t80) REVERT: B 318 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7737 (mtp85) REVERT: B 434 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7471 (t0) REVERT: C 109 ARG cc_start: 0.7432 (ptt90) cc_final: 0.7034 (ptt90) REVERT: C 180 PHE cc_start: 0.8081 (t80) cc_final: 0.7822 (t80) REVERT: C 318 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7776 (mtp85) REVERT: C 338 MET cc_start: 0.8929 (mmm) cc_final: 0.8519 (mmp) REVERT: C 434 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7437 (t0) REVERT: D 124 ASP cc_start: 0.7403 (p0) cc_final: 0.7183 (p0) REVERT: D 180 PHE cc_start: 0.8075 (t80) cc_final: 0.7768 (t80) REVERT: D 318 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7784 (mtp85) REVERT: D 338 MET cc_start: 0.8946 (mmm) cc_final: 0.8555 (mmp) REVERT: D 434 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7499 (t0) outliers start: 62 outliers final: 49 residues processed: 184 average time/residue: 0.2986 time to fit residues: 78.8619 Evaluate side-chains 187 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 135 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 20.0000 chunk 149 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 77 optimal weight: 0.2980 chunk 13 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 overall best weight: 2.2764 ------------------------------------------------------------------------------- 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: 0.8423 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13896 Z= 0.209 Angle : 0.489 5.005 18744 Z= 0.266 Chirality : 0.042 0.147 2060 Planarity : 0.003 0.028 2396 Dihedral : 4.904 29.754 1852 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.43 % Allowed : 16.60 % Favored : 79.97 % 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: -1.21 (0.20), residues: 1696 helix: 0.57 (0.20), residues: 748 sheet: -0.31 (0.34), residues: 228 loop : -2.54 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 311 HIS 0.005 0.002 HIS C 75 PHE 0.016 0.001 PHE A 180 TYR 0.013 0.001 TYR D 162 ARG 0.003 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 128 time to evaluate : 1.554 Fit side-chains REVERT: A 124 ASP cc_start: 0.7367 (p0) cc_final: 0.7140 (p0) REVERT: B 25 ILE cc_start: 0.7721 (mm) cc_final: 0.7492 (mm) REVERT: B 180 PHE cc_start: 0.8076 (t80) cc_final: 0.7780 (t80) REVERT: B 434 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7437 (t70) REVERT: C 109 ARG cc_start: 0.7425 (ptt90) cc_final: 0.6953 (ptt90) REVERT: C 180 PHE cc_start: 0.8038 (t80) cc_final: 0.7830 (t80) REVERT: C 434 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7416 (t70) REVERT: D 180 PHE cc_start: 0.8029 (t80) cc_final: 0.7754 (t80) REVERT: D 338 MET cc_start: 0.8864 (mmm) cc_final: 0.8548 (mmp) REVERT: D 434 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7429 (t70) outliers start: 51 outliers final: 47 residues processed: 167 average time/residue: 0.2616 time to fit residues: 63.5615 Evaluate side-chains 177 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 127 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.0470 chunk 94 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.9682 ------------------------------------------------------------------------------- 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: 0.8410 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13896 Z= 0.188 Angle : 0.477 5.004 18744 Z= 0.258 Chirality : 0.042 0.158 2060 Planarity : 0.003 0.027 2396 Dihedral : 4.742 28.343 1852 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.76 % Allowed : 16.26 % Favored : 79.97 % 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: -1.13 (0.20), residues: 1696 helix: 0.72 (0.20), residues: 748 sheet: -0.00 (0.37), residues: 188 loop : -2.56 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 311 HIS 0.004 0.001 HIS B 75 PHE 0.014 0.001 PHE A 108 TYR 0.012 0.001 TYR C 162 ARG 0.002 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 132 time to evaluate : 1.467 Fit side-chains REVERT: A 124 ASP cc_start: 0.7348 (p0) cc_final: 0.7123 (p0) REVERT: B 25 ILE cc_start: 0.7700 (mm) cc_final: 0.7469 (mm) REVERT: B 180 PHE cc_start: 0.8103 (t80) cc_final: 0.7755 (t80) REVERT: B 434 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7350 (t70) REVERT: C 109 ARG cc_start: 0.7443 (ptt90) cc_final: 0.6944 (ptt90) REVERT: C 180 PHE cc_start: 0.8022 (t80) cc_final: 0.7797 (t80) REVERT: C 434 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7350 (t70) REVERT: D 124 ASP cc_start: 0.7164 (p0) cc_final: 0.6951 (p0) REVERT: D 180 PHE cc_start: 0.8014 (t80) cc_final: 0.7790 (t80) REVERT: D 338 MET cc_start: 0.8843 (mmm) cc_final: 0.8345 (mmt) REVERT: D 434 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7353 (t70) outliers start: 56 outliers final: 46 residues processed: 173 average time/residue: 0.2600 time to fit residues: 65.9995 Evaluate side-chains 177 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 128 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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: 0.8418 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13896 Z= 0.211 Angle : 0.490 5.807 18744 Z= 0.264 Chirality : 0.042 0.163 2060 Planarity : 0.003 0.028 2396 Dihedral : 4.774 28.310 1852 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.83 % Allowed : 16.20 % Favored : 79.97 % 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: -1.10 (0.20), residues: 1696 helix: 0.73 (0.20), residues: 748 sheet: 0.04 (0.37), residues: 188 loop : -2.55 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 311 HIS 0.005 0.001 HIS B 75 PHE 0.020 0.001 PHE A 180 TYR 0.012 0.001 TYR C 162 ARG 0.002 