Starting phenix.real_space_refine on Sun Feb 18 20:24:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef8_9046/02_2024/6ef8_9046_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef8_9046/02_2024/6ef8_9046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef8_9046/02_2024/6ef8_9046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef8_9046/02_2024/6ef8_9046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef8_9046/02_2024/6ef8_9046_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef8_9046/02_2024/6ef8_9046_neut_updated.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.101 sd= 0.576 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 Fe 42 7.16 5 S 140 5.16 5 C 14385 2.51 5 N 3927 2.21 5 O 4417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22911 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3015 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 388} Chain: "B" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3015 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 388} Chain: "C" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3015 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 388} Chain: "D" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3015 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 388} Chain: "E" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3015 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 388} Chain: "F" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3015 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 388} Chain: "G" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3015 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 388} Chain: "A" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {'HEC': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {'HEC': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {'HEC': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {'HEC': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {'HEC': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {'HEC': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {'HEC': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 11.08, per 1000 atoms: 0.48 Number of scatterers: 22911 At special positions: 0 Unit cell: (85.05, 84, 358.05, 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) Fe 42 26.01 S 140 16.00 O 4417 8.00 N 3927 7.00 C 14385 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=119, symmetry=0 Number of additional bonds: simple=119, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.78 Conformation dependent library (CDL) restraints added in 3.8 seconds 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 14 sheets defined 13.5% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 9 through 12 No H-bonds generated for 'chain 'A' and resid 9 through 12' Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 45 through 48 No H-bonds generated for 'chain 'A' and resid 45 through 48' Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 267 through 275 Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 377 through 383 Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'B' and resid 9 through 12 No H-bonds generated for 'chain 'B' and resid 9 through 12' Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 45 through 48 No H-bonds generated for 'chain 'B' and resid 45 through 48' Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 267 through 275 Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'C' and resid 9 through 12 No H-bonds generated for 'chain 'C' and resid 9 through 12' Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 45 through 48 No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 235 through 239 Processing helix chain 'C' and resid 267 through 275 Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' Processing helix chain 'C' and resid 303 through 308 Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 377 through 383 Processing helix chain 'C' and resid 399 through 401 No H-bonds generated for 'chain 'C' and resid 399 through 401' Processing helix chain 'D' and resid 9 through 12 No H-bonds generated for 'chain 'D' and resid 9 through 12' Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 45 through 48 No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 303 through 308 Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'D' and resid 399 through 401 No H-bonds generated for 'chain 'D' and resid 399 through 401' Processing helix chain 'E' and resid 9 through 12 No H-bonds generated for 'chain 'E' and resid 9 through 12' Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 45 through 48 No H-bonds generated for 'chain 'E' and resid 45 through 48' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 235 through 239 Processing helix chain 'E' and resid 267 through 275 Processing helix chain 'E' and resid 292 through 294 No H-bonds generated for 'chain 'E' and resid 292 through 294' Processing helix chain 'E' and resid 303 through 308 Processing helix chain 'E' and resid 314 through 316 No H-bonds generated for 'chain 'E' and resid 314 through 316' Processing helix chain 'E' and resid 377 through 383 Processing helix chain 'E' and resid 399 through 401 No H-bonds generated for 'chain 'E' and resid 399 through 401' Processing helix chain 'F' and resid 9 through 12 No H-bonds generated for 'chain 'F' and resid 9 through 12' Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 45 through 48 No H-bonds generated for 'chain 'F' and resid 45 through 48' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 235 through 239 Processing helix chain 'F' and resid 267 through 275 Processing helix chain 'F' and resid 292 through 294 No H-bonds generated for 'chain 'F' and resid 292 through 294' Processing helix chain 'F' and resid 303 through 308 Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 377 through 383 Processing helix chain 'F' and resid 399 through 401 No H-bonds generated for 'chain 'F' and resid 399 through 401' Processing helix chain 'G' and resid 9 through 12 No H-bonds generated for 'chain 'G' and resid 9 through 12' Processing helix chain 'G' and resid 35 through 37 No H-bonds generated for 'chain 'G' and resid 35 through 37' Processing helix chain 'G' and resid 45 through 48 No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'G' and resid 140 through 142 No H-bonds generated for 'chain 'G' and resid 140 through 142' Processing helix chain 'G' and resid 235 through 239 Processing helix chain 'G' and resid 267 through 275 Processing helix chain 'G' and resid 292 through 294 No H-bonds generated for 'chain 'G' and resid 292 through 294' Processing helix chain 'G' and resid 303 through 308 Processing helix chain 'G' and resid 314 through 316 No H-bonds generated for 'chain 'G' and resid 314 through 316' Processing helix chain 'G' and resid 377 through 383 Processing helix chain 'G' and resid 399 through 401 No H-bonds generated for 'chain 'G' and resid 399 through 401' Processing sheet with id= A, first strand: chain 'A' and resid 93 through 95 removed outlier: 3.578A pdb=" N TRP A 95 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.930A pdb=" N ASN A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 93 through 95 removed outlier: 3.577A pdb=" N TRP B 95 " --> pdb=" O ASN B 101 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.931A pdb=" N ASN B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 93 through 95 removed outlier: 3.577A pdb=" N TRP C 95 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.931A pdb=" N ASN C 360 " --> pdb=" O ASP C 356 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 93 through 95 removed outlier: 3.578A pdb=" N TRP D 95 " --> pdb=" O ASN D 101 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 354 through 356 removed outlier: 3.931A pdb=" N ASN D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 93 through 95 removed outlier: 3.577A pdb=" N TRP E 95 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 354 through 356 removed outlier: 3.932A pdb=" N ASN E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 93 through 95 removed outlier: 3.578A pdb=" N TRP F 95 " --> pdb=" O ASN F 101 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 354 through 356 removed outlier: 3.931A pdb=" N ASN F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 93 through 95 removed outlier: 3.577A pdb=" N TRP G 95 " --> pdb=" O ASN G 101 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 354 through 356 removed outlier: 3.931A pdb=" N ASN G 360 " --> pdb=" O ASP G 356 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 9.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 10137 1.39 - 1.56: 13226 1.56 - 1.73: 3 1.73 - 1.90: 196 1.90 - 2.06: 168 Bond restraints: 23730 Sorted by residual: bond pdb=" CB CYS G 140 " pdb=" SG CYS G 140 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.82e+00 bond pdb=" CB CYS E 140 " pdb=" SG CYS E 140 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.81e+00 bond pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.81e+00 bond pdb=" CB CYS C 140 " pdb=" SG CYS C 140 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.80e+00 bond pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.75e+00 ... (remaining 23725 not shown) Histogram of bond angle deviations from ideal: 81.50 - 101.09: 210 101.09 - 120.68: 22429 120.68 - 140.27: 10170 140.27 - 