Starting phenix.real_space_refine on Fri Mar 15 16:01:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/03_2024/7lid_23374_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/03_2024/7lid_23374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/03_2024/7lid_23374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/03_2024/7lid_23374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/03_2024/7lid_23374_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/03_2024/7lid_23374_updated.pdb" } resolution = 2.9 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= 0.002 sd= 0.105 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 120 5.16 5 C 7992 2.51 5 N 1936 2.21 5 O 2092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A ASP 317": "OD1" <-> "OD2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "B PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ASP 220": "OD1" <-> "OD2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B ASP 317": "OD1" <-> "OD2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 422": "NH1" <-> "NH2" Residue "C PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 169": "OD1" <-> "OD2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C ASP 317": "OD1" <-> "OD2" Residue "C TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "D PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D ASP 317": "OD1" <-> "OD2" Residue "D TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 422": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12140 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3023 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain breaks: 2 Chain: "B" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3023 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain breaks: 2 Chain: "C" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3023 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain breaks: 2 Chain: "D" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3023 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain breaks: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'EOL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'EOL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'EOL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'EOL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.56, per 1000 atoms: 0.54 Number of scatterers: 12140 At special positions: 0 Unit cell: (112.27, 112.27, 92.7, 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 120 16.00 O 2092 8.00 N 1936 7.00 C 7992 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: 4.58 Conformation dependent library (CDL) restraints added in 2.3 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 0 sheets defined 77.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 14 through 30 removed outlier: 3.601A pdb=" N ARG A 18 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 49 through 74 removed outlier: 3.718A pdb=" N CYS A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 73 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 104 removed outlier: 4.344A pdb=" N THR A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 126 through 168 removed outlier: 3.919A pdb=" N SER A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 195 through 246 removed outlier: 4.410A pdb=" N ALA A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 319 through 365 removed outlier: 4.166A pdb=" N SER A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 406 removed outlier: 3.771A pdb=" N LEU A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 432 removed outlier: 3.693A pdb=" N GLN A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 468 removed outlier: 3.677A pdb=" N ILE A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 30 removed outlier: 3.601A pdb=" N ARG B 18 " --> pdb=" O TYR B 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 49 through 74 removed outlier: 3.716A pdb=" N CYS B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 73 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 104 removed outlier: 4.344A pdb=" N THR B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 126 through 168 removed outlier: 3.919A pdb=" N SER B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 195 through 246 removed outlier: 4.411A pdb=" N ALA B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 319 through 365 removed outlier: 4.166A pdb=" N SER B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 406 removed outlier: 3.771A pdb=" N LEU B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 419 through 432 removed outlier: 3.693A pdb=" N GLN B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 468 removed outlier: 3.676A pdb=" N ILE