Starting phenix.real_space_refine on Wed Feb 14 16:38:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/02_2024/7wk0_32554.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/02_2024/7wk0_32554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/02_2024/7wk0_32554.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/02_2024/7wk0_32554.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/02_2024/7wk0_32554.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/02_2024/7wk0_32554.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 6154 2.51 5 N 1646 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 408": "NH1" <-> "NH2" Residue "F ARG 454": "NH1" <-> "NH2" Residue "F ARG 457": "NH1" <-> "NH2" Residue "F ARG 466": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9724 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1699 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "B" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "C" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1572 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1699 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "E" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "F" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1572 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.32, per 1000 atoms: 0.55 Number of scatterers: 9724 At special positions: 0 Unit cell: (88.312, 155.344, 110.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1890 8.00 N 1646 7.00 C 6154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " " NAG F 601 " - " ASN F 343 " Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 25 sheets defined 2.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.131A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.804A pdb=" N GLU B 126 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.567A pdb=" N ASP E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 82' Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.798A pdb=" N GLN F 506 " --> pdb=" O VAL F 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 60 removed outlier: 5.936A pdb=" N GLY A 50 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR A 60 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 48 " --> pdb=" O TYR A 60 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 92 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 94 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 120 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.873A pdb=" N GLY A 152 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.507A pdb=" N THR A 164 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS A 209 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS A 222 " --> pdb=" O CYS A 209 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 220 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS A 213 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 218 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.868A pdb=" N VAL B 10 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.747A pdb=" N ILE B 74 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 20 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 117 through 120 removed outlier: 3.503A pdb=" N ILE B 138 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 176 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 140 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR B 174 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.752A pdb=" N THR B 147 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS B 195 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 206 " --> pdb=" O CYS B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.726A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.726A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.534A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.628A pdb=" N TYR D 94 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL D 48 " --> pdb=" O TYR D 60 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR D 60 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY D 50 " --> pdb=" O ILE D 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.533A pdb=" N LEU D 151 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 193 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER D 192 " --> pdb=" O PHE D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 Processing sheet with id=AB8, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.887A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'E' and resid 44 through 47 removed outlier: 5.626A pdb=" N LEU E 45 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN E 36 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E 47 " --> pdb=" O TRP E 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 117 through 120 removed outlier: 3.899A pdb=" N VAL E 135 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE E 138 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP E 140 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR E 174 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 194 through 196 removed outlier: 3.674A pdb=" N CYS E 195 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS E 206 " --> pdb=" O CYS E 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 357 through 358 removed outlier: 4.190A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA F 435 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 357 through 358 removed outlier: 4.190A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'F' and resid 473 through 474 183 hydrogen bonds defined for protein. 