Starting phenix.real_space_refine on Mon Mar 18 01:28:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3g_13791/03_2024/7q3g_13791.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3g_13791/03_2024/7q3g_13791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3g_13791/03_2024/7q3g_13791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3g_13791/03_2024/7q3g_13791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3g_13791/03_2024/7q3g_13791.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3g_13791/03_2024/7q3g_13791.pdb" } resolution = 3.5 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= 0.002 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 40 5.16 5 C 12585 2.51 5 N 3270 2.21 5 O 3670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 497": "OE1" <-> "OE2" Residue "C PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19570 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3913 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain breaks: 6 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 125 Chain: "E" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3913 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain breaks: 6 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 125 Chain: "D" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3913 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain breaks: 6 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 125 Chain: "C" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3913 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain breaks: 6 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3913 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain breaks: 6 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 125 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.25, per 1000 atoms: 0.52 Number of scatterers: 19570 At special positions: 0 Unit cell: (137.76, 136.94, 149.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 40 16.00 O 3670 8.00 N 3270 7.00 C 12585 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: 7.75 Conformation dependent library (CDL) restraints added in 3.6 seconds 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4820 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 25 sheets defined 31.0% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.550A pdb=" N GLY A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.781A pdb=" N ARG A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.756A pdb=" N CYS A 371 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 Processing helix chain 'A' and resid 437 through 441 removed outlier: 4.425A pdb=" N ALA A 440 " --> pdb=" O ASP A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 522 removed outlier: 3.787A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 536 Processing helix chain 'A' and resid 543 through 564 Processing helix chain 'A' and resid 574 through 604 Processing helix chain 'A' and resid 606 through 637 Proline residue: A 621 - end of helix removed outlier: 3.707A pdb=" N THR A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 98 removed outlier: 3.550A pdb=" N GLY E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 117 Processing helix chain 'E' and resid 308 through 313 removed outlier: 3.813A pdb=" N ARG E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 365 Processing helix chain 'E' and resid 367 through 372 removed outlier: 4.459A pdb=" N CYS E 371 " --> pdb=" O SER E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 390 Processing helix chain 'E' and resid 437 through 441 removed outlier: 4.396A pdb=" N ALA E 440 " --> pdb=" O ASP E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 522 removed outlier: 3.755A pdb=" N TYR E 518 " --> pdb=" O ASN E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 536 Processing helix chain 'E' and resid 543 through 564 Processing helix chain 'E' and resid 574 through 604 Processing helix chain 'E' and resid 606 through 637 Proline residue: E 621 - end of helix removed outlier: 3.710A pdb=" N THR E 637 " --> pdb=" O LEU E 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.540A pdb=" N GLY D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 117 Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.778A pdb=" N ARG D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.771A pdb=" N CYS D 371 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 390 Processing helix chain 'D' and resid 437 through 441 removed outlier: 4.406A pdb=" N ALA D 440 " --> pdb=" O ASP D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 522 removed outlier: 3.715A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 536 Processing helix chain 'D' and resid 543 through 564 Processing helix chain 'D' and resid 574 through 604 Processing helix chain 'D' and resid 606 through 637 Proline residue: D 621 - end of helix removed outlier: 3.704A pdb=" N THR D 637 " --> pdb=" O LEU D 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 removed outlier: 3.550A pdb=" N GLY C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 117 Processing helix chain 'C' and resid 308 through 313 removed outlier: 3.784A pdb=" N ARG C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.756A pdb=" N CYS C 371 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 390 Processing helix chain 'C' and resid 437 through 441 removed outlier: 4.405A pdb=" N ALA C 440 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 522 removed outlier: 3.746A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 536 removed outlier: 3.542A pdb=" N LEU C 526 " --> pdb=" O ILE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 564 Processing helix chain 'C' and resid 574 through 604 Processing helix chain 'C' and resid 606 through 637 Proline residue: C 621 - end of helix removed outlier: 3.700A pdb=" N THR C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.555A pdb=" N GLY B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.798A pdb=" N ARG B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.756A pdb=" N CYS B 371 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 Processing helix chain 'B' and resid 437 through 441 removed outlier: 4.395A pdb=" N ALA B 440 " --> pdb=" O ASP B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 522 removed outlier: 