159.86: 0 159.86 - 179.45: 84 Bond angle restraints: 32893 Sorted by residual: angle pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" C ILE A 188 " ideal model delta sigma weight residual 109.34 120.83 -11.49 2.08e+00 2.31e-01 3.05e+01 angle pdb=" N ILE D 188 " pdb=" CA ILE D 188 " pdb=" C ILE D 188 " ideal model delta sigma weight residual 109.34 120.83 -11.49 2.08e+00 2.31e-01 3.05e+01 angle pdb=" N ILE E 188 " pdb=" CA ILE E 188 " pdb=" C ILE E 188 " ideal model delta sigma weight residual 109.34 120.82 -11.48 2.08e+00 2.31e-01 3.05e+01 angle pdb=" N ILE G 188 " pdb=" CA ILE G 188 " pdb=" C ILE G 188 " ideal model delta sigma weight residual 109.34 120.82 -11.48 2.08e+00 2.31e-01 3.05e+01 angle pdb=" N ILE C 188 " pdb=" CA ILE C 188 " pdb=" C ILE C 188 " ideal model delta sigma weight residual 109.34 120.82 -11.48 2.08e+00 2.31e-01 3.04e+01 ... (remaining 32888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 12120 17.44 - 34.88: 529 34.88 - 52.32: 84 52.32 - 69.76: 42 69.76 - 87.20: 98 Dihedral angle restraints: 12873 sinusoidal: 4809 harmonic: 8064 Sorted by residual: dihedral pdb=" CA ASN E 327 " pdb=" C ASN E 327 " pdb=" N CYS E 328 " pdb=" CA CYS E 328 " ideal model delta harmonic sigma weight residual 180.00 132.00 48.00 0 5.00e+00 4.00e-02 9.22e+01 dihedral pdb=" CA ASN D 327 " pdb=" C ASN D 327 " pdb=" N CYS D 328 " pdb=" CA CYS D 328 " ideal model delta harmonic sigma weight residual 180.00 132.01 47.99 0 5.00e+00 4.00e-02 9.21e+01 dihedral pdb=" CA ASN C 327 " pdb=" C ASN C 327 " pdb=" N CYS C 328 " pdb=" CA CYS C 328 " ideal model delta harmonic sigma weight residual 180.00 132.02 47.98 0 5.00e+00 4.00e-02 9.21e+01 ... (remaining 12870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1917 0.046 - 0.092: 890 0.092 - 0.138: 266 0.138 - 0.184: 63 0.184 - 0.229: 21 Chirality restraints: 3157 Sorted by residual: chirality pdb=" CB VAL E 6 " pdb=" CA VAL E 6 " pdb=" CG1 VAL E 6 " pdb=" CG2 VAL E 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL C 6 " pdb=" CA VAL C 6 " pdb=" CG1 VAL C 6 " pdb=" CG2 VAL C 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL F 6 " pdb=" CA VAL F 6 " pdb=" CG1 VAL F 6 " pdb=" CG2 VAL F 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3154 not shown) Planarity restraints: 4179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 504 " -0.011 2.00e-02 2.50e+03 5.68e-02 7.25e+01 pdb=" C2C HEC C 504 " 0.153 2.00e-02 2.50e+03 pdb=" C3C HEC C 504 " -0.037 2.00e-02 2.50e+03 pdb=" C4C HEC C 504 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC C 504 " -0.013 2.00e-02 2.50e+03 pdb=" CHC HEC C 504 " -0.020 2.00e-02 2.50e+03 pdb=" CHD HEC C 504 " -0.001 2.00e-02 2.50e+03 pdb=" CMC HEC C 504 " -0.057 2.00e-02 2.50e+03 pdb=" NC HEC C 504 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 504 " 0.011 2.00e-02 2.50e+03 5.68e-02 7.25e+01 pdb=" C2C HEC D 504 " -0.153 2.00e-02 2.50e+03 pdb=" C3C HEC D 504 " 0.037 2.00e-02 2.50e+03 pdb=" C4C HEC D 504 " 0.006 2.00e-02 2.50e+03 pdb=" CAC HEC D 504 " 0.013 2.00e-02 2.50e+03 pdb=" CHC HEC D 504 " 0.020 2.00e-02 2.50e+03 pdb=" CHD HEC D 504 " 0.001 2.00e-02 2.50e+03 pdb=" CMC HEC D 504 " 0.057 2.00e-02 2.50e+03 pdb=" NC HEC D 504 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 504 " -0.011 2.00e-02 2.50e+03 5.68e-02 7.25e+01 pdb=" C2C HEC A 504 " 0.153 2.00e-02 2.50e+03 pdb=" C3C HEC A 504 " -0.037 2.00e-02 2.50e+03 pdb=" C4C HEC A 504 " -0.006 2.00e-02 2.50e+03 pdb=" CAC HEC A 504 " -0.013 2.00e-02 2.50e+03 pdb=" CHC HEC A 504 " -0.020 2.00e-02 2.50e+03 pdb=" CHD HEC A 504 " -0.001 2.00e-02 2.50e+03 pdb=" CMC HEC A 504 " -0.057 2.00e-02 2.50e+03 pdb=" NC HEC A 504 " -0.007 2.00e-02 2.50e+03 ... (remaining 4176 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 332 2.60 - 3.17: 19594 3.17 - 3.75: 38120 3.75 - 4.32: 56691 4.32 - 4.90: 89050 Nonbonded interactions: 203787 Sorted by model distance: nonbonded pdb=" NE2 HIS A 332 " pdb="FE HEC A 501 " model vdw 2.023 3.080 nonbonded pdb=" NE2 HIS D 335 " pdb="FE HEC D 504 " model vdw 2.044 3.080 nonbonded pdb=" NE2 HIS E 335 " pdb="FE HEC E 504 " model vdw 2.044 3.080 nonbonded pdb=" NE2 HIS G 335 " pdb="FE HEC G 504 " model vdw 2.044 3.080 nonbonded pdb=" NE2 HIS C 335 " pdb="FE HEC C 504 " model vdw 2.044 3.080 ... (remaining 203782 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' selection = chain 'F' selection = chain 'G' } 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.270 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 53.950 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.150 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 : 0.007 0.064 23730 Z= 0.424 Angle : 1.377 12.428 32893 Z= 0.631 Chirality : 