447 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: 2.88 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1593 1.31 - 1.44: 2884 1.44 - 1.56: 5469 1.56 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 9982 Sorted by residual: bond pdb=" CA LYS D 65 " pdb=" C LYS D 65 " ideal model delta sigma weight residual 1.524 1.445 0.079 1.31e-02 5.83e+03 3.62e+01 bond pdb=" N ASN C 448 " pdb=" CA ASN C 448 " ideal model delta sigma weight residual 1.455 1.397 0.059 1.25e-02 6.40e+03 2.19e+01 bond pdb=" N GLU F 406 " pdb=" CA GLU F 406 " ideal model delta sigma weight residual 1.457 1.405 0.052 1.16e-02 7.43e+03 2.02e+01 bond pdb=" C ILE C 358 " pdb=" O ILE C 358 " ideal model delta sigma weight residual 1.237 1.188 0.050 1.13e-02 7.83e+03 1.93e+01 bond pdb=" CA ASN C 354 " pdb=" C ASN C 354 " ideal model delta sigma weight residual 1.523 1.469 0.053 1.23e-02 6.61e+03 1.89e+01 ... (remaining 9977 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.41: 450 107.41 - 114.06: 5473 114.06 - 120.71: 3689 120.71 - 127.36: 3881 127.36 - 134.01: 121 Bond angle restraints: 13614 Sorted by residual: angle pdb=" N ASN C 370 " pdb=" CA ASN C 370 " pdb=" C ASN C 370 " ideal model delta sigma weight residual 114.31 104.48 9.83 1.29e+00 6.01e-01 5.81e+01 angle pdb=" N VAL F 407 " pdb=" CA VAL F 407 " pdb=" C VAL F 407 " ideal model delta sigma weight residual 111.58 104.58 7.00 1.06e+00 8.90e-01 4.36e+01 angle pdb=" N GLY D 66 " pdb=" CA GLY D 66 " pdb=" C GLY D 66 " ideal model delta sigma weight residual 115.27 107.54 7.73 1.41e+00 5.03e-01 3.00e+01 angle pdb=" N ASN C 448 " pdb=" CA ASN C 448 " pdb=" C ASN C 448 " ideal model delta sigma weight residual 109.24 101.13 8.11 1.67e+00 3.59e-01 2.36e+01 angle pdb=" N SER C 359 " pdb=" CA SER C 359 " pdb=" C SER C 359 " ideal model delta sigma weight residual 108.74 114.66 -5.92 1.38e+00 5.25e-01 1.84e+01 ... (remaining 13609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5574 17.71 - 35.42: 306 35.42 - 53.14: 45 53.14 - 70.85: 18 70.85 - 88.56: 1 Dihedral angle restraints: 5944 sinusoidal: 2288 harmonic: 3656 Sorted by residual: dihedral pdb=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N SER B 192 " pdb=" CA SER B 192 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" N ASN C 448 " pdb=" C ASN C 448 " pdb=" CA ASN C 448 " pdb=" CB ASN C 448 " ideal model delta harmonic sigma weight residual 122.80 111.49 11.31 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" CA GLU A 161 " pdb=" C GLU A 161 " pdb=" N PRO A 162 " pdb=" CA PRO A 162 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 5941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1322 0.071 - 0.142: 169 0.142 - 0.212: 4 0.212 - 0.283: 2 0.283 - 0.354: 1 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA LYS D 65 " pdb=" N LYS D 65 " pdb=" C LYS D 65 " pdb=" CB LYS D 65 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA ASN F 448 " pdb=" N ASN F 448 " pdb=" C ASN F 448 " pdb=" CB ASN F 448 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ALA C 372 " pdb=" N ALA C 372 " pdb=" C ALA C 372 " pdb=" CB ALA C 372 " both_signs ideal model delta sigma weight residual False 2.48 2.27 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1495 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 601 " 0.257 2.00e-02 2.50e+03 2.18e-01 5.92e+02 pdb=" C7 NAG F 601 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG F 601 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG F 601 " -0.371 2.00e-02 2.50e+03 pdb=" O7 NAG F 601 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 400 " -0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C PHE C 400 " 0.075 2.00e-02 2.50e+03 pdb=" O PHE C 400 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL C 401 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 353 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C TRP C 353 " -0.058 2.00e-02 2.50e+03 pdb=" O TRP C 353 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN C 354 " 0.020 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1603 2.77 - 3.30: 9290 3.30 - 3.83: 15901 3.83 - 4.37: 18585 4.37 - 4.90: 31950 Nonbonded interactions: 77329 Sorted by model distance: nonbonded pdb=" OG SER E 62 " pdb=" OG1 THR E 73 " model vdw 2.233 2.440 nonbonded pdb=" OG SER B 64 " pdb=" OG1 THR B 71 " model vdw 2.263 2.440 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.272 2.440 nonbonded pdb=" OD2 ASP E 91 " pdb=" OG SER E 94 " model vdw 2.278 2.440 nonbonded pdb=" OE1 GLU E 126 " pdb=" OG1 THR E 133 " model vdw 2.286 2.440 ... (remaining 77324 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 22.150 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.960 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9982 Z= 0.273 Angle : 0.655 9.922 13614 Z= 0.387 Chirality : 0.045 0.354 1498 Planarity : 0.007 0.218 1764 Dihedral : 11.091 88.559 3568 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.22 % Favored : 87.54 % Rotamer: Outliers : 7.71 % Allowed : 7.99 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.20), residues: 1252 helix: -5.35 (0.10), residues: 70 sheet: -2.88 (0.22), residues: 452 loop : -3.46 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 167 HIS 0.002 0.001 HIS B 199 PHE 0.008 0.001 PHE C 375 TYR 0.008 0.001 TYR A 112 ARG 0.005 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 237 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.7978 (m) cc_final: 0.7616 (t) REVERT: A 154 LEU cc_start: 0.8591 (tp) cc_final: 0.8217 (tp) REVERT: B 21 THR cc_start: 0.8338 (p) cc_final: 0.8136 (t) REVERT: B 116 SER cc_start: 0.7575 (t) cc_final: 0.7274 (p) REVERT: C 346 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8251 (mtt90) REVERT: C 438 SER cc_start: 0.8294 (m) cc_final: 0.8077 (p) REVERT: C 445 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.8103 (p) REVERT: C 448 ASN cc_start: 0.7715 (OUTLIER) cc_final: 0.7425 (p0) REVERT: C 459 SER cc_start: 0.8501 (p) cc_final: 0.8280 (m) REVERT: C 467 ASP cc_start: 0.7055 (p0) cc_final: 0.6626 (p0) REVERT: C 508 TYR cc_start: 0.8308 (m-80) cc_final: 0.7897 (m-80) REVERT: D 25 SER cc_start: 0.8443 (t) cc_final: 0.8099 (p) REVERT: D 37 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8025 (m) REVERT: D 70 ILE cc_start: 0.8809 (tt) cc_final: 0.8585 (tt) REVERT: D 126 SER cc_start: 0.8376 (m) cc_final: 0.8124 (p) REVERT: D 134 VAL cc_start: 0.8661 (t) cc_final: 0.8455 (m) REVERT: E 78 GLU cc_start: 0.7089 (pm20) cc_final: 0.6506 (pm20) REVERT: E 81 ASP cc_start: 0.8128 (t70) cc_final: 0.7921 (t70) REVERT: E 147 THR cc_start: 0.8027 (m) cc_final: 0.7546 (p) REVERT: F 355 ARG cc_start: 0.7473 (mtp85) cc_final: 0.7100 (mtp85) REVERT: F 362 VAL cc_start: 0.8501 (t) cc_final: 0.8069 (p) REVERT: F 375 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6576 (m-10) REVERT: F 377 PHE cc_start: 0.7852 (t80) cc_final: 0.7636 (t80) REVERT: F 394 ASN cc_start: 0.7326 (m-40) cc_final: 0.6887 (m-40) REVERT: F 439 ASN cc_start: 0.8213 (t0) cc_final: 0.7927 (t0) REVERT: F 503 VAL cc_start: 0.8803 (p) cc_final: 0.8588 (t) REVERT: F 517 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6655 (tm) outliers start: 82 outliers final: 35 residues processed: 296 average time/residue: 0.2385 time to fit residues: 95.1705 Evaluate side-chains 250 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 210 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 474 GLN Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.0970 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 33 HIS B 88 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS C 409 GLN C 437 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN D 118 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 172 ASN ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 9982 Z= 0.480 Angle : 0.722 8.172 13614 Z= 0.372 Chirality : 0.048 0.211 1498 Planarity : 0.005 0.060 1764 Dihedral : 8.625 72.196 1517 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.86 % Favored : 85.06 % Rotamer: Outliers : 6.30 % Allowed : 13.91 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.21), residues: 1252 helix: -4.93 (0.35), residues: 56 sheet: -2.32 (0.24), residues: 424 loop : -3.05 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 167 HIS 0.007 0.001 HIS D 100 PHE 0.030 0.002 PHE C 377 TYR 0.021 0.002 TYR A 189 ARG 0.004 0.001 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 238 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8015 (m) cc_final: 0.7749 (p) REVERT: A 32 TYR cc_start: 0.8512 (m-80) cc_final: 0.8111 (m-80) REVERT: A 55 SER cc_start: 0.8241 (m) cc_final: 0.7836 (t) REVERT: A 85 SER cc_start: 0.8253 (t) cc_final: 0.8014 (t) REVERT: A 154 LEU cc_start: 0.8652 (tp) cc_final: 0.8210 (tp) REVERT: B 14 PRO cc_start: 0.8527 (Cg_endo) cc_final: 0.8304 (Cg_exo) REVERT: B 53 ARG cc_start: 0.8191 (ptp90) cc_final: 0.7880 (ptp90) REVERT: B 116 SER cc_start: 0.7824 (t) cc_final: 0.7139 (p) REVERT: B 138 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7441 (mt) REVERT: C 346 ARG cc_start: 0.8594 (mtt-85) cc_final: 0.8120 (mtt180) REVERT: C 354 ASN cc_start: 0.8092 (t0) cc_final: 0.7801 (t0) REVERT: C 355 ARG cc_start: 0.7665 (ttt90) cc_final: 0.7361 (ttm170) REVERT: C 481 ASN cc_start: 0.8190 (m-40) cc_final: 0.7899 (t0) REVERT: C 508 TYR cc_start: 0.8442 (m-80) cc_final: 0.8228 (m-80) REVERT: C 518 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8259 (mp) REVERT: D 25 SER cc_start: 0.8532 (t) cc_final: 0.8169 (p) REVERT: D 70 ILE cc_start: 0.8844 (tt) cc_final: 0.8607 (tt) REVERT: D 126 SER cc_start: 0.8598 (m) cc_final: 0.8300 (p) REVERT: D 139 PRO cc_start: 0.8107 (Cg_endo) cc_final: 0.7888 (Cg_exo) REVERT: D 158 TYR cc_start: 0.7909 (p90) cc_final: 0.7661 (p90) REVERT: E 51 SER cc_start: 0.8124 (m) cc_final: 0.7845 (p) REVERT: E 77 VAL cc_start: 0.7557 (OUTLIER) cc_final: 0.7170 (t) REVERT: E 81 ASP cc_start: 0.8142 (t70) cc_final: 0.7647 (t70) REVERT: E 119 LEU cc_start: 0.6655 (mm) cc_final: 0.6309 (tp) REVERT: E 198 THR cc_start: 0.7625 (m) cc_final: 0.7371 (p) REVERT: F 354 ASN cc_start: 0.7394 (t0) cc_final: 0.7061 (t0) REVERT: F 375 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.6964 (m-80) REVERT: F 394 ASN cc_start: 0.7253 (m-40) cc_final: 0.6941 (m-40) REVERT: F 438 SER cc_start: 0.8490 (m) cc_final: 0.8132 (p) outliers start: 67 outliers final: 42 residues processed: 287 average time/residue: 0.2190 time to fit residues: 86.8300 Evaluate side-chains 257 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 211 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 0.4980 chunk 121 optimal weight: 0.1980 chunk 100 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 168 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS C 448 ASN D 3 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 ASN F 450 ASN F 481 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9982 Z= 0.355 Angle : 0.668 8.159 13614 Z= 0.343 Chirality : 0.046 0.197 1498 Planarity : 0.005 0.051 1764 Dihedral : 8.057 73.274 