B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 465 " --> pdb=" O TYR B 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 30 removed outlier: 3.600A pdb=" N ARG C 18 " --> pdb=" O TYR C 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 49 through 74 removed outlier: 3.716A pdb=" N CYS C 56 " --> pdb=" O GLN C 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS C 74 " --> pdb=" O CYS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 104 removed outlier: 4.345A pdb=" N THR C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 115 Processing helix chain 'C' and resid 126 through 168 removed outlier: 3.918A pdb=" N SER C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 195 through 246 removed outlier: 4.411A pdb=" N ALA C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 319 through 365 removed outlier: 4.165A pdb=" N SER C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL C 341 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 406 removed outlier: 3.771A pdb=" N LEU C 379 " --> pdb=" O PRO C 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 432 removed outlier: 3.692A pdb=" N GLN C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 468 removed outlier: 3.677A pdb=" N ILE C 463 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 464 " --> pdb=" O THR C 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 465 " --> pdb=" O TYR C 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 30 removed outlier: 3.601A pdb=" N ARG D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY D 25 " --> pdb=" O ILE D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 49 through 74 removed outlier: 3.716A pdb=" N CYS D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 104 removed outlier: 4.344A pdb=" N THR D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 115 Processing helix chain 'D' and resid 126 through 168 removed outlier: 3.918A pdb=" N SER D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Proline residue: D 162 - end of helix Processing helix chain 'D' and resid 195 through 246 removed outlier: 4.411A pdb=" N ALA D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 319 through 365 removed outlier: 4.166A pdb=" N SER D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 342 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 406 removed outlier: 3.772A pdb=" N LEU D 379 " --> pdb=" O PRO D 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET D 382 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 419 through 432 removed outlier: 3.693A pdb=" N GLN D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 468 removed outlier: 3.676A pdb=" N ILE D 463 " --> pdb=" O LEU D 459 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 464 " --> pdb=" O THR D 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 465 " --> pdb=" O TYR D 461 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.48 Time building geometry restraints manager: 4.94 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: 3354 1.34 - 1.46: 2242 1.46 - 1.57: 6648 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 12416 Sorted by residual: bond pdb=" C8 EOL B 900 " pdb=" C9 EOL B 900 " ideal model delta sigma weight residual 1.328 1.525 -0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C8 EOL A 900 " pdb=" C9 EOL A 900 " ideal model delta sigma weight residual 1.328 1.525 -0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C8 EOL D 900 " pdb=" C9 EOL D 900 " ideal model delta sigma weight residual 1.328 1.525 -0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" C8 EOL C 900 " pdb=" C9 EOL C 900 " ideal model delta sigma weight residual 1.328 1.525 -0.197 2.00e-02 2.50e+03 9.65e+01 bond pdb=" C SER D 195 " pdb=" N PRO D 196 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.23e-02 6.61e+03 1.13e+01 ... (remaining 12411 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.62: 264 106.62 - 113.48: 6990 113.48 - 120.33: 4844 120.33 - 127.19: 4628 127.19 - 134.04: 114 Bond angle restraints: 16840 Sorted by residual: angle pdb=" C7 EOL D 900 " pdb=" C8 EOL D 900 " pdb=" C9 EOL D 900 " ideal model delta sigma weight residual 124.74 111.99 12.75 3.00e+00 1.11e-01 1.81e+01 angle pdb=" C7 EOL A 900 " pdb=" C8 EOL A 900 " pdb=" C9 EOL A 900 " ideal model delta sigma weight residual 124.74 112.02 12.72 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C7 EOL C 900 " pdb=" C8 EOL C 900 " pdb=" C9 EOL C 900 " ideal model delta sigma weight residual 124.74 112.05 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C7 EOL B 900 " pdb=" C8 EOL B 900 " pdb=" C9 EOL B 900 " ideal model delta sigma weight residual 124.74 112.05 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C THR D 194 " pdb=" N SER D 195 " pdb=" CA SER D 195 " ideal model delta sigma weight residual 120.26 125.27 -5.01 1.34e+00 5.57e-01 1.40e+01 ... (remaining 16835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6487 17.99 - 35.98: 610 35.98 - 53.97: 155 53.97 - 71.96: 28 71.96 - 89.96: 4 Dihedral angle restraints: 7284 sinusoidal: 2776 harmonic: 4508 Sorted by residual: dihedral pdb=" CA ILE C 21 " pdb=" C ILE C 21 " pdb=" N LYS C 22 " pdb=" CA LYS C 22 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE D 21 " pdb=" C ILE D 21 " pdb=" N LYS D 22 " pdb=" CA LYS D 22 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE B 21 " pdb=" C ILE B 21 " pdb=" N LYS B 22 " pdb=" CA LYS B 22 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 7281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1151 0.032 - 0.064: 593 0.064 - 0.095: 180 0.095 - 0.127: 60 0.127 - 0.159: 32 Chirality restraints: 2016 Sorted by residual: chirality pdb=" CB VAL B 184 " pdb=" CA VAL B 184 " pdb=" CG1 VAL B 184 " pdb=" CG2 VAL B 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CB VAL C 184 " pdb=" CA VAL C 184 " pdb=" CG1 VAL C 184 " pdb=" CG2 VAL C 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CB VAL D 184 " pdb=" CA VAL D 184 " pdb=" CG1 VAL D 184 " pdb=" CG2 VAL D 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 2013 not shown) Planarity restraints: 2016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 38 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO B 39 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 38 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO A 39 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 38 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO C 39 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 39 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 39 " 0.035 5.00e-02 4.00e+02 ... (remaining 2013 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4077 2.84 - 3.36: 11778 3.36 - 3.87: 20108 3.87 - 4.39: 21484 4.39 - 4.90: 37801 Nonbonded interactions: 95248 Sorted by model distance: nonbonded pdb=" O THR A 348 " pdb=" OG1 THR A 352 " model vdw 2.330 2.440 nonbonded pdb=" O THR C 348 " pdb=" OG1 THR C 352 " model vdw 2.330 2.440 nonbonded pdb=" O THR D 348 " pdb=" OG1 THR D 352 " model vdw 2.330 2.440 nonbonded pdb=" O THR B 348 " pdb=" OG1 THR B 352 " model vdw 2.331 2.440 nonbonded pdb=" OG SER D 78 " pdb=" OE1 GLN D 81 " model vdw 2.388 2.440 ... (remaining 95243 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.230 Check model and map are aligned: 0.190 Set scattering table: 0.100 Process input model: 33.930 Find NCS groups from input model: 0.780 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:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 : 0.006 0.197 12416 Z= 0.405 Angle : 0.877 12.753 16840 Z= 0.494 Chirality : 0.044 0.159 2016 Planarity : 0.007 0.062 2016 Dihedral : 15.329 89.956 4356 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.47 % Allowed : 5.90 % Favored : 92.63 % 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: -2.01 (0.19), residues: 1500 helix: -0.77 (0.13), residues: 1188 sheet: None (None), residues: 0 loop : -3.07 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 158 HIS 0.003 0.001 HIS C 46 PHE 0.021 0.002 PHE D 363 TYR 0.023 0.002 TYR A 380 ARG 0.002 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 251 time to evaluate : 1.381 Fit side-chains REVERT: A 371 PHE cc_start: 0.7433 (t80) cc_final: 0.7220 (t80) REVERT: B 371 PHE cc_start: 0.7726 (t80) cc_final: 0.7448 (t80) REVERT: C 191 ASP cc_start: 0.7574 (p0) cc_final: 0.7371 (p0) REVERT: D 191 ASP cc_start: 0.7901 (p0) cc_final: 0.7669 (p0) REVERT: D 371 PHE cc_start: 0.7493 (t80) cc_final: 0.7246 (t80) outliers start: 20 outliers final: 9 residues processed: 268 average time/residue: 0.7351 time to fit residues: 223.9457 Evaluate side-chains 165 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 178 GLN B 52 GLN B 105 ASN B 467 GLN C 52 GLN C 198 ASN C 467 GLN D 52 GLN D 105 ASN D 178 GLN D 467 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12416 Z= 0.217 Angle : 0.553 6.602 16840 Z= 0.280 Chirality : 0.037 0.137 2016 Planarity : 0.004 0.040 2016 Dihedral : 6.188 59.995 1672 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.98 % Allowed : 16.45 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.22), residues: 1500 helix: 0.92 (0.15), residues: 1212 sheet: None (None), residues: 0 loop : -2.72 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 158 HIS 0.003 0.001 HIS A 16 PHE 0.025 0.001 PHE C 371 TYR 0.009 0.001 TYR C 380 ARG 0.008 0.001 ARG C 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 191 time to evaluate : 1.448 Fit side-chains REVERT: A 355 