3.843A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 536 Processing helix chain 'B' and resid 543 through 564 Processing helix chain 'B' and resid 574 through 604 Processing helix chain 'B' and resid 606 through 637 Proline residue: B 621 - end of helix removed outlier: 3.703A pdb=" N THR B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 73 Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 212 removed outlier: 4.070A pdb=" N LEU A 208 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN A 272 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N PHE A 259 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A 274 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N LEU A 257 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASP A 251 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY A 260 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A 247 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.885A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL A 415 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A 420 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASN A 348 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY A 341 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER A 350 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE A 339 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 352 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS A 360 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU A 329 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 398 removed outlier: 5.037A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS A 512 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL A 484 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 70 through 73 Processing sheet with id=AA7, first strand: chain 'E' and resid 151 through 152 Processing sheet with id=AA8, first strand: chain 'E' and resid 208 through 212 removed outlier: 4.061A pdb=" N LEU E 208 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN E 272 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N PHE E 259 " --> pdb=" O ASN E 272 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR E 274 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N LEU E 257 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP E 251 " --> pdb=" O PRO E 256 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY E 260 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU E 247 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 376 through 379 removed outlier: 3.896A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL E 415 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG E 420 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN E 348 " --> pdb=" O GLY E 341 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY E 341 " --> pdb=" O ASN E 348 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER E 350 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE E 339 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL E 352 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS E 360 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU E 329 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL E 332 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE E 466 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU E 334 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 397 through 398 removed outlier: 5.083A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS E 512 " --> pdb=" O VAL E 484 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL E 484 " --> pdb=" O LYS E 512 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 70 through 73 Processing sheet with id=AB3, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AB4, first strand: chain 'D' and resid 208 through 212 removed outlier: 4.109A pdb=" N LEU D 208 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN D 272 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE D 259 " --> pdb=" O ASN D 272 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR D 274 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N LEU D 257 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP D 251 " --> pdb=" O PRO D 256 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY D 260 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU D 247 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 376 through 379 removed outlier: 3.889A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL D 415 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG D 420 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN D 348 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY D 341 " --> pdb=" O ASN D 348 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER D 350 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE D 339 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 352 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS D 360 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU D 329 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL D 332 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE D 466 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU D 334 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 397 through 398 removed outlier: 5.079A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS D 512 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL D 484 " --> pdb=" O LYS D 512 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AB8, first strand: chain 'C' and resid 151 through 152 Processing sheet with id=AB9, first strand: chain 'C' and resid 205 through 212 removed outlier: 3.747A pdb=" N VAL C 304 " --> pdb=" O GLN C 206 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU C 208 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN C 272 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N PHE C 259 " --> pdb=" O ASN C 272 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C 274 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N LEU C 257 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP C 251 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY C 260 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU C 247 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.882A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL C 415 