1488 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.74 % Favored : 86.18 % Rotamer: Outliers : 7.05 % Allowed : 15.98 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.22), residues: 1252 helix: -4.95 (0.29), residues: 56 sheet: -1.97 (0.25), residues: 408 loop : -2.83 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 436 HIS 0.010 0.001 HIS B 190 PHE 0.027 0.002 PHE C 377 TYR 0.016 0.002 TYR D 95 ARG 0.006 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 217 time to evaluate : 1.081 Fit side-chains REVERT: A 17 SER cc_start: 0.7959 (m) cc_final: 0.7673 (p) REVERT: A 55 SER cc_start: 0.8188 (m) cc_final: 0.7776 (t) REVERT: A 85 SER cc_start: 0.8169 (t) cc_final: 0.7922 (t) REVERT: A 154 LEU cc_start: 0.8652 (tp) cc_final: 0.8174 (tp) REVERT: A 188 LEU cc_start: 0.7780 (mm) cc_final: 0.7437 (mt) REVERT: B 6 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7304 (mt0) REVERT: B 76 ARG cc_start: 0.7438 (tpp80) cc_final: 0.7176 (mpp80) REVERT: B 138 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7387 (mt) REVERT: B 148 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8340 (m) REVERT: B 200 GLU cc_start: 0.5024 (OUTLIER) cc_final: 0.4792 (pm20) REVERT: C 346 ARG cc_start: 0.8503 (mtt-85) cc_final: 0.8069 (mtt180) REVERT: C 354 ASN cc_start: 0.8050 (t0) cc_final: 0.7785 (t0) REVERT: C 355 ARG cc_start: 0.7643 (ttt90) cc_final: 0.7395 (ttm170) REVERT: C 481 ASN cc_start: 0.8176 (m-40) cc_final: 0.7922 (t0) REVERT: C 508 TYR cc_start: 0.8450 (m-80) cc_final: 0.8150 (m-80) REVERT: C 511 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8319 (t) REVERT: C 518 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8277 (mp) REVERT: D 25 SER cc_start: 0.8513 (t) cc_final: 0.8169 (p) REVERT: D 80 TYR cc_start: 0.8228 (m-80) cc_final: 0.7837 (m-80) REVERT: D 100 HIS cc_start: 0.6089 (OUTLIER) cc_final: 0.5751 (m90) REVERT: D 101 GLN cc_start: 0.6335 (OUTLIER) cc_final: 0.6085 (mp10) REVERT: D 126 SER cc_start: 0.8592 (m) cc_final: 0.8272 (p) REVERT: D 158 TYR cc_start: 0.7970 (p90) cc_final: 0.7359 (p90) REVERT: E 51 SER cc_start: 0.8127 (m) cc_final: 0.7856 (p) REVERT: E 81 ASP cc_start: 0.8014 (t70) cc_final: 0.7578 (t70) REVERT: E 119 LEU cc_start: 0.6641 (mm) cc_final: 0.6353 (tp) REVERT: E 180 LEU cc_start: 0.7840 (tp) cc_final: 0.7578 (tt) REVERT: E 198 THR cc_start: 0.7574 (m) cc_final: 0.7322 (p) REVERT: F 354 ASN cc_start: 0.7392 (t0) cc_final: 0.7065 (t0) REVERT: F 394 ASN cc_start: 0.7220 (m-40) cc_final: 0.6864 (m-40) outliers start: 75 outliers final: 45 residues processed: 270 average time/residue: 0.2252 time to fit residues: 83.7497 Evaluate side-chains 266 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 213 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 chunk 58 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 0.0970 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 107 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN C 394 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS F 450 ASN F 481 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9982 Z= 0.279 Angle : 0.626 7.640 13614 Z= 0.321 Chirality : 0.045 0.200 1498 Planarity : 0.005 0.049 1764 Dihedral : 7.858 75.357 1487 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.78 % Favored : 87.14 % Rotamer: Outliers : 6.11 % Allowed : 17.67 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.59 (0.22), residues: 1252 helix: -5.01 (0.23), residues: 56 sheet: -1.79 (0.25), residues: 428 loop : -2.63 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 436 HIS 0.003 0.001 HIS D 99 PHE 0.015 0.001 PHE C 375 TYR 0.013 0.001 TYR D 95 ARG 0.005 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 215 time to evaluate : 1.142 Fit side-chains REVERT: A 17 SER cc_start: 0.7845 (m) cc_final: 0.7601 (p) REVERT: A 32 TYR cc_start: 0.8524 (m-80) cc_final: 0.8107 (m-80) REVERT: A 55 SER cc_start: 0.8103 (m) cc_final: 0.7680 (t) REVERT: A 85 SER cc_start: 0.8112 (t) cc_final: 0.7858 (t) REVERT: A 154 LEU cc_start: 0.8609 (tp) cc_final: 0.8150 (tp) REVERT: A 188 LEU cc_start: 0.7815 (mm) cc_final: 0.7472 (mt) REVERT: B 6 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7282 (mt0) REVERT: B 76 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7196 (mpp80) REVERT: B 138 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7370 (mt) REVERT: C 346 ARG cc_start: 0.8483 (mtt-85) cc_final: 0.8036 (mtt180) REVERT: C 354 ASN cc_start: 0.8042 (t0) cc_final: 0.7756 (t0) REVERT: C 355 ARG cc_start: 0.7644 (ttt90) cc_final: 0.7393 (ttm170) REVERT: C 448 ASN cc_start: 0.7512 (p0) cc_final: 0.7284 (p0) REVERT: C 508 TYR cc_start: 0.8422 (m-80) cc_final: 0.8166 (m-80) REVERT: C 511 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8267 (t) REVERT: C 518 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8240 (mp) REVERT: D 25 SER cc_start: 0.8503 (t) cc_final: 0.8154 (p) REVERT: D 80 TYR cc_start: 0.8188 (m-80) cc_final: 0.7752 (m-80) REVERT: D 100 HIS cc_start: 0.6094 (OUTLIER) cc_final: 0.5778 (m90) REVERT: D 101 GLN cc_start: 0.6312 (OUTLIER) cc_final: 0.6092 (mp10) REVERT: D 126 SER cc_start: 0.8601 (m) cc_final: 0.8266 (p) REVERT: D 158 TYR cc_start: 0.7936 (p90) cc_final: 0.7418 (p90) REVERT: E 51 SER cc_start: 0.8110 (m) cc_final: 0.7839 (p) REVERT: E 81 ASP cc_start: 0.7942 (t70) cc_final: 0.7621 (t0) REVERT: E 180 LEU cc_start: 0.7852 (tp) cc_final: 0.7586 (tt) REVERT: E 198 THR cc_start: 0.7375 (m) cc_final: 0.7097 (p) REVERT: F 350 VAL cc_start: 0.8238 (t) cc_final: 0.7948 (p) REVERT: F 354 ASN