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7537 (mp) REVERT: B 355 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7535 (mp) REVERT: B 371 PHE cc_start: 0.7669 (t80) cc_final: 0.7408 (t80) REVERT: C 355 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7388 (mp) REVERT: D 191 ASP cc_start: 0.8001 (p0) cc_final: 0.7761 (p0) REVERT: D 355 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7623 (mp) REVERT: D 371 PHE cc_start: 0.7506 (t80) cc_final: 0.7261 (t80) outliers start: 54 outliers final: 24 residues processed: 224 average time/residue: 0.6875 time to fit residues: 176.7719 Evaluate side-chains 193 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 178 GLN B 46 HIS B 467 GLN C 46 HIS C 52 GLN D 46 HIS D 178 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12416 Z= 0.256 Angle : 0.569 9.071 16840 Z= 0.284 Chirality : 0.038 0.141 2016 Planarity : 0.003 0.034 2016 Dihedral : 4.892 38.558 1666 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.98 % Allowed : 18.95 % Favored : 77.06 % 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: 1.17 (0.22), residues: 1500 helix: 1.49 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : -2.41 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 158 HIS 0.004 0.001 HIS B 407 PHE 0.023 0.001 PHE D 142 TYR 0.009 0.001 TYR D 380 ARG 0.006 0.001 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 173 time to evaluate : 1.472 Fit side-chains REVERT: A 355 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7525 (mp) REVERT: A 377 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7135 (mtt) REVERT: B 355 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7545 (mp) REVERT: B 371 PHE cc_start: 0.7734 (t80) cc_final: 0.7498 (t80) REVERT: C 191 ASP cc_start: 0.7641 (p0) cc_final: 0.7292 (p0) REVERT: C 355 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7577 (mp) REVERT: C 371 PHE cc_start: 0.7736 (t80) cc_final: 0.7395 (t80) REVERT: D 191 ASP cc_start: 0.7918 (p0) cc_final: 0.7578 (p0) REVERT: D 355 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7599 (mp) REVERT: D 371 PHE cc_start: 0.7613 (t80) cc_final: 0.7350 (t80) outliers start: 54 outliers final: 35 residues processed: 203 average time/residue: 0.6765 time to fit residues: 158.6181 Evaluate side-chains 198 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 158 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 52 GLN C 178 GLN D 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12416 Z= 0.259 Angle : 0.564 9.277 16840 Z= 0.279 Chirality : 0.038 0.137 2016 Planarity : 0.003 0.031 2016 Dihedral : 4.397 32.757 1666 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.50 % Allowed : 20.50 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.22), residues: 1500 helix: 1.80 (0.15), residues: 1208 sheet: None (None), residues: 0 loop : -2.00 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 187 HIS 0.004 0.001 HIS C 407 PHE 0.024 0.001 PHE C 50 TYR 0.010 0.001 TYR D 332 ARG 0.004 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 162 time to evaluate : 1.463 Fit side-chains REVERT: A 355 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7574 (mp) REVERT: A 377 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7113 (mtt) REVERT: B 355 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7500 (mp) REVERT: B 371 PHE cc_start: 0.7700 (t80) cc_final: 0.7460 (t80) REVERT: B 377 MET cc_start: 0.7380 (mtt) cc_final: 0.7050 (mtt) REVERT: C 191 ASP cc_start: 0.7818 (p0) cc_final: 0.7495 (p0) REVERT: C 355 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7483 (mp) REVERT: C 371 PHE cc_start: 0.7734 (t80) cc_final: 0.7397 (t80) REVERT: D 191 ASP cc_start: 0.8014 (p0) cc_final: 0.7706 (p0) REVERT: D 355 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7541 (mp) REVERT: D 371 PHE cc_start: 0.7642 (t80) cc_final: 0.7410 (t80) outliers start: 61 outliers final: 41 residues processed: 199 average time/residue: 0.6527 time to fit residues: 150.3716 Evaluate side-chains 199 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 52 GLN C 178 GLN D 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12416 Z= 0.220 Angle : 0.547 9.088 16840 Z= 0.270 Chirality : 0.037 0.137 2016 Planarity : 0.003 0.029 2016 Dihedral : 4.328 32.485 1666 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.47 % Allowed : 23.45 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.23), residues: 1500 helix: 2.02 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.88 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 187 HIS 0.003 0.001 HIS D 407 PHE 0.025 0.001 PHE C 50 TYR 0.010 0.001 TYR D 332 ARG 0.004 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 166 time to evaluate : 1.165 Fit