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG C 420 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN C 348 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY C 341 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER C 350 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE C 339 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 352 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N HIS C 360 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU C 329 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 397 through 398 removed outlier: 5.025A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS C 512 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL C 484 " --> pdb=" O LYS C 512 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 70 through 73 Processing sheet with id=AC4, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AC5, first strand: chain 'B' and resid 208 through 212 removed outlier: 4.085A pdb=" N LEU B 208 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN B 272 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE B 259 " --> pdb=" O ASN B 272 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR B 274 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N LEU B 257 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP B 251 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 260 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 247 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.895A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N VAL B 415 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG B 420 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASN B 348 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY B 341 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER B 350 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE B 339 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 352 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS B 360 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU B 329 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 397 through 398 removed outlier: 5.036A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 512 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL B 484 " --> pdb=" O LYS B 512 " (cutoff:3.500A) 921 hydrogen bonds defined for protein. 2646 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: 6.30 Time building geometry restraints manager: 8.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6365 1.34 - 1.46: 4256 1.46 - 1.58: 9314 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 19985 Sorted by residual: bond pdb=" CB PRO C 161 " pdb=" CG PRO C 161 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.30e+00 bond pdb=" CG1 ILE D 530 " pdb=" CD1 ILE D 530 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.12e+00 bond pdb=" CG1 ILE C 530 " pdb=" CD1 ILE C 530 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.10e+00 bond pdb=" CG LEU D 553 " pdb=" CD2 LEU D 553 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CG LEU E 553 " pdb=" CD2 LEU E 553 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 ... (remaining 19980 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.91: 392 105.91 - 112.93: 10820 112.93 - 119.95: 6413 119.95 - 126.97: 9398 126.97 - 133.99: 217 Bond angle restraints: 27240 Sorted by residual: angle pdb=" C GLU C 379 " pdb=" N ASP C 380 " pdb=" CA ASP C 380 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C GLU A 379 " pdb=" N ASP A 380 " pdb=" CA ASP A 380 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C GLU D 379 " pdb=" N ASP D 380 " pdb=" CA ASP D 380 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.57e+00 angle pdb=" C GLU B 379 " pdb=" N ASP B 380 " pdb=" CA ASP B 380 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.31e+00 angle pdb=" C GLU E 379 " pdb=" N ASP E 380 " pdb=" CA ASP E 380 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.01e+00 ... (remaining 27235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 10543 16.66 - 33.33: 967 33.33 - 49.99: 136 49.99 - 66.65: 23 66.65 - 83.32: 11 Dihedral angle restraints: 11680 sinusoidal: 4225 harmonic: 7455 Sorted by residual: dihedral pdb=" CA GLN D 338 " pdb=" C GLN D 338 " pdb=" N ILE D 339 " pdb=" CA ILE D 339 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA GLN E 338 " pdb=" C GLN E 338 " pdb=" N ILE E 339 " pdb=" CA ILE E 339 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLN C 338 " pdb=" C GLN C 338 " pdb=" N ILE C 339 " pdb=" CA ILE C 339 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 11677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1900 0.033 - 0.066: 836 0.066 - 0.099: 299 0.099 - 0.132: 114 0.132 - 0.165: 26 Chirality restraints: 3175 Sorted by residual: chirality pdb=" CG LEU B 329 " pdb=" CB LEU B 329 " pdb=" CD1 LEU B 329 " pdb=" CD2 LEU B 329 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CG LEU C 329 " pdb=" CB LEU C 329 " pdb=" CD1 LEU C 329 " pdb=" CD2 LEU C 329 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CB ILE A 413 " pdb=" CA ILE A 413 " pdb=" CG1 ILE A 413 " pdb=" CG2 ILE A 413 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 3172 not shown) Planarity restraints: 3505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 160 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO C 161 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 161 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 161 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 160 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO D 161 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 416 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO D 417 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 417 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 417 " -0.032 5.00e-02 4.00e+02 ... (remaining 3502 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 485 2.69 - 3.25: 19389 3.25 - 3.80: 30327 3.80 - 4.35: 38700 4.35 - 4.90: 64784 Nonbonded interactions: 153685 Sorted by model distance: nonbonded pdb=" OG SER B 533 " pdb=" OD1 ASN B 552 " model vdw 2.142 2.440 nonbonded pdb=" OG SER A 533 " pdb=" OD1 ASN A 552 " model vdw 2.145 2.440 nonbonded pdb=" OG SER E 533 " pdb=" OD1 ASN E 552 " model vdw 2.148 2.440 nonbonded pdb=" OG SER C 533 " pdb=" OD1 ASN C 552 " model vdw 2.149 