cc_start: 0.7389 (t0) cc_final: 0.7141 (t0) REVERT: F 386 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7729 (mmpt) REVERT: F 394 ASN cc_start: 0.7183 (m-40) cc_final: 0.6887 (m-40) REVERT: F 438 SER cc_start: 0.8472 (m) cc_final: 0.8121 (p) outliers start: 65 outliers final: 45 residues processed: 263 average time/residue: 0.2289 time to fit residues: 82.8700 Evaluate side-chains 265 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 213 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.0010 chunk 68 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 102 optimal weight: 0.0570 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 196 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9982 Z= 0.276 Angle : 0.623 7.532 13614 Z= 0.320 Chirality : 0.045 0.200 1498 Planarity : 0.005 0.047 1764 Dihedral : 7.714 76.314 1482 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.94 % Favored : 86.98 % Rotamer: Outliers : 6.39 % Allowed : 18.52 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.23), residues: 1252 helix: -5.03 (0.21), residues: 56 sheet: -1.52 (0.25), residues: 440 loop : -2.61 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 436 HIS 0.004 0.001 HIS A 213 PHE 0.020 0.002 PHE C 377 TYR 0.014 0.001 TYR B 179 ARG 0.004 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 219 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8503 (m-80) cc_final: 0.8050 (m-80) REVERT: A 55 SER cc_start: 0.8075 (m) cc_final: 0.7622 (t) REVERT: A 85 SER cc_start: 0.8062 (t) cc_final: 0.7805 (t) REVERT: A 154 LEU cc_start: 0.8561 (tp) cc_final: 0.8112 (tp) REVERT: A 188 LEU cc_start: 0.7828 (mm) cc_final: 0.7495 (mt) REVERT: B 6 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7264 (mt0) REVERT: B 76 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7208 (mpp80) REVERT: B 138 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7381 (mt) REVERT: B 173 LYS cc_start: 0.7243 (mmtp) cc_final: 0.7013 (mmmm) REVERT: C 346 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.8030 (mtt180) REVERT: C 354 ASN cc_start: 0.8013 (t0) cc_final: 0.7730 (t0) REVERT: C 355 ARG cc_start: 0.7657 (ttt90) cc_final: 0.7380 (ttm170) REVERT: C 448 ASN cc_start: 0.7571 (p0) cc_final: 0.7314 (p0) REVERT: C 508 TYR cc_start: 0.8400 (m-80) cc_final: 0.8133 (m-80) REVERT: C 511 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8279 (t) REVERT: C 518 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8239 (mp) REVERT: D 25 SER cc_start: 0.8489 (t) cc_final: 0.8144 (p) REVERT: D 80 TYR cc_start: 0.8184 (m-80) cc_final: 0.7852 (m-80) REVERT: D 100 HIS cc_start: 0.6151 (OUTLIER) cc_final: 0.5811 (m90) REVERT: D 101 GLN cc_start: 0.6333 (OUTLIER) cc_final: 0.6115 (mp10) REVERT: D 126 SER cc_start: 0.8614 (m) cc_final: 0.8274 (p) REVERT: D 158 TYR cc_start: 0.7934 (p90) cc_final: 0.7415 (p90) REVERT: E 5 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8479 (p) REVERT: E 51 SER cc_start: 0.8118 (m) cc_final: 0.7860 (p) REVERT: E 81 ASP cc_start: 0.7912 (t70) cc_final: 0.7605 (t0) REVERT: E 147 THR cc_start: 0.8074 (m) cc_final: 0.7567 (p) REVERT: E 180 LEU cc_start: 0.7845 (tp) cc_final: 0.7581 (tt) REVERT: E 198 THR cc_start: 0.7409 (m) cc_final: 0.7141 (p) REVERT: F 354 ASN cc_start: 0.7340 (t0) cc_final: 0.7099 (t0) REVERT: F 386 LYS cc_start: 0.8016 (mmtt) cc_final: 0.7705 (mmpt) REVERT: F 394 ASN cc_start: 0.7276 (m-40) cc_final: 0.6944 (m-40) REVERT: F 438 SER cc_start: 0.8464 (m) cc_final: 0.8121 (p) outliers start: 68 outliers final: 52 residues processed: 264 average time/residue: 0.2244 time to fit residues: 81.4126 Evaluate side-chains 273 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 213 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 0.0270 chunk 119 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 9982 Z= 0.479 Angle : 0.720 8.683 13614 Z= 0.370 Chirality : 0.048 0.211 1498 Planarity : 0.005 0.051 1764 Dihedral : 8.050 77.229 1482 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.18 % Favored : 84.74 % Rotamer: Outliers : 6.77 % Allowed : 18.89 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.22), residues: 1252 helix: -5.03 (0.22), residues: 56 sheet: -1.53 (0.26), residues: 416 loop : -2.68 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 167 HIS 0.005 0.001 HIS D 99 PHE 0.019 0.002 PHE C 375 TYR 0.019 0.002 TYR D 95 ARG 0.004 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 224 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.7979 (m) cc_final: 0.7741 (p) REVERT: A 55 SER cc_start: 0.8174 (m) cc_final: 0.7752 (t) REVERT: A 85 SER cc_start: 0.7998 (t) cc_final: 0.7738 (t) REVERT: A 93 LEU cc_start: 0.8080 (mt) cc_final: 0.7865 (mp) REVERT: A 154 LEU cc_start: 0.8621 (tp) cc_final: 0.8168 (tp) REVERT: A 164 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7532 (p) REVERT: A 188 LEU cc_start: 0.8031 (mm) cc_final: 0.7691 (mt) REVERT: B 6 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7409 (mt0) REVERT: B 55 SER cc_start: 0.7894 (t) cc_final: 0.7526 (m) REVERT: B 76 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7242 (mpp80) REVERT: B 200 GLU cc_start: 0.4811 (OUTLIER) cc_final: 0.4565 (pm20) REVERT: C 346 ARG cc_start: 0.8510 (mtt-85) cc_final: 0.8096 (mtt180) REVERT: C 354 ASN cc_start: 0.7935 (t0) cc_final: 0.7722 (t0) REVERT: C 355 ARG cc_start: 0.7686 (ttt90) cc_final: 0.7403 (ttm170) REVERT: C 481 ASN cc_start: 0.8135 (t0) cc_final: 0.7879 (t0) REVERT: C 508 TYR cc_start: 0.8412 (m-80) cc_final: 0.8129 (m-80) REVERT: C 511 