side-chains REVERT: A 355 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7443 (mp) REVERT: A 377 MET cc_start: 0.7404 (mtt) cc_final: 0.7038 (mtt) REVERT: B 355 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7360 (mp) REVERT: B 371 PHE cc_start: 0.7721 (t80) cc_final: 0.7491 (t80) REVERT: C 191 ASP cc_start: 0.7916 (p0) cc_final: 0.7612 (p0) REVERT: C 355 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7524 (mp) REVERT: C 371 PHE cc_start: 0.7744 (t80) cc_final: 0.7417 (t80) REVERT: D 191 ASP cc_start: 0.8065 (p0) cc_final: 0.7775 (p0) REVERT: D 355 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7478 (mp) REVERT: D 371 PHE cc_start: 0.7696 (t80) cc_final: 0.7422 (t80) REVERT: D 377 MET cc_start: 0.7291 (mtt) cc_final: 0.6948 (mtt) outliers start: 47 outliers final: 27 residues processed: 192 average time/residue: 0.6831 time to fit residues: 151.1422 Evaluate side-chains 188 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 0.0070 chunk 77 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 178 GLN C 467 GLN D 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12416 Z= 0.162 Angle : 0.529 8.736 16840 Z= 0.259 Chirality : 0.036 0.149 2016 Planarity : 0.003 0.027 2016 Dihedral : 4.203 29.790 1666 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.43 % Allowed : 25.37 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.23), residues: 1500 helix: 2.26 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.81 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 187 HIS 0.002 0.000 HIS D 407 PHE 0.026 0.001 PHE D 50 TYR 0.013 0.001 TYR B 188 ARG 0.004 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.482 Fit side-chains REVERT: A 377 MET cc_start: 0.7359 (mtt) cc_final: 0.7043 (mtt) REVERT: B 371 PHE cc_start: 0.7643 (t80) cc_final: 0.7430 (t80) REVERT: C 191 ASP cc_start: 0.7896 (p0) cc_final: 0.7605 (p0) REVERT: C 355 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7170 (mp) REVERT: C 371 PHE cc_start: 0.7660 (t80) cc_final: 0.7371 (t80) REVERT: D 191 ASP cc_start: 0.8048 (p0) cc_final: 0.7765 (p0) REVERT: D 355 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7337 (mp) REVERT: D 371 PHE cc_start: 0.7640 (t80) cc_final: 0.7391 (t80) REVERT: D 377 MET cc_start: 0.7223 (mtt) cc_final: 0.6935 (mtt) outliers start: 33 outliers final: 25 residues processed: 184 average time/residue: 0.7455 time to fit residues: 156.4193 Evaluate side-chains 187 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 0.0670 chunk 146 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 178 GLN C 467 GLN D 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12416 Z= 0.269 Angle : 0.598 9.843 16840 Z= 0.289 Chirality : 0.038 0.152 2016 Planarity : 0.003 0.026 2016 Dihedral : 4.260 31.467 1666 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.95 % Allowed : 25.81 % Favored : 71.24 % 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: 2.16 (0.23), residues: 1500 helix: 2.16 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.70 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 187 HIS 0.004 0.001 HIS D 407 PHE 0.026 0.001 PHE C 50 TYR 0.011 0.001 TYR B 188 ARG 0.002 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 159 time to evaluate : 1.352 Fit side-chains REVERT: A 377 MET cc_start: 0.7349 (mtt) cc_final: 0.7077 (mtt) REVERT: C 191 ASP cc_start: 0.7939 (p0) cc_final: 0.7659 (p0) REVERT: C 355 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7379 (mp) REVERT: C 371 PHE cc_start: 0.7599 (t80) cc_final: 0.7323 (t80) REVERT: D 191 ASP cc_start: 0.8053 (p0) cc_final: 0.7792 (p0) REVERT: D 355 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7568 (mp) REVERT: D 371 PHE cc_start: 0.7770 (t80) cc_final: 0.7521 (t80) REVERT: D 377 MET cc_start: 0.7211 (mtt) cc_final: 0.6973 (mtt) outliers start: 40 outliers final: 30 residues processed: 179 average time/residue: 0.7261 time to fit residues: 148.8167 Evaluate side-chains 187 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 93 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 467 GLN B 467 GLN C 52 GLN C 178 GLN C 467 GLN D 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12416 Z= 0.182 Angle : 0.572 9.535 16840 Z= 0.272 Chirality : 0.037 0.157 2016 Planarity : 0.003 0.026 2016 Dihedral : 4.200 29.668 1666 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.43 % Allowed : 27.21 % Favored : 70.35 % 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: 2.35 (0.23), residues: 1500 helix: 2.30 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.64 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 187 HIS 0.002 0.000 HIS C 407 PHE 0.028 0.001 PHE C 50 TYR 0.009 0.001 TYR A 332 ARG 0.003 