2.440 nonbonded pdb=" OG SER D 533 " pdb=" OD1 ASN D 552 " model vdw 2.161 2.440 ... (remaining 153680 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' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 4.740 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 51.570 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 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 : 0.004 0.057 19985 Z= 0.270 Angle : 0.639 7.682 27240 Z= 0.327 Chirality : 0.045 0.165 3175 Planarity : 0.004 0.076 3505 Dihedral : 13.013 83.316 6860 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2515 helix: 1.62 (0.20), residues: 670 sheet: -0.59 (0.20), residues: 560 loop : -1.94 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 407 HIS 0.003 0.001 HIS A 285 PHE 0.024 0.002 PHE A 414 TYR 0.017 0.002 TYR E 441 ARG 0.009 0.001 ARG B 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 439 LEU cc_start: 0.8000 (tp) cc_final: 0.7722 (tp) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3269 time to fit residues: 128.8786 Evaluate side-chains 152 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 20.0000 chunk 193 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 199 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 121 optimal weight: 50.0000 chunk 148 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 597 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN D 597 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN B 410 ASN B 597 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19985 Z= 0.310 Angle : 0.606 11.530 27240 Z= 0.306 Chirality : 0.043 0.156 3175 Planarity : 0.004 0.049 3505 Dihedral : 4.366 19.427 2735 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.19 % Allowed : 12.29 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2515 helix: 1.79 (0.19), residues: 680 sheet: -0.50 (0.19), residues: 640 loop : -1.79 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 407 HIS 0.004 0.001 HIS D 233 PHE 0.020 0.002 PHE B 561 TYR 0.014 0.002 TYR B 441 ARG 0.005 0.001 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 515 LEU cc_start: 0.7260 (pt) cc_final: 0.6995 (pp) REVERT: B 439 LEU cc_start: 0.8241 (tp) cc_final: 0.8029 (tp) outliers start: 24 outliers final: 20 residues processed: 194 average time/residue: 0.2990 time to fit residues: 91.6609 Evaluate side-chains 173 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 622 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 63 optimal weight: 40.0000 chunk 231 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 206 optimal weight: 0.2980 chunk 230 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19985 Z= 0.221 Angle : 0.573 12.444 27240 Z= 0.284 Chirality : 0.042 0.158 3175 Planarity : 0.003 0.043 3505 Dihedral : 4.148 18.731 2735 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.59 % Allowed : 14.58 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2515 helix: 1.84 (0.20), residues: 685 sheet: -0.37 (0.19), residues: 640 loop : -1.72 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 407 HIS 0.003 0.001 HIS C 233 PHE 0.026 0.001 PHE D 561 TYR 0.016 0.002 TYR D 624 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 581 ILE cc_start: 0.7958 (mm) cc_final: 0.7743 (mt) outliers start: 32 outliers final: 29 residues processed: 197 average time/residue: 0.2817 time to fit residues: 88.9561 Evaluate side-chains 183 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 622 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 121 optimal weight: 0.1980 chunk 220 optimal weight: 50.0000 chunk 66 optimal weight: 50.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 233 HIS E 410 ASN D 514 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 19985 Z= 0.274 Angle : 0.581 12.096 27240 Z= 0.290 Chirality : 0.042 0.181 3175 Planarity : 0.003 0.040 3505 Dihedral : 4.182 18.892 2735 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.29 % Allowed : 16.37 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2515 helix: 1.90 (0.20), residues: 685 sheet: -0.39 (0.19), residues: 660 loop : -1.61 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 407 HIS 0.004 0.001 HIS C 233 PHE 0.028 0.001 PHE D 561 TYR 0.015 0.002 TYR B 441 ARG 0.004 0.000 ARG E 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 155 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.6853 (mp0) cc_final: 0.6463 (mp0) outliers start: 46 outliers final: 34 residues processed: 190 average time/residue: 0.2703 time to fit residues: 82.7108 Evaluate side-chains 173 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 622 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 210 optimal weight: 30.0000 chunk 170 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 125 optimal weight: 10.0000 chunk 221 optimal weight: 50.0000 chunk 62 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19985 Z= 0.279 Angle : 0.580 12.367 27240 Z= 0.290 Chirality : 0.042 0.163 3175 Planarity : 0.003 0.039 3505 Dihedral : 4.197 18.334 2735 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.49 % Allowed : 17.76 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2515 helix: 1.90 (0.20), residues: 685 sheet: -0.36 (0.19), residues: 660 loop : -1.58 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 407 HIS 0.004 0.001 HIS B 233 PHE 0.023 0.001 PHE D 561 TYR 0.014 0.002 TYR B 627 ARG 0.004 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 148 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 LEU cc_start: 0.7522 (pt) cc_final: 0.7286 (pp) REVERT: B 439 LEU cc_start: 0.8151 (tp) cc_final: 0.7921 (tp) outliers start: 50 outliers final: 31 residues processed: 184 average time/residue: 0.2830 time to fit residues: 83.7528 Evaluate side-chains 168 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 562 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 1.9990 chunk 221 optimal weight: 50.0000 chunk 48 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 204 optimal weight: 40.0000 chunk 114 optimal weight: 40.0000 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19985 Z= 0.279 Angle : 0.581 12.392 27240 Z= 0.291 Chirality : 0.042 0.156 3175 Planarity : 0.003 0.037 3505 Dihedral : 4.197 18.270 2735 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.49 % Allowed : 18.26 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2515 