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8282 (t) REVERT: C 518 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8267 (mp) REVERT: D 25 SER cc_start: 0.8506 (t) cc_final: 0.8154 (p) REVERT: D 80 TYR cc_start: 0.8248 (m-80) cc_final: 0.7989 (m-80) REVERT: D 100 HIS cc_start: 0.6710 (OUTLIER) cc_final: 0.6384 (m170) REVERT: D 101 GLN cc_start: 0.6830 (OUTLIER) cc_final: 0.6515 (mp10) REVERT: D 120 THR cc_start: 0.8621 (t) cc_final: 0.8271 (p) REVERT: D 126 SER cc_start: 0.8700 (m) cc_final: 0.8370 (p) REVERT: D 133 SER cc_start: 0.8136 (t) cc_final: 0.7825 (t) REVERT: D 158 TYR cc_start: 0.7995 (p90) cc_final: 0.7491 (p90) REVERT: E 5 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8494 (p) REVERT: E 51 SER cc_start: 0.8210 (m) cc_final: 0.7978 (p) REVERT: E 81 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7663 (t0) REVERT: E 147 THR cc_start: 0.8068 (m) cc_final: 0.7552 (p) REVERT: E 178 SER cc_start: 0.8515 (t) cc_final: 0.8237 (t) REVERT: E 180 LEU cc_start: 0.7846 (tp) cc_final: 0.7558 (tt) REVERT: E 198 THR cc_start: 0.7532 (m) cc_final: 0.7272 (p) REVERT: F 354 ASN cc_start: 0.7344 (t0) cc_final: 0.7116 (t0) REVERT: F 386 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7733 (mmpt) REVERT: F 394 ASN cc_start: 0.7504 (m-40) cc_final: 0.7260 (m-40) REVERT: F 438 SER cc_start: 0.8463 (m) cc_final: 0.8143 (p) outliers start: 72 outliers final: 55 residues processed: 271 average time/residue: 0.2220 time to fit residues: 83.2952 Evaluate side-chains 282 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 217 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 68 optimal weight: 0.0060 chunk 87 optimal weight: 0.2980 chunk 67 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9982 Z= 0.274 Angle : 0.639 7.815 13614 Z= 0.327 Chirality : 0.045 0.198 1498 Planarity : 0.005 0.057 1764 Dihedral : 7.730 77.372 1479 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.42 % Favored : 86.50 % Rotamer: Outliers : 6.30 % Allowed : 20.21 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.23), residues: 1252 helix: -5.03 (0.21), residues: 56 sheet: -1.42 (0.26), residues: 412 loop : -2.49 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 167 HIS 0.003 0.001 HIS D 99 PHE 0.016 0.001 PHE C 392 TYR 0.016 0.001 TYR E 193 ARG 0.003 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 204 time to evaluate : 1.063 Fit side-chains REVERT: A 17 SER cc_start: 0.7864 (m) cc_final: 0.7611 (p) REVERT: A 32 TYR cc_start: 0.8500 (m-80) cc_final: 0.8148 (m-80) REVERT: A 55 SER cc_start: 0.8053 (m) cc_final: 0.7606 (t) REVERT: A 85 SER cc_start: 0.7957 (t) cc_final: 0.7704 (t) REVERT: A 154 LEU cc_start: 0.8567 (tp) cc_final: 0.8127 (tp) REVERT: A 188 LEU cc_start: 0.7952 (mm) cc_final: 0.7624 (mt) REVERT: B 32 VAL cc_start: 0.7898 (t) cc_final: 0.7638 (p) REVERT: B 76 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7252 (mpp80) REVERT: B 138 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7413 (mt) REVERT: C 346 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.8035 (mtt180) REVERT: C 354 ASN cc_start: 0.7970 (t0) cc_final: 0.7711 (t0) REVERT: C 355 ARG cc_start: 0.7669 (ttt90) cc_final: 0.7406 (ttm170) REVERT: C 481 ASN cc_start: 0.8105 (t0) cc_final: 0.7834 (t0) REVERT: C 489 TYR cc_start: 0.8280 (m-80) cc_final: 0.7896 (m-80) REVERT: C 508 TYR cc_start: 0.8383 (m-80) cc_final: 0.8106 (m-80) REVERT: C 511 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8297 (t) REVERT: C 518 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8192 (mp) REVERT: D 25 SER cc_start: 0.8481 (t) cc_final: 0.8149 (p) REVERT: D 80 TYR cc_start: 0.8218 (m-80) cc_final: 0.7949 (m-80) REVERT: D 100 HIS cc_start: 0.6332 (OUTLIER) cc_final: 0.5890 (m90) REVERT: D 101 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.6195 (mp10) REVERT: D 126 SER cc_start: 0.8657 (m) cc_final: 0.8297 (p) REVERT: D 151 LEU cc_start: 0.8211 (pp) cc_final: 0.7999 (pp) REVERT: D 158 TYR cc_start: 0.7972 (p90) cc_final: 0.7447 (p90) REVERT: E 5 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8489 (p) REVERT: E 51 SER cc_start: 0.8118 (m) cc_final: 0.7868 (p) REVERT: E 64 SER cc_start: 0.8598 (p) cc_final: 0.8332 (m) REVERT: E 81 ASP cc_start: 0.7880 (t70) cc_final: 0.7677 (m-30) REVERT: E 147 THR cc_start: 0.8059 (m) cc_final: 0.7570 (p) REVERT: E 178 SER cc_start: 0.8507 (t) cc_final: 0.8217 (t) REVERT: E 180 LEU cc_start: 0.7854 (tp) cc_final: 0.7566 (tt) REVERT: E 198 THR cc_start: 0.7402 (m) cc_final: 0.7160 (p) REVERT: F 350 VAL cc_start: 0.8201 (t) cc_final: 0.7978 (p) REVERT: F 354 ASN cc_start: 0.7340 (t0) cc_final: 0.7087 (t0) REVERT: F 394 ASN cc_start: 0.7419 (m-40) cc_final: 0.7090 (m-40) REVERT: F 438 SER cc_start: 0.8475 (m) cc_final: 0.8168 (p) outliers start: 67 outliers final: 51 residues processed: 249 average time/residue: 0.2261 time to fit residues: 77.1313 Evaluate side-chains 261 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 203 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9982 Z= 0.351 Angle : 0.672 7.543 13614 Z= 0.344 Chirality : 0.047 0.221 1498 Planarity : 0.005 0.049 1764 Dihedral : 7.762 77.725 1475 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.74 % Favored : 86.18 % Rotamer: Outliers : 6.30 % Allowed : 19.74 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.23), residues: 1252 helix: -4.98 (0.28), residues: 44 sheet: -1.35 (0.28), residues: 380 loop : -2.50 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 167 HIS 0.005 0.001 HIS A 213 PHE 0.017 0.002 PHE C 