Starting phenix.real_space_refine on Thu Feb 15 08:44:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/02_2024/6v6d_21071.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/02_2024/6v6d_21071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/02_2024/6v6d_21071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/02_2024/6v6d_21071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/02_2024/6v6d_21071.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/02_2024/6v6d_21071.pdb" } resolution = 3.77 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= 0.004 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 63 5.16 5 C 7924 2.51 5 N 1778 2.21 5 O 1974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ASP 242": "OD1" <-> "OD2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ASP 242": "OD1" <-> "OD2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ASP 242": "OD1" <-> "OD2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ASP 327": "OD1" <-> "OD2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ASP 327": "OD1" <-> "OD2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ASP 242": "OD1" <-> "OD2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E ASP 327": "OD1" <-> "OD2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F ASP 242": "OD1" <-> "OD2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F ARG 300": "NH1" <-> "NH2" Residue "F ASP 327": "OD1" <-> "OD2" Residue "F GLU 336": "OE1" <-> "OE2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G ARG 217": "NH1" <-> "NH2" Residue "G ASP 242": "OD1" <-> "OD2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G ARG 300": "NH1" <-> "NH2" Residue "G ASP 327": "OD1" <-> "OD2" Residue "G GLU 336": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11739 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Chain: "B" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Chain: "D" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Chain: "E" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Chain: "F" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Chain: "G" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Time building chain proxies: 6.03, per 1000 atoms: 0.51 Number of scatterers: 11739 At special positions: 0 Unit cell: (110, 110, 94.6, 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 63 16.00 O 1974 8.00 N 1778 7.00 C 7924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " 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 Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 2.1 seconds 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 71.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.800A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 108 through 139 Proline residue: A 123 - end of helix removed outlier: 3.754A pdb=" N PHE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 208 through 237 removed outlier: 3.574A pdb=" N LEU A 237 " --> pdb=" O TYR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.458A pdb=" N ASN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.716A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.800A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 108 through 139 Proline residue: B 123 - end of helix removed outlier: 3.754A pdb=" N PHE B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Proline residue: B 133 - end of helix Processing helix chain 'B' and resid 208 through 237 removed outlier: 3.575A pdb=" N LEU B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.459A pdb=" N ASN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Proline residue: B 289 - end of helix removed outlier: 3.716A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.799A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 86 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 108 through 139 Proline residue: C 123 - end of helix removed outlier: 3.754A pdb=" N PHE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 130 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Proline residue: C 133 - end of helix Processing helix chain 'C' and resid 208 through 237 removed outlier: 3.574A pdb=" N LEU C 237 " --> pdb=" O TYR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.457A pdb=" N ASN C 255 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 removed outlier: 3.646A pdb=" N LEU