helix: 1.91 (0.20), residues: 685 sheet: -0.34 (0.19), residues: 660 loop : -1.55 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 407 HIS 0.003 0.001 HIS D 233 PHE 0.023 0.001 PHE D 561 TYR 0.013 0.002 TYR E 441 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 515 LEU cc_start: 0.7494 (pt) cc_final: 0.7252 (pp) outliers start: 50 outliers final: 33 residues processed: 187 average time/residue: 0.2838 time to fit residues: 85.6995 Evaluate side-chains 169 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 562 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 153 optimal weight: 30.0000 chunk 149 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 464 ASN C 233 HIS ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19985 Z= 0.142 Angle : 0.560 13.841 27240 Z= 0.275 Chirality : 0.042 0.174 3175 Planarity : 0.003 0.038 3505 Dihedral : 3.930 17.210 2735 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.34 % Allowed : 20.30 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2515 helix: 1.96 (0.19), residues: 685 sheet: -0.29 (0.19), residues: 660 loop : -1.45 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 407 HIS 0.004 0.001 HIS A 233 PHE 0.022 0.001 PHE D 561 TYR 0.012 0.001 TYR B 620 ARG 0.003 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 2.454 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 21 residues processed: 180 average time/residue: 0.2688 time to fit residues: 79.9387 Evaluate side-chains 164 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain B residue 413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 167 optimal weight: 30.0000 chunk 121 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 193 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19985 Z= 0.147 Angle : 0.558 13.470 27240 Z= 0.273 Chirality : 0.042 0.172 3175 Planarity : 0.003 0.038 3505 Dihedral : 3.850 17.041 2735 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.34 % Allowed : 20.95 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2515 helix: 1.97 (0.19), residues: 685 sheet: -0.20 (0.19), residues: 655 loop : -1.44 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 407 HIS 0.003 0.001 HIS A 285 PHE 0.028 0.001 PHE A 561 TYR 0.011 0.001 TYR C 620 ARG 0.002 0.000 ARG E 406 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 2.357 Fit side-chains revert: symmetry clash REVERT: C 409 GLN cc_start: 0.6948 (tp40) cc_final: 0.6731 (mm-40) outliers start: 27 outliers final: 22 residues processed: 177 average time/residue: 0.2602 time to fit residues: 76.0328 Evaluate side-chains 162 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 533 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 0.8980 chunk 235 optimal weight: 0.0370 chunk 214 optimal weight: 40.0000 chunk 229 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 70 optimal weight: 50.0000 chunk 206 optimal weight: 0.0040 chunk 216 optimal weight: 30.0000 chunk 228 optimal weight: 1.9990 overall best weight: 1.9874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 154 GLN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19985 Z= 0.173 Angle : 0.563 13.336 27240 Z= 0.276 Chirality : 0.042 0.161 3175 Planarity : 0.003 0.038 3505 Dihedral : 3.848 18.205 2735 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.34 % Allowed : 21.29 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2515 helix: 1.99 (0.19), residues: 685 sheet: -0.19 (0.19), residues: 655 loop : -1.41 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP E 407 HIS 0.002 0.001 HIS A 285 PHE 0.031 0.001 PHE A 561 TYR 0.011 0.001 TYR C 620 ARG 0.004 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 2.509 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 26 residues processed: 170 average time/residue: 0.2842 time to fit residues: 80.5617 Evaluate side-chains 165 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 533 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 114 optimal weight: 40.0000 chunk 168 optimal weight: 30.0000 chunk 254 optimal weight: 2.9990 chunk 233 optimal weight: 20.0000 chunk 202 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 221 GLN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19985 Z= 0.312 Angle : 0.601 12.229 27240 Z= 0.303 Chirality : 0.043 0.168 3175 Planarity : 0.003 0.037 3505 Dihedral : 4.157 19.157 2735 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.54 % Allowed : 21.09 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2515 helix: 2.01 (0.20), residues: 680 sheet: -0.25 (0.19), residues: 660 loop : -1.46 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 407 HIS 0.004 0.001 HIS B 233 PHE 0.035 0.002 PHE A 561 TYR 0.015 0.002 TYR A 441 ARG 0.006 0.000 ARG B 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 2.303 Fit side-chains revert: symmetry clash REVERT: A 515 LEU cc_start: 0.7472 (pt) cc_final: 0.7170 (pp) outliers start: 31 outliers final: 27 residues processed: 166 average time/residue: 0.2635 time to fit residues: 72.1483 Evaluate side-chains 158 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 533 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 50.0000 chunk 202 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 208 optimal weight: 30.0000 chunk 25 optimal weight: 0.0270 chunk 37 optimal weight: 7.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.083138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.056418 restraints weight = 69877.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.058074 restraints weight = 34107.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.059139 restraints weight = 22050.127| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19985 Z= 0.216 Angle : 0.580 12.958 27240 Z= 0.287 Chirality : 0.042 0.162 3175 Planarity : 0.003 0.100 3505 Dihedral : 4.046 18.979 2735 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.24 % Allowed : 21.49 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2515 helix: 1.92 (0.20), residues: 690 sheet: -0.25 (0.19), residues: 660 loop : -1.36 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 407 HIS 0.003 0.001 HIS D 233 PHE 0.029 0.001 PHE A 561 TYR 0.011 0.001 TYR B 627 ARG 0.007 0.000 ARG B 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3180.64 seconds wall clock time: 60 minutes 26.46 seconds (3626.46 seconds total)