375 TYR 0.017 0.002 TYR B 179 ARG 0.003 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 207 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.7911 (m) cc_final: 0.7678 (p) REVERT: A 32 TYR cc_start: 0.8486 (m-80) cc_final: 0.8138 (m-80) REVERT: A 55 SER cc_start: 0.8073 (m) cc_final: 0.7627 (t) REVERT: A 85 SER cc_start: 0.7931 (t) cc_final: 0.7678 (t) REVERT: A 93 LEU cc_start: 0.8001 (mt) cc_final: 0.7782 (mp) REVERT: A 154 LEU cc_start: 0.8570 (tp) cc_final: 0.8115 (tp) REVERT: A 188 LEU cc_start: 0.7976 (mm) cc_final: 0.7638 (mt) REVERT: B 6 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7329 (mt0) REVERT: B 32 VAL cc_start: 0.7899 (t) cc_final: 0.7636 (p) REVERT: B 76 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7279 (mpp80) REVERT: B 138 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7398 (mt) REVERT: C 346 ARG cc_start: 0.8470 (mtt-85) cc_final: 0.8052 (mtt180) REVERT: C 350 VAL cc_start: 0.8459 (t) cc_final: 0.8184 (p) REVERT: C 354 ASN cc_start: 0.7941 (t0) cc_final: 0.7708 (t0) REVERT: C 355 ARG cc_start: 0.7674 (ttt90) cc_final: 0.7416 (ttm170) REVERT: C 425 LEU cc_start: 0.8231 (mp) cc_final: 0.7998 (mt) REVERT: C 448 ASN cc_start: 0.7726 (p0) cc_final: 0.7485 (p0) REVERT: C 481 ASN cc_start: 0.8141 (t0) cc_final: 0.7903 (t0) REVERT: C 508 TYR cc_start: 0.8373 (m-80) cc_final: 0.8107 (m-80) REVERT: C 511 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8272 (t) REVERT: C 518 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8263 (mp) REVERT: D 25 SER cc_start: 0.8493 (t) cc_final: 0.8156 (p) REVERT: D 80 TYR cc_start: 0.8201 (m-80) cc_final: 0.7931 (m-80) REVERT: D 100 HIS cc_start: 0.6466 (OUTLIER) cc_final: 0.5962 (m90) REVERT: D 101 GLN cc_start: 0.6568 (OUTLIER) cc_final: 0.6298 (mp10) REVERT: D 126 SER cc_start: 0.8685 (m) cc_final: 0.8332 (p) REVERT: D 133 SER cc_start: 0.8142 (t) cc_final: 0.7812 (t) REVERT: D 151 LEU cc_start: 0.8168 (pp) cc_final: 0.7961 (pp) REVERT: D 158 TYR cc_start: 0.7999 (p90) cc_final: 0.7470 (p90) REVERT: E 5 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8491 (p) REVERT: E 51 SER cc_start: 0.8131 (m) cc_final: 0.7900 (p) REVERT: E 64 SER cc_start: 0.8557 (p) cc_final: 0.8266 (m) REVERT: E 81 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7630 (t0) REVERT: E 116 SER cc_start: 0.8640 (p) cc_final: 0.8401 (p) REVERT: E 147 THR cc_start: 0.8089 (m) cc_final: 0.7609 (p) REVERT: E 178 SER cc_start: 0.8484 (t) cc_final: 0.8212 (t) REVERT: E 198 THR cc_start: 0.7473 (m) cc_final: 0.7217 (p) REVERT: F 350 VAL cc_start: 0.8197 (t) cc_final: 0.7946 (p) REVERT: F 354 ASN cc_start: 0.7322 (t0) cc_final: 0.7085 (t0) REVERT: F 394 ASN cc_start: 0.7447 (m-40) cc_final: 0.7112 (m-40) REVERT: F 438 SER cc_start: 0.8465 (m) cc_final: 0.8180 (p) outliers start: 67 outliers final: 52 residues processed: 253 average time/residue: 0.2273 time to fit residues: 78.8608 Evaluate side-chains 266 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 205 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 87 optimal weight: 0.3980 chunk 34 optimal weight: 0.3980 chunk 100 optimal weight: 0.5980 chunk 105 optimal weight: 0.2980 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9982 Z= 0.286 Angle : 0.644 7.101 13614 Z= 0.330 Chirality : 0.046 0.212 1498 Planarity : 0.005 0.045 1764 Dihedral : 7.695 77.785 1475 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.34 % Favored : 86.58 % Rotamer: Outliers : 5.92 % Allowed : 20.21 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.23), residues: 1252 helix: -4.98 (0.26), residues: 44 sheet: -1.16 (0.29), residues: 360 loop : -2.45 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 167 HIS 0.008 0.001 HIS B 199 PHE 0.017 0.001 PHE C 375 TYR 0.015 0.001 TYR B 179 ARG 0.006 0.000 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 204 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8523 (m-80) cc_final: 0.8212 (m-80) REVERT: A 55 SER cc_start: 0.8037 (m) cc_final: 0.7580 (t) REVERT: A 85 SER cc_start: 0.7938 (t) cc_final: 0.7691 (t) REVERT: A 154 LEU cc_start: 0.8539 (tp) cc_final: 0.8098 (tp) REVERT: A 188 LEU cc_start: 0.7961 (mm) cc_final: 0.7623 (mt) REVERT: B 6 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7308 (mt0) REVERT: B 32 VAL cc_start: 0.7900 (t) cc_final: 0.7652 (p) REVERT: B 76 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7272 (mpp80) REVERT: B 138 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7417 (mt) REVERT: C 346 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.8028 (mtt180) REVERT: C 350 VAL cc_start: 0.8471 (t) cc_final: 0.8163 (p) REVERT: C 354 ASN cc_start: 0.7961 (t0) cc_final: 0.7698 (t0) REVERT: C 355 ARG cc_start: 0.7673 (ttt90) cc_final: 0.7402 (ttm170) REVERT: C 425 LEU cc_start: 0.8219 (mp) cc_final: 0.7991 (mt) REVERT: C 448 ASN cc_start: 0.7730 (p0) cc_final: 0.7464 (p0) REVERT: C 481 ASN cc_start: 0.8135 (t0) cc_final: 0.7909 (t0) REVERT: C 508 TYR cc_start: 0.8363 (m-80) cc_final: 0.8082 (m-80) REVERT: C 511 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8286 (t) REVERT: C 518 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8192 (mp) REVERT: D 25 SER cc_start: 0.8491 (t) cc_final: 0.8158 (p) REVERT: D 80 TYR cc_start: 0.8193 (m-80) cc_final: 0.7952 (m-80) REVERT: D 100 HIS cc_start: 0.6265 (OUTLIER) cc_final: 0.5853 (m90) REVERT: D 101 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.6193 (mp10) REVERT: D 126 SER cc_start: 0.8661 (m) cc_final: 0.8297 (p) REVERT: D 133 SER cc_start: 0.8122 (t) cc_final: 