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 1.457 Fit side-chains REVERT: C 191 ASP cc_start: 0.7894 (p0) cc_final: 0.7641 (p0) REVERT: C 355 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7228 (mp) REVERT: C 371 PHE cc_start: 0.7596 (t80) cc_final: 0.7313 (t80) REVERT: D 191 ASP cc_start: 0.8122 (p0) cc_final: 0.7848 (p0) REVERT: D 355 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7347 (mp) REVERT: D 371 PHE cc_start: 0.7738 (t80) cc_final: 0.7508 (t80) REVERT: D 377 MET cc_start: 0.7185 (mtt) cc_final: 0.6968 (mtt) outliers start: 33 outliers final: 28 residues processed: 172 average time/residue: 0.7256 time to fit residues: 142.4921 Evaluate side-chains 183 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 0.0570 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 467 GLN C 52 GLN C 178 GLN C 467 GLN D 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12416 Z= 0.193 Angle : 0.586 9.859 16840 Z= 0.277 Chirality : 0.037 0.158 2016 Planarity : 0.003 0.026 2016 Dihedral : 4.117 29.071 1666 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.51 % Allowed : 27.65 % Favored : 69.84 % 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: 2.42 (0.23), residues: 1500 helix: 2.34 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.58 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 187 HIS 0.003 0.000 HIS D 407 PHE 0.029 0.001 PHE A 50 TYR 0.008 0.001 TYR B 188 ARG 0.003 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 1.437 Fit side-chains REVERT: C 191 ASP cc_start: 0.7950 (p0) cc_final: 0.7707 (p0) REVERT: C 355 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7191 (mp) REVERT: C 371 PHE cc_start: 0.7514 (t80) cc_final: 0.7224 (t80) REVERT: D 191 ASP cc_start: 0.8085 (p0) cc_final: 0.7829 (p0) REVERT: D 355 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7351 (mp) REVERT: D 371 PHE cc_start: 0.7684 (t80) cc_final: 0.7473 (t80) outliers start: 34 outliers final: 30 residues processed: 181 average time/residue: 0.7348 time to fit residues: 152.3926 Evaluate side-chains 191 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 120 optimal weight: 0.0060 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 178 GLN B 467 GLN C 52 GLN C 178 GLN C 467 GLN D 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12416 Z= 0.176 Angle : 0.591 9.970 16840 Z= 0.276 Chirality : 0.037 0.162 2016 Planarity : 0.003 0.026 2016 Dihedral : 4.079 27.993 1666 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.36 % Allowed : 28.24 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.23), residues: 1500 helix: 2.42 (0.15), residues: 1196 sheet: None (None), residues: 0 loop : -1.56 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 187 HIS 0.002 0.000 HIS D 407 PHE 0.030 0.001 PHE A 50 TYR 0.007 0.001 TYR B 188 ARG 0.003 0.000 ARG D 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 1.413 Fit side-chains REVERT: C 191 ASP cc_start: 0.7871 (p0) cc_final: 0.7639 (p0) REVERT: C 355 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7193 (mp) REVERT: C 371 PHE cc_start: 0.7468 (t80) cc_final: 0.7192 (t80) REVERT: C 377 MET cc_start: 0.7322 (mtm) cc_final: 0.6895 (mtt) REVERT: D 191 ASP cc_start: 0.8065 (p0) cc_final: 0.7848 (p0) REVERT: D 355 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7355 (mp) outliers start: 32 outliers final: 27 residues processed: 182 average time/residue: 0.7111 time to fit residues: 148.3377 Evaluate side-chains 187 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 0.0000 chunk 50 optimal weight: 0.7980 chunk 124 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 6 optimal weight: 0.0010 overall best weight: 0.2708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 178 GLN B 467 GLN C 52 GLN C 178 GLN C 467 GLN D 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.153292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122285 restraints weight = 17548.041| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.27 r_work: 0.3427 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12416 Z= 0.148 Angle : 0.580 10.103 16840 Z= 0.271 Chirality : 0.036 0.174 2016 Planarity : 0.003 0.026 2016 Dihedral : 4.012 26.102 1666 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.84 % Allowed : 29.13 % Favored : 69.03 % 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: 2.65 (0.23), residues: 1500 helix: 2.52 (0.15), residues: 1196 sheet: None (None), residues: 0 loop : -1.57 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 187 HIS 0.001 0.000 HIS D 407 PHE 0.030 0.001 PHE D 50 TYR 0.006 0.001 TYR C 204 ARG 0.003 0.000 ARG D 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3519.20 seconds wall clock time: 63 minutes 39.26 seconds (3819.26 seconds total)