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 130 time to evaluate : 1.641 Fit side-chains REVERT: A 124 ASP cc_start: 0.7361 (p0) cc_final: 0.7137 (p0) REVERT: A 170 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6225 (tt) REVERT: B 25 ILE cc_start: 0.7688 (mm) cc_final: 0.7446 (mm) REVERT: B 180 PHE cc_start: 0.8069 (t80) cc_final: 0.7736 (t80) REVERT: B 434 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7220 (t70) REVERT: C 109 ARG cc_start: 0.7406 (ptt90) cc_final: 0.6914 (ptt90) REVERT: C 170 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6283 (tt) REVERT: C 180 PHE cc_start: 0.8021 (t80) cc_final: 0.7789 (t80) REVERT: C 434 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7206 (t70) REVERT: D 170 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6260 (tt) REVERT: D 180 PHE cc_start: 0.8020 (t80) cc_final: 0.7783 (t80) REVERT: D 338 MET cc_start: 0.8862 (mmm) cc_final: 0.8315 (mmt) REVERT: D 434 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7210 (t70) outliers start: 57 outliers final: 49 residues processed: 173 average time/residue: 0.2576 time to fit residues: 65.3093 Evaluate side-chains 181 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 126 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 163 optimal weight: 0.5980 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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: 0.8435 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13896 Z= 0.251 Angle : 0.514 5.131 18744 Z= 0.277 Chirality : 0.043 0.172 2060 Planarity : 0.003 0.027 2396 Dihedral : 4.911 29.359 1852 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 3.97 % Allowed : 16.40 % Favored : 79.64 % 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: -1.12 (0.20), residues: 1696 helix: 0.70 (0.19), residues: 748 sheet: 0.07 (0.38), residues: 188 loop : -2.54 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 351 HIS 0.005 0.002 HIS B 75 PHE 0.015 0.001 PHE C 108 TYR 0.013 0.001 TYR C 162 ARG 0.002 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 129 time to evaluate : 1.602 Fit side-chains REVERT: A 124 ASP cc_start: 0.7367 (p0) cc_final: 0.7141 (p0) REVERT: A 170 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6299 (tt) REVERT: B 25 ILE cc_start: 0.7620 (mm) cc_final: 0.7410 (mm) REVERT: B 180 PHE cc_start: 0.8079 (t80) cc_final: 0.7791 (t80) REVERT: B 318 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7792 (mtp85) REVERT: C 109 ARG cc_start: 0.7433 (ptt90) cc_final: 0.6923 (ptt90) REVERT: C 170 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6288 (tt) REVERT: C 180 PHE cc_start: 0.8039 (t80) cc_final: 0.7785 (t80) REVERT: D 180 PHE cc_start: 0.8025 (t80) cc_final: 0.7779 (t80) REVERT: D 338 MET cc_start: 0.8907 (mmm) cc_final: 0.8548 (mmp) outliers start: 59 outliers final: 56 residues processed: 176 average time/residue: 0.2642 time to fit residues: 67.9837 Evaluate side-chains 186 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 128 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8428 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13896 Z= 0.232 Angle : 0.504 5.110 18744 Z= 0.272 Chirality : 0.043 0.172 2060 Planarity : 0.003 0.029 2396 Dihedral : 4.863 29.152 1852 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.23 % Allowed : 16.53 % Favored : 79.23 % 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: -1.06 (0.20), residues: 1696 helix: 0.74 (0.20), residues: 748 sheet: 0.10 (0.38), residues: 188 loop : -2.50 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 351 HIS 0.005 0.002 HIS B 75 PHE 0.015 0.001 PHE A 108 TYR 0.013 0.001 TYR C 162 ARG 0.002 0.000 ARG C 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 127 time to evaluate : 1.571 Fit side-chains REVERT: A 124 ASP cc_start: 0.7363 (p0) cc_final: 0.7138 (p0) REVERT: A 170 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6284 (tt) REVERT: B 25 ILE cc_start: 0.7622 (mm) cc_final: 0.7405 (mm) REVERT: B 180 PHE cc_start: 0.8068 (t80) cc_final: 0.7774 (t80) REVERT: B 434 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7425 (t70) REVERT: C 109 ARG cc_start: 0.7410 (ptt90) cc_final: 0.6897 (ptt90) REVERT: C 170 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6327 (tt) REVERT: C 180 PHE cc_start: 0.8028 (t80) cc_final: 0.7790 (t80) REVERT: D 170 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6275 (tt) REVERT: D 180 PHE cc_start: 0.8012 (t80) cc_final: 0.7770 (t80) REVERT: D 338 MET cc_start: 0.8877 (mmm) cc_final: 0.8310 (mmt) outliers start: 63 outliers final: 58 residues processed: 177 average time/residue: 0.2530 time to fit residues: 66.1157 Evaluate side-chains 189 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 127 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.148896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113984 restraints weight = 19537.005| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.26 r_work: 0.3001 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13896 Z= 0.271 Angle : 0.525 5.127 18744 Z= 0.283 Chirality : 0.043 0.170 2060 Planarity : 0.003 0.028 2396 Dihedral : 4.985 30.228 1852 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 4.30 % Allowed : 16.53 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.11 (0.20), residues: 1696 helix: 0.66 (0.20), residues: 748 sheet: 0.07 (0.38), residues: 188 loop : -2.48 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 351 HIS 0.005 0.002 HIS B 75 PHE 0.041 0.002 PHE A 180 TYR 0.013 0.002 TYR C 162 ARG 0.002 0.000 ARG C 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2585.57 seconds wall clock time: 48 minutes 14.58 seconds (2894.58 seconds total)