C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Proline residue: C 289 - end of helix removed outlier: 3.716A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.800A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 108 through 139 Proline residue: D 123 - end of helix removed outlier: 3.754A pdb=" N PHE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 130 " --> pdb=" O PHE D 126 " (cutoff:3.500A) Proline residue: D 133 - end of helix Processing helix chain 'D' and resid 208 through 237 removed outlier: 3.575A pdb=" N LEU D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 4.458A pdb=" N ASN D 255 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Proline residue: D 289 - end of helix removed outlier: 3.716A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.800A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 86 Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 108 through 139 Proline residue: E 123 - end of helix removed outlier: 3.754A pdb=" N PHE E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 130 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Proline residue: E 133 - end of helix Processing helix chain 'E' and resid 208 through 237 removed outlier: 3.574A pdb=" N LEU E 237 " --> pdb=" O TYR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 removed outlier: 4.458A pdb=" N ASN E 255 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Proline residue: E 289 - end of helix removed outlier: 3.717A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.800A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 86 Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 108 through 139 Proline residue: F 123 - end of helix removed outlier: 3.754A pdb=" N PHE F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 130 " --> pdb=" O PHE F 126 " (cutoff:3.500A) Proline residue: F 133 - end of helix Processing helix chain 'F' and resid 208 through 237 removed outlier: 3.574A pdb=" N LEU F 237 " --> pdb=" O TYR F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 removed outlier: 4.459A pdb=" N ASN F 255 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Proline residue: F 289 - end of helix removed outlier: 3.716A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 336 removed outlier: 3.726A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.800A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 86 Processing helix chain 'G' and resid 103 through 108 Processing helix chain 'G' and resid 108 through 139 Proline residue: G 123 - end of helix removed outlier: 3.754A pdb=" N PHE G 129 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA G 130 " --> pdb=" O PHE G 126 " (cutoff:3.500A) Proline residue: G 133 - end of helix Processing helix chain 'G' and resid 208 through 237 removed outlier: 3.575A pdb=" N LEU G 237 " --> pdb=" O TYR G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 removed outlier: 4.458A pdb=" N ASN G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU G 286 " --> pdb=" O VAL G 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) Proline residue: G 289 - end of helix removed outlier: 3.717A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 728 hydrogen bonds defined for protein. 2121 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3374 1.34 - 1.46: 2809 1.46 - 1.58: 5787 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 12040 Sorted by residual: bond pdb=" N ILE E 41 " pdb=" CA ILE E 41 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.21e-02 6.83e+03 9.11e+00 bond pdb=" N ILE B 41 " pdb=" CA ILE B 41 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.21e-02 6.83e+03 9.03e+00 bond pdb=" N ILE F 41 " pdb=" CA ILE F 41 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.21e-02 6.83e+03 9.03e+00 bond pdb=" N ILE D 41 " pdb=" CA ILE D 41 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.21e-02 6.83e+03 8.88e+00 bond pdb=" N ILE G 41 " pdb=" CA ILE G 41 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.21e-02 6.83e+03 8.85e+00 ... (remaining 12035 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.21: 343 107.21 - 113.91: 6878 113.91 - 120.60: 5162 120.60 - 127.30: 3899 127.30 - 134.00: 140 Bond angle restraints: 16422 Sorted by residual: angle pdb=" N GLY C 61 " pdb=" CA GLY C 61 " pdb=" C GLY C 61 " ideal model delta sigma weight residual 112.73 124.86 -12.13 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N GLY G 61 " pdb=" CA GLY G 61 " pdb=" C GLY G 61 " ideal model delta sigma weight residual 112.73 124.86 -12.13 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N GLY E 61 " pdb=" CA GLY E 61 " pdb=" C GLY E 61 " ideal model delta sigma weight residual 112.73 124.85 -12.12 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N GLY F 61 " pdb=" CA GLY F 61 " pdb=" C GLY F 61 " ideal model delta sigma weight residual 112.73 124.83 -12.10 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N GLY D 61 " pdb=" CA GLY D 61 " pdb=" C GLY D 61 " ideal model delta sigma weight residual 112.73 124.83 -12.10 1.20e+00 6.94e-01 1.02e+02 ... (remaining 16417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 6405 17.09 - 34.18: 581 34.18 - 51.27: 77 51.27 - 68.36: 7 68.36 - 85.45: 7 Dihedral angle restraints: 7077 sinusoidal: 2709 harmonic: 4368 Sorted by residual: dihedral pdb=" C ASP B 35 " pdb=" N ASP B 35 " pdb=" CA ASP B 35 " pdb=" CB ASP B 35 " ideal model delta harmonic sigma weight residual -122.60 -131.85 9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C ASP F 35 " pdb=" N ASP F 35 " pdb=" CA ASP F 35 " pdb=" CB ASP F 35 " ideal model delta harmonic sigma weight residual -122.60 -131.84 9.24 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C ASP A 35 " pdb=" N ASP A 35 " pdb=" CA ASP A 35 " pdb=" CB ASP A 35 " ideal model delta harmonic sigma weight residual -122.60 -131.82 9.22 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 7074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1559 0.057 - 0.114: 308 0.114 - 0.171: 107 0.171 - 0.229: 7 0.229 - 0.286: 14 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CA LEU D 32 " pdb=" N LEU D 32 " pdb=" C LEU D 32 " pdb=" CB LEU D 32 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA LEU C 32 " pdb=" N LEU C 32 " pdb=" C LEU C 32 " pdb=" CB LEU C 32 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA LEU B 32 " pdb=" N LEU B 32 " pdb=" C LEU B 32 " pdb=" CB LEU B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1992 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 132 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.02e+00 pdb=" N PRO E 133 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO E 133 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 133 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 132 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO G 133 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 133 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 133 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 132 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO F 133 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO F 133 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 133 " -0.035 5.00e-02 4.00e+02 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3326 2.80 - 3.33: 11144 3.33 - 3.85: 18671 3.85 - 4.38: 20454 4.38 - 4.90: 36759 Nonbonded interactions: 90354 Sorted by model distance: nonbonded pdb=" OH TYR E 111 " pdb=" O LEU F 52 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR D 111 " pdb=" O LEU E 52 " model vdw 2.307 2.440 nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.323 2.440 nonbonded pdb=" OH TYR F 111 " pdb=" O LEU G 52 " model vdw 2.325 2.440 nonbonded pdb=" O SER D 241 " pdb=" OG SER D 241 " model vdw 2.350 2.440 ... (remaining 90349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 3.600 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 31.330 Find NCS groups from input model: 0.770 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12040 Z= 0.348 Angle : 0.948 12.128 16422 Z= 0.571 Chirality : 0.058 0.286 1995 Planarity : 0.007 0.061 1953 Dihedral : 13.309 85.452 4179 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.20), residues: 1407 helix: -0.43 (0.15), residues: 1001 sheet: -2.75 (0.55), residues: 84 loop : -4.03 (0.18), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 74 HIS 0.001 0.000 HIS E 134 PHE 0.010 0.001 PHE G 129 TYR 0.009 0.001 TYR E 230 ARG 0.002 0.000 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8764 (tptt) cc_final: 0.8538 (tttt) REVERT: A 75 ARG cc_start: 0.8539 (mmm160) cc_final: 0.8292 (mmt180) REVERT: A 212 LYS cc_start: 0.7283 (mttp) cc_final: 0.7010 (mttp) REVERT: A 326 