0.059 0.229 3157 Planarity : 0.009 0.071 4179 Dihedral : 14.341 87.197 7805 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.36 % Favored : 88.15 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.22 % 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: -4.03 (0.12), residues: 2835 helix: -3.87 (0.14), residues: 294 sheet: None (None), residues: 0 loop : -2.84 (0.10), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP D 238 HIS 0.009 0.003 HIS D 335 PHE 0.021 0.003 PHE B 345 TYR 0.018 0.002 TYR B 150 ARG 0.008 0.001 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 2.683 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ASP cc_start: 0.7961 (m-30) cc_final: 0.7589 (t0) REVERT: C 107 ARG cc_start: 0.8402 (mmp80) cc_final: 0.7649 (mmp80) REVERT: C 111 ASN cc_start: 0.8048 (m-40) cc_final: 0.7843 (m-40) REVERT: D 221 THR cc_start: 0.8498 (t) cc_final: 0.8192 (p) REVERT: D 377 VAL cc_start: 0.9263 (m) cc_final: 0.9060 (t) REVERT: E 235 MET cc_start: 0.8587 (tpt) cc_final: 0.8223 (tpt) REVERT: E 274 ASN cc_start: 0.8392 (m-40) cc_final: 0.8187 (m-40) REVERT: F 10 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8039 (mm-30) REVERT: F 107 ARG cc_start: 0.8468 (mmp80) cc_final: 0.7964 (mmp80) REVERT: F 235 MET cc_start: 0.8427 (tpt) cc_final: 0.8079 (tpt) REVERT: G 10 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8030 (mm-30) REVERT: G 111 ASN cc_start: 0.8372 (m-40) cc_final: 0.8085 (m-40) REVERT: G 377 VAL cc_start: 0.9260 (m) cc_final: 0.9043 (t) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.3339 time to fit residues: 207.0631 Evaluate side-chains 182 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 254 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 63 HIS A 111 ASN A 139 HIS ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN A 404 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 63 HIS B 111 ASN B 139 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS C 52 GLN C 63 HIS C 111 ASN C 139 HIS ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS D 51 HIS D 52 GLN D 63 HIS D 111 ASN D 139 HIS ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS E 52 GLN E 63 HIS E 111 ASN E 139 HIS ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 HIS F 52 GLN F 63 HIS F 111 ASN F 139 HIS ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 HIS G 52 GLN G 63 HIS G 111 ASN G 139 HIS ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 404 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 23730 Z= 0.398 Angle : 0.966 21.991 32893 Z= 0.395 Chirality : 0.047 0.162 3157 Planarity : 0.005 0.072 4179 Dihedral : 15.434 88.866 3430 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.70 % Favored : 87.02 % Rotamer: Outliers : 2.66 % Allowed : 9.25 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.14), residues: 2835 helix: -2.93 (0.18), residues: 378 sheet: None (None), residues: 0 loop : -2.31 (0.12), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP G 238 HIS 0.013 0.002 HIS F 332 PHE 0.020 0.003 PHE E 31 TYR 0.019 0.002 TYR C 150 ARG 0.003 0.001 ARG E 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 181 time to evaluate : 2.328 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8577 (mmp80) cc_final: 0.8297 (mmp80) REVERT: A 278 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8220 (mtmm) REVERT: A 340 ASP cc_start: 0.7889 (m-30) cc_final: 0.7645 (t0) REVERT: B 118 ASN cc_start: 0.8474 (m-40) cc_final: 0.7931 (p0) REVERT: C 118 ASN cc_start: 0.8351 (m-40) cc_final: 0.8005 (p0) REVERT: C 165 ILE cc_start: 0.8823 (mt) cc_final: 0.8573 (mt) REVERT: C 380 MET cc_start: 0.9008 (tpp) cc_final: 0.8632 (tpp) REVERT: D 340 ASP cc_start: 0.8247 (t0) cc_final: 0.8003 (t0) REVERT: F 107 ARG cc_start: 0.8655 (mmp80) cc_final: 0.8306 (mmp80) REVERT: F 297 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: G 15 MET cc_start: 0.7362 (mmm) cc_final: 0.6856 (mmt) REVERT: G 342 MET cc_start: 0.8204 (ttp) cc_final: 0.7929 (ttp) outliers start: 58 outliers final: 34 residues processed: 219 average time/residue: 0.2926 time to fit residues: 107.3386 Evaluate side-chains 175 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 351 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 chunk 211 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 254 optimal weight: 8.9990 chunk 275 optimal weight: 30.0000 chunk 226 optimal weight: 20.0000 chunk 252 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 373 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 ASN ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 23730 Z= 0.289 Angle : 0.836 19.508 32893 Z= 0.342 Chirality : 0.044 0.165 3157 Planarity : 0.005 0.047 4179 Dihedral : 15.130 