0.7885 (t) REVERT: D 151 LEU cc_start: 0.8184 (pp) cc_final: 0.7972 (pp) REVERT: D 158 TYR cc_start: 0.7972 (p90) cc_final: 0.7436 (p90) REVERT: E 5 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8511 (p) REVERT: E 51 SER cc_start: 0.8101 (m) cc_final: 0.7852 (p) REVERT: E 64 SER cc_start: 0.8564 (p) cc_final: 0.8262 (m) REVERT: E 116 SER cc_start: 0.8595 (p) cc_final: 0.8310 (p) REVERT: E 147 THR cc_start: 0.8085 (m) cc_final: 0.7608 (p) REVERT: E 178 SER cc_start: 0.8481 (t) cc_final: 0.8230 (t) REVERT: E 198 THR cc_start: 0.7436 (m) cc_final: 0.7207 (p) REVERT: F 350 VAL cc_start: 0.8189 (t) cc_final: 0.7956 (p) REVERT: F 354 ASN cc_start: 0.7329 (t0) cc_final: 0.7077 (t0) REVERT: F 394 ASN cc_start: 0.7384 (m-40) cc_final: 0.7065 (m-40) REVERT: F 438 SER cc_start: 0.8466 (m) cc_final: 0.8229 (p) REVERT: F 517 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6642 (tm) outliers start: 63 outliers final: 53 residues processed: 247 average time/residue: 0.2215 time to fit residues: 75.2814 Evaluate side-chains 263 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 201 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 81 optimal weight: 0.4980 chunk 123 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 0.0870 chunk 75 optimal weight: 0.1980 chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9982 Z= 0.299 Angle : 0.655 7.280 13614 Z= 0.334 Chirality : 0.046 0.210 1498 Planarity : 0.005 0.049 1764 Dihedral : 7.598 78.093 1473 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.58 % Favored : 86.34 % Rotamer: Outliers : 5.55 % Allowed : 20.58 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.23), residues: 1252 helix: -4.99 (0.25), residues: 44 sheet: -1.38 (0.27), residues: 398 loop : -2.33 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 167 HIS 0.004 0.001 HIS A 213 PHE 0.032 0.002 PHE C 377 TYR 0.015 0.001 TYR B 179 ARG 0.006 0.000 ARG F 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 194 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8470 (m-80) cc_final: 0.8141 (m-80) REVERT: A 55 SER cc_start: 0.8064 (m) cc_final: 0.7611 (t) REVERT: A 85 SER cc_start: 0.7925 (t) cc_final: 0.7658 (t) REVERT: A 154 LEU cc_start: 0.8557 (tp) cc_final: 0.8097 (tp) REVERT: A 188 LEU cc_start: 0.7963 (mm) cc_final: 0.7630 (mt) REVERT: B 6 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7315 (mt0) REVERT: B 32 VAL cc_start: 0.7899 (t) cc_final: 0.7651 (p) REVERT: B 76 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7308 (mpp80) REVERT: B 138 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7422 (mt) REVERT: B 193 TYR cc_start: 0.6563 (m-80) cc_final: 0.6193 (m-80) REVERT: C 346 ARG cc_start: 0.8465 (mtt-85) cc_final: 0.8040 (mtt180) REVERT: C 350 VAL cc_start: 0.8461 (t) cc_final: 0.8159 (p) REVERT: C 354 ASN cc_start: 0.7963 (t0) cc_final: 0.7700 (t0) REVERT: C 355 ARG cc_start: 0.7677 (ttt90) cc_final: 0.7402 (ttm170) REVERT: C 448 ASN cc_start: 0.7740 (p0) cc_final: 0.7462 (p0) REVERT: C 481 ASN cc_start: 0.8151 (t0) cc_final: 0.7917 (t0) REVERT: C 508 TYR cc_start: 0.8355 (m-80) cc_final: 0.8086 (m-80) REVERT: C 511 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8285 (t) REVERT: D 25 SER cc_start: 0.8493 (t) cc_final: 0.8156 (p) REVERT: D 80 TYR cc_start: 0.8181 (m-80) cc_final: 0.7945 (m-80) REVERT: D 100 HIS cc_start: 0.6238 (OUTLIER) cc_final: 0.5837 (m90) REVERT: D 126 SER cc_start: 0.8666 (m) cc_final: 0.8305 (p) REVERT: D 133 SER cc_start: 0.8194 (t) cc_final: 0.7885 (t) REVERT: D 151 LEU cc_start: 0.8188 (pp) cc_final: 0.7975 (pp) REVERT: D 158 TYR cc_start: 0.8004 (p90) cc_final: 0.7462 (p90) REVERT: E 51 SER cc_start: 0.8105 (m) cc_final: 0.7858 (p) REVERT: E 64 SER cc_start: 0.8555 (p) cc_final: 0.8256 (m) REVERT: E 116 SER cc_start: 0.8593 (p) cc_final: 0.8289 (p) REVERT: E 147 THR cc_start: 0.8088 (m) cc_final: 0.7616 (p) REVERT: E 178 SER cc_start: 0.8482 (t) cc_final: 0.8221 (t) REVERT: E 198 THR cc_start: 0.7469 (m) cc_final: 0.7227 (p) REVERT: F 350 VAL cc_start: 0.8180 (t) cc_final: 0.7946 (p) REVERT: F 354 ASN cc_start: 0.7317 (t0) cc_final: 0.7076 (t0) REVERT: F 394 ASN cc_start: 0.7382 (m-40) cc_final: 0.7077 (m-40) REVERT: F 438 SER cc_start: 0.8462 (m) cc_final: 0.8234 (p) REVERT: F 517 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6655 (tm) outliers start: 59 outliers final: 52 residues processed: 235 average time/residue: 0.2262 time to fit residues: 73.7144 Evaluate side-chains 252 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 194 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 14 optimal weight: 0.0870 chunk 27 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111685 restraints weight = 14358.706| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.20 r_work: 0.3287 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 9982 Z= 0.400 Angle : 0.705 7.935 13614 Z= 0.360 Chirality : 0.048 0.214 1498 Planarity : 0.005 0.049 1764 Dihedral : 7.778 77.947 1473 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.54 % Favored : 85.38 % Rotamer: Outliers : 5.92 % Allowed : 20.49 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.23), residues: 1252 helix: -4.97 (0.28), residues: 44 sheet: -1.38 (0.27), residues: 390 loop : -2.32 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 167 HIS 0.005 0.001 HIS A 213 PHE 0.034 0.002 PHE C 377 TYR 0.018 0.002 TYR D 95 ARG 0.006 0.001 ARG F 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2862.83 seconds wall clock time: 52 minutes 30.21 seconds (3150.21 seconds total)