ASN cc_start: 0.6408 (p0) cc_final: 0.5651 (p0) REVERT: B 36 LYS cc_start: 0.8908 (tptt) cc_final: 0.8494 (tttt) REVERT: B 293 TYR cc_start: 0.9148 (t80) cc_final: 0.8889 (t80) REVERT: B 326 ASN cc_start: 0.6800 (p0) cc_final: 0.5894 (p0) REVERT: B 333 LEU cc_start: 0.8827 (pp) cc_final: 0.8497 (pp) REVERT: C 36 LYS cc_start: 0.8986 (tptt) cc_final: 0.8585 (tttt) REVERT: C 126 PHE cc_start: 0.8798 (t80) cc_final: 0.8498 (t80) REVERT: C 275 LEU cc_start: 0.8998 (tt) cc_final: 0.8666 (tp) REVERT: C 326 ASN cc_start: 0.6433 (p0) cc_final: 0.5564 (p0) REVERT: C 327 ASP cc_start: 0.8749 (m-30) cc_final: 0.8495 (m-30) REVERT: C 333 LEU cc_start: 0.8664 (pp) cc_final: 0.8384 (pp) REVERT: D 36 LYS cc_start: 0.8900 (tptt) cc_final: 0.8631 (tttt) REVERT: D 75 ARG cc_start: 0.8692 (mmm160) cc_final: 0.8270 (mmt180) REVERT: D 326 ASN cc_start: 0.6895 (p0) cc_final: 0.6028 (p0) REVERT: D 331 TYR cc_start: 0.8608 (m-80) cc_final: 0.8374 (m-80) REVERT: D 333 LEU cc_start: 0.8780 (pp) cc_final: 0.8361 (pp) REVERT: E 36 LYS cc_start: 0.8892 (tptt) cc_final: 0.8565 (tttt) REVERT: E 327 ASP cc_start: 0.8831 (m-30) cc_final: 0.8505 (m-30) REVERT: F 36 LYS cc_start: 0.9053 (tptt) cc_final: 0.8542 (tttt) REVERT: F 75 ARG cc_start: 0.8616 (mmm160) cc_final: 0.8296 (mmt180) REVERT: F 208 ASN cc_start: 0.8407 (p0) cc_final: 0.8171 (p0) REVERT: F 212 LYS cc_start: 0.7540 (mttp) cc_final: 0.7196 (mttt) REVERT: F 230 TYR cc_start: 0.9330 (t80) cc_final: 0.9076 (t80) REVERT: F 293 TYR cc_start: 0.9128 (t80) cc_final: 0.8675 (t80) REVERT: G 29 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7837 (mtm180) REVERT: G 36 LYS cc_start: 0.8877 (tptt) cc_final: 0.8609 (tttt) REVERT: G 212 LYS cc_start: 0.7452 (mttp) cc_final: 0.7081 (mttp) REVERT: G 326 ASN cc_start: 0.6795 (p0) cc_final: 0.5933 (p0) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2809 time to fit residues: 130.8615 Evaluate side-chains 251 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 332 ASN B 106 HIS B 332 ASN C 106 HIS D 106 HIS ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS G 106 HIS ** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12040 Z= 0.211 Angle : 0.641 8.211 16422 Z= 0.317 Chirality : 0.040 0.132 1995 Planarity : 0.005 0.049 1953 Dihedral : 4.197 15.618 1554 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.12 % Allowed : 15.42 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1407 helix: 1.00 (0.16), residues: 1008 sheet: -2.55 (0.51), residues: 84 loop : -3.33 (0.22), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 74 HIS 0.001 0.000 HIS C 106 PHE 0.017 0.001 PHE A 299 TYR 0.018 0.001 TYR E 213 ARG 0.003 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 291 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9003 (tptt) cc_final: 0.8601 (tttt) REVERT: A 75 ARG cc_start: 0.8589 (mmm160) cc_final: 0.8367 (mmt180) REVERT: A 212 LYS cc_start: 0.7570 (mttp) cc_final: 0.7249 (mttp) REVERT: A 326 ASN cc_start: 0.6364 (p0) cc_final: 0.5579 (p0) REVERT: B 36 LYS cc_start: 0.9029 (tptt) cc_final: 0.8548 (tttt) REVERT: B 111 TYR cc_start: 0.8549 (m-10) cc_final: 0.8055 (m-10) REVERT: B 326 ASN cc_start: 0.6704 (p0) cc_final: 0.5921 (p0) REVERT: B 333 LEU cc_start: 0.8655 (pp) cc_final: 0.8321 (pp) REVERT: C 36 LYS cc_start: 0.9125 (tptt) cc_final: 0.8718 (tttt) REVERT: C 212 LYS cc_start: 0.7962 (mttp) cc_final: 0.7546 (mttp) REVERT: C 248 ILE cc_start: 0.9107 (pt) cc_final: 0.8861 (tp) REVERT: C 275 LEU cc_start: 0.9056 (tt) cc_final: 0.8656 (tp) REVERT: C 326 ASN cc_start: 0.6377 (p0) cc_final: 0.5570 (p0) REVERT: D 36 LYS cc_start: 0.9133 (tptt) cc_final: 0.8709 (tttt) REVERT: D 75 ARG cc_start: 0.8613 (mmm160) cc_final: 0.8200 (mmt180) REVERT: D 83 TYR cc_start: 0.8621 (t80) cc_final: 0.8130 (t80) REVERT: D 212 LYS cc_start: 0.7744 (mttp) cc_final: 0.7370 (mttp) REVERT: D 276 LEU cc_start: 0.9276 (mt) cc_final: 0.9029 (mt) REVERT: D 326 ASN cc_start: 0.6835 (p0) cc_final: 0.6051 (p0) REVERT: D 333 LEU cc_start: 0.8624 (pp) cc_final: 0.8255 (pp) REVERT: E 36 LYS cc_start: 0.9119 (tptt) cc_final: 0.8632 (tttm) REVERT: E 327 ASP cc_start: 0.8807 (m-30) cc_final: 0.8530 (m-30) REVERT: E 333 LEU cc_start: 0.8722 (pp) cc_final: 0.8379 (pp) REVERT: F 36 LYS cc_start: 0.9155 (tptt) cc_final: 0.8607 (tttt) REVERT: F 75 ARG cc_start: 0.8650 (mmm160) cc_final: 