89.784 3430 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.50 % Favored : 88.01 % Rotamer: Outliers : 3.16 % Allowed : 11.72 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -2.83 (0.15), residues: 2835 helix: -1.89 (0.24), residues: 378 sheet: None (None), residues: 0 loop : -2.10 (0.12), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 238 HIS 0.008 0.001 HIS F 332 PHE 0.015 0.002 PHE A 351 TYR 0.015 0.001 TYR C 150 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 175 time to evaluate : 2.328 Fit side-chains REVERT: A 342 MET cc_start: 0.8739 (tpp) cc_final: 0.8269 (ttm) REVERT: B 354 ILE cc_start: 0.9069 (mm) cc_final: 0.8787 (mt) REVERT: C 71 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6621 (ptp) REVERT: C 165 ILE cc_start: 0.8770 (mt) cc_final: 0.8551 (mt) REVERT: C 342 MET cc_start: 0.8176 (ttp) cc_final: 0.7966 (ttp) REVERT: C 380 MET cc_start: 0.8981 (tpp) cc_final: 0.8682 (tpp) REVERT: D 340 ASP cc_start: 0.8398 (t0) cc_final: 0.8024 (t0) REVERT: G 15 MET cc_start: 0.7132 (mmm) cc_final: 0.6592 (mmt) REVERT: G 342 MET cc_start: 0.8104 (ttp) cc_final: 0.7847 (ttp) REVERT: G 396 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7682 (tp40) outliers start: 69 outliers final: 40 residues processed: 213 average time/residue: 0.2732 time to fit residues: 100.7538 Evaluate side-chains 188 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 146 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 396 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 8.9990 chunk 191 optimal weight: 40.0000 chunk 132 optimal weight: 0.0050 chunk 28 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 255 optimal weight: 9.9990 chunk 270 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 23730 Z= 0.278 Angle : 0.818 18.930 32893 Z= 0.329 Chirality : 0.043 0.165 3157 Planarity : 0.004 0.047 4179 Dihedral : 14.931 89.331 3430 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.20 % Favored : 87.55 % Rotamer: Outliers : 3.98 % Allowed : 12.36 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -2.53 (0.16), residues: 2835 helix: -1.36 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -1.93 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 238 HIS 0.007 0.001 HIS A 332 PHE 0.013 0.002 PHE A 351 TYR 0.014 0.001 TYR C 150 ARG 0.004 0.000 ARG F 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 171 time to evaluate : 2.309 Fit side-chains revert: symmetry clash REVERT: B 118 ASN cc_start: 0.8310 (m-40) cc_final: 0.8043 (p0) REVERT: B 247 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8164 (p-80) REVERT: B 354 ILE cc_start: 0.9029 (mm) cc_final: 0.8766 (mt) REVERT: C 71 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6703 (ptp) REVERT: C 380 MET cc_start: 0.8977 (tpp) cc_final: 0.8731 (tpp) REVERT: D 85 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: D 340 ASP cc_start: 0.8499 (t0) cc_final: 0.8110 (t0) REVERT: G 189 LEU cc_start: 0.8792 (mt) cc_final: 0.8582 (mt) REVERT: G 342 MET cc_start: 0.8119 (ttp) cc_final: 0.7877 (ttp) REVERT: G 396 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7727 (tp40) outliers start: 87 outliers final: 57 residues processed: 229 average time/residue: 0.2634 time to fit residues: 106.7264 Evaluate side-chains 214 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 153 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 403 CYS Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 396 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 111 optimal weight: 30.0000 chunk 230 optimal weight: 20.0000 chunk 187 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 242 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 23730 Z= 0.370 Angle : 0.909 21.927 32893 Z= 0.356 Chirality : 0.045 0.171 3157 Planarity : 0.004 0.043 4179 Dihedral : 15.246 89.768 3430 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.09 % Favored : 86.42 % Rotamer: Outliers : 5.13 % Allowed : 12.04 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -2.46 (0.16), residues: 2835 helix: -1.31 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.88 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 95 HIS 0.009 0.002 HIS A 332 PHE 0.020 0.002 PHE F 86 TYR 0.016 0.001 TYR C 150 ARG 0.003 0.000 ARG F 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 148 time to evaluate : 2.217 Fit side-chains revert: symmetry clash REVERT: A 342 MET cc_start: 0.8890 (tpp) cc_final: 0.8679 (tpp) REVERT: B 15 MET cc_start: 0.8119 (tpp) cc_final: 0.7871 (tpp) REVERT: B 118 ASN cc_start: 0.8363 (m-40) cc_final: 0.7996 (p0) REVERT: B 247 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.8042 (p-80) REVERT: C 71 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6727 (ptp) REVERT: C 85 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: C 138 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7140 (tt) REVERT: C 380 MET cc_start: 0.8993 (tpp) cc_final: 0.8707 (tpp) REVERT: D 85 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: D 138 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7017 (tt) REVERT: D 340 ASP cc_start: 0.8601 (t0) cc_final: 0.8213 (t0) REVERT: E 138 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7270 (tp) REVERT: F 118 ASN cc_start: 0.8237 (m-40) cc_final: 0.7858 (p0) REVERT: F 235 MET cc_start: 0.7782 (tpt) cc_final: 0.7355 (tpt) REVERT: F 340 ASP cc_start: 0.8652 (t0) cc_final: 0.8425 (t0) REVERT: G 138 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7244 (tp) REVERT: G 342 MET cc_start: 0.8311 (ttp) cc_final: 0.8105 (ttp) REVERT: G 396 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7878 (tp40) outliers start: 112 outliers final: 79 residues processed: 231 average time/residue: 0.2724 time to fit residues: 109.9944 Evaluate side-chains 228 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 140 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 247 HIS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 247 HIS Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 403 CYS Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 396 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 270 optimal weight: 0.0970 chunk 224 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 overall best weight: 7.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 23730 Z= 0.392 Angle : 0.927 22.010 32893 Z= 0.363 Chirality : 0.046 0.182 3157 Planarity : 0.004 0.044 4179 Dihedral : 15.367 89.931 3430 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.54 % Favored : 86.21 % Rotamer: Outliers : 5.27 % Allowed : 12.32 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -2.45 (0.16), residues: 2835 helix: -1.35 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.86 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 238 HIS 0.008 0.002 HIS A 332 PHE 0.020 0.002 PHE F 86 TYR 0.017 0.001 TYR C 150 ARG 0.003 0.000 ARG F 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 149 time to evaluate : 2.480 Fit side-chains revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8287 (m110) cc_final: 0.8066 (m-40) REVERT: B 15 MET cc_start: 0.8206 (tpp) cc_final: 0.7941 (tpp) REVERT: B 118 ASN cc_start: 0.8401 (m-40) cc_final: 0.7992 (p0) REVERT: B 247 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.7953 (p-80) REVERT: C 71 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6662 (ptp) REVERT: C 85 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: C 138 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7191 (tt) REVERT: C 380 MET cc_start: 0.8989 (tpp) cc_final: 0.8722 (tpp) REVERT: D 85 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: D 138 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6896 (tt) REVERT: D 340 ASP cc_start: 0.8653 (t0) cc_final: 0.8295 (t0) REVERT: E 138 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7261 (tp) REVERT: F 118 ASN cc_start: 0.8394 (m-40) cc_final: 0.7972 (p0) REVERT: G 138 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7299 (tp) REVERT: G 396 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7876 (tp40) outliers start: 115 outliers final: 86 residues processed: 234 average time/residue: 0.2682 time to fit residues: 109.7460 Evaluate side-chains 239 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 144 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 247 HIS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 247 HIS Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 396 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 154 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 228 optimal weight: 30.0000 chunk 151 optimal weight: 30.0000 chunk 269 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 HIS ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23730 Z= 0.218 Angle : 0.758 16.347 32893 Z= 0.310 Chirality : 0.042 0.168 3157 Planarity : 0.004 0.045 4179 Dihedral : 14.884 89.850 3430 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.04 % Favored : 88.71 % Rotamer: Outliers : 4.08 % Allowed : 13.92 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -2.30 (0.16), residues: 2835 helix: -1.08 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -1.78 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 95 HIS 0.005 0.001 HIS A 332 PHE 0.011 0.001 PHE A 351 TYR 0.011 0.001 TYR F 150 ARG 0.003 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 186 time to evaluate : 2.450 Fit side-chains revert: symmetry clash REVERT: A 342 MET cc_start: 0.8934 (tpp) cc_final: 0.8384 (ttm) REVERT: B 247 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.8187 (p-80) REVERT: B 354 ILE cc_start: 0.9086 (mm) cc_final: 0.8849 (mt) REVERT: C 85 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: C 138 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7199 (tp) REVERT: C 380 MET cc_start: 0.8990 (tpp) cc_final: 0.8784 (tpp) REVERT: D 85 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7444 (m-30) REVERT: D 138 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7081 (tt) REVERT: D 340 ASP cc_start: 0.8492 (t0) cc_final: 0.8195 (t0) REVERT: E 138 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7214 (tp) REVERT: E 340 ASP cc_start: 0.8336 (t0) cc_final: 0.8105 (t0) REVERT: F 118 ASN cc_start: 0.8216 (m-40) cc_final: 0.7917 (p0) REVERT: F 340 ASP cc_start: 0.8446 (t0) cc_final: 0.8230 (t0) REVERT: G 149 LYS cc_start: 0.7951 (mttt) cc_final: 0.7428 (mmtt) REVERT: G 297 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7394 (tt0) outliers start: 89 outliers final: 59 residues processed: 246 average time/residue: 0.2621 time to fit residues: 112.9791 Evaluate side-chains 229 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 164 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 403 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 133 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 212 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 23730 Z= 0.364 Angle : 0.902 21.158 32893 Z= 0.351 Chirality : 0.045 0.174 3157 Planarity : 0.004 0.047 4179 Dihedral : 15.164 89.777 3430 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.69 % Favored : 86.07 % Rotamer: Outliers : 4.58 % Allowed : 13.60 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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 (0.16), residues: 2835 helix: -1.19 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.80 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 238 HIS 0.007 0.002 HIS A 332 PHE 0.016 0.002 PHE E 86 TYR 0.016 0.001 TYR B 150 ARG 0.003 0.000 ARG F 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 149 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.9016 (tpp) cc_final: 0.8355 (ttm) REVERT: B 247 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.8007 (p-80) REVERT: C 71 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6696 (ptp) REVERT: C 85 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: C 138 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7161 (tt) REVERT: C 380 MET cc_start: 0.8992 (tpp) cc_final: 0.8750 (tpp) REVERT: D 85 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: D 138 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6988 (tt) REVERT: D 340 ASP cc_start: 0.8644 (t0) cc_final: 0.8301 (t0) REVERT: E 138 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7248 (tp) REVERT: F 118 ASN cc_start: 0.8359 (m-40) cc_final: 0.7979 (p0) REVERT: F 340 ASP cc_start: 0.8671 (t0) cc_final: 0.8457 (t0) REVERT: G 138 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7329 (tp) outliers start: 100 outliers final: 73 residues processed: 221 average time/residue: 0.2686 time to fit residues: 103.4362 Evaluate side-chains 225 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 144 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 390 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 9.9990 chunk 258 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 250 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 23730 Z= 0.353 Angle : 0.894 20.965 32893 Z= 0.350 Chirality : 0.045 0.174 3157 Planarity : 0.004 0.046 4179 Dihedral : 15.207 89.481 3430 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.87 % Favored : 86.88 % Rotamer: Outliers : 4.30 % Allowed : 13.97 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -2.37 (0.16), residues: 2835 helix: -1.25 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.81 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 238 HIS 0.007 0.001 HIS A 332 PHE 0.018 0.002 PHE E 86 TYR 0.016 0.001 TYR C 150 ARG 0.002 0.000 ARG F 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 147 time to evaluate : 2.606 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.8134 (mmm) cc_final: 0.7733 (mmm) REVERT: A 342 MET cc_start: 0.9007 (tpp) cc_final: 0.8345 (ttm) REVERT: B 247 HIS cc_start: 0.8840 (OUTLIER) cc_final: 0.8000 (p-80) REVERT: C 71 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.6678 (ptp) REVERT: C 85 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: C 138 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7192 (tt) REVERT: C 380 MET cc_start: 0.8994 (tpp) cc_final: 0.8756 (tpp) REVERT: D 85 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7699 (m-30) REVERT: D 138 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6973 (tt) REVERT: D 340 ASP cc_start: 0.8611 (t0) cc_final: 0.8305 (t0) REVERT: E 138 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7236 (tp) REVERT: F 118 ASN cc_start: 0.8368 (m-40) cc_final: 0.7997 (p0) REVERT: G 138 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7390 (tp) outliers start: 94 outliers final: 81 residues processed: 213 average time/residue: 0.2557 time to fit residues: 96.0553 Evaluate side-chains 233 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 144 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 247 HIS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 247 HIS Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 390 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 278 optimal weight: 20.0000 chunk 256 optimal weight: 0.9980 chunk 222 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 23730 Z= 0.317 Angle : 0.858 20.036 32893 Z= 0.339 Chirality : 0.044 0.173 3157 Planarity : 0.004 0.048 4179 Dihedral : 15.087 89.610 3430 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.05 % Favored : 86.70 % Rotamer: Outliers : 4.44 % Allowed : 14.01 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 (0.16), residues: 2835 helix: -1.22 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.80 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 238 HIS 0.006 0.001 HIS A 332 PHE 0.014 0.002 PHE E 86 TYR 0.014 0.001 TYR C 150 ARG 0.002 0.000 ARG F 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 154 time to evaluate : 2.365 Fit side-chains revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: A 342 MET cc_start: 0.8974 (tpp) cc_final: 0.8334 (ttm) REVERT: B 247 HIS cc_start: 0.8783 (OUTLIER) cc_final: 0.8009 (p-80) REVERT: C 71 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6636 (ptp) REVERT: C 85 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: C 138 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7181 (tt) REVERT: C 380 MET cc_start: 0.8998 (tpp) cc_final: 0.8769 (tpp) REVERT: D 85 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: D 138 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7012 (tt) REVERT: D 340 ASP cc_start: 0.8560 (t0) cc_final: 0.8303 (t0) REVERT: E 138 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7217 (tp) REVERT: F 118 ASN cc_start: 0.8379 (m-40) cc_final: 0.8024 (p0) REVERT: G 138 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7387 (tp) REVERT: G 297 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7327 (tt0) outliers start: 97 outliers final: 84 residues processed: 224 average time/residue: 0.2567 time to fit residues: 100.6510 Evaluate side-chains 246 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 153 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 403 CYS Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 247 HIS Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 390 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 68 optimal weight: 30.0000 chunk 204 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 222 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 228 optimal weight: 30.0000 chunk 28 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 overall best weight: 10.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS E 63 HIS ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 HIS F 63 HIS ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 373 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.071952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.065392 restraints weight = 52860.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.067497 restraints weight = 22297.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.068784 restraints weight = 11849.937| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.112 23730 Z= 0.538 Angle : 1.048 23.608 32893 Z= 0.412 Chirality : 0.049 0.184 3157 Planarity : 0.005 0.055 4179 Dihedral : 15.565 89.913 3430 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.39 % Allowed : 14.71 % Favored : 84.90 % Rotamer: Outliers : 4.40 % Allowed : 14.06 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -2.62 (0.15), residues: 2835 helix: -1.57 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -1.97 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP G 238 HIS 0.009 0.002 HIS D 147 PHE 0.027 0.003 PHE F 86 TYR 0.020 0.002 TYR C 150 ARG 0.004 0.001 ARG F 107 =============================================================================== Job complete usr+sys time: 3298.60 seconds wall clock time: 62 minutes 59.90 seconds (3779.90 seconds total)