0.8289 (mmt180) REVERT: F 276 LEU cc_start: 0.9282 (mt) cc_final: 0.9065 (mt) REVERT: F 333 LEU cc_start: 0.8693 (pp) cc_final: 0.8397 (pp) REVERT: G 36 LYS cc_start: 0.9092 (tptt) cc_final: 0.8702 (tttt) REVERT: G 75 ARG cc_start: 0.8513 (mmm160) cc_final: 0.8229 (mmt180) REVERT: G 326 ASN cc_start: 0.6670 (p0) cc_final: 0.5921 (p0) REVERT: G 333 LEU cc_start: 0.8678 (pp) cc_final: 0.8446 (pp) REVERT: G 334 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7660 (t80) outliers start: 28 outliers final: 18 residues processed: 307 average time/residue: 0.2856 time to fit residues: 117.4016 Evaluate side-chains 281 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 262 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 ASN G 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12040 Z= 0.175 Angle : 0.605 6.562 16422 Z= 0.295 Chirality : 0.039 0.136 1995 Planarity : 0.005 0.041 1953 Dihedral : 3.852 12.845 1554 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.19 % Allowed : 18.22 % Favored : 79.59 % 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: 0.50 (0.23), residues: 1407 helix: 1.58 (0.17), residues: 1008 sheet: -2.49 (0.49), residues: 84 loop : -3.04 (0.23), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 74 HIS 0.001 0.000 HIS E 106 PHE 0.015 0.001 PHE C 126 TYR 0.019 0.001 TYR G 293 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 300 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9052 (tptt) cc_final: 0.8652 (tttt) REVERT: A 75 ARG cc_start: 0.8534 (mmm160) cc_final: 0.8291 (mmt180) REVERT: A 326 ASN cc_start: 0.6511 (p0) cc_final: 0.5710 (p0) REVERT: B 36 LYS cc_start: 0.9006 (tptt) cc_final: 0.8523 (tttt) REVERT: B 111 TYR cc_start: 0.8518 (m-10) cc_final: 0.8121 (m-10) REVERT: B 213 TYR cc_start: 0.8806 (t80) cc_final: 0.8586 (t80) REVERT: B 326 ASN cc_start: 0.6796 (p0) cc_final: 0.6078 (p0) REVERT: B 333 LEU cc_start: 0.8623 (pp) cc_final: 0.8326 (pp) REVERT: C 36 LYS cc_start: 0.9134 (tptt) cc_final: 0.8719 (tttt) REVERT: C 212 LYS cc_start: 0.8096 (mttp) cc_final: 0.7590 (mttp) REVERT: C 248 ILE cc_start: 0.9090 (pt) cc_final: 0.8874 (tp) REVERT: C 275 LEU cc_start: 0.8986 (tt) cc_final: 0.8585 (tp) REVERT: C 326 ASN cc_start: 0.6467 (p0) cc_final: 0.5765 (p0) REVERT: D 36 LYS cc_start: 0.9124 (tptt) cc_final: 0.8688 (tttt) REVERT: D 75 ARG cc_start: 0.8596 (mmm160) cc_final: 0.8167 (mmt180) REVERT: D 83 TYR cc_start: 0.8603 (t80) cc_final: 0.8070 (t80) REVERT: D 212 LYS cc_start: 0.7826 (mttp) cc_final: 0.7390 (mttp) REVERT: D 326 ASN cc_start: 0.6876 (p0) cc_final: 0.6062 (p0) REVERT: E 36 LYS cc_start: 0.9127 (tptt) cc_final: 0.8663 (tttm) REVERT: E 276 LEU cc_start: 0.9306 (mt) cc_final: 0.9057 (mt) REVERT: F 36 LYS cc_start: 0.9159 (tptt) cc_final: 0.8624 (tttt) REVERT: F 75 ARG cc_start: 0.8658 (mmm160) cc_final: 0.8296 (mmt180) REVERT: F 248 ILE cc_start: 0.9016 (pt) cc_final: 0.8770 (tp) REVERT: F 276 LEU cc_start: 0.9229 (mt) cc_final: 0.9014 (mt) REVERT: G 36 LYS cc_start: 0.9087 (tptt) cc_final: 0.8684 (tttt) REVERT: G 75 ARG cc_start: 0.8476 (mmm160) cc_final: 0.8175 (mmt180) REVERT: G 111 TYR cc_start: 0.8677 (m-10) cc_final: 0.8223 (m-10) REVERT: G 326 ASN cc_start: 0.6812 (p0) cc_final: 0.6038 (p0) REVERT: G 334 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7767 (t80) outliers start: 29 outliers final: 23 residues processed: 312 average time/residue: 0.2645 time to fit residues: 111.9597 Evaluate side-chains 310 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 286 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12040 Z= 0.167 Angle : 0.607 9.941 16422 Z= 0.286 Chirality : 0.039 0.133 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.648 11.952 1554 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.04 % Allowed : 21.47 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1407 helix: 1.83 (0.17), residues: 1001 sheet: -2.36 (0.48), residues: 84 loop : -2.91 (0.24), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS E 106 PHE 0.015 0.001 PHE C 126 TYR 0.019 0.001 TYR B 293 ARG 0.004 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 299 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9086 (tptt) cc_final: 0.8678 (tttt) REVERT: A 75 ARG cc_start: 0.8617 (mmm160) cc_final: 0.8367 (mmt180) REVERT: A 326 ASN cc_start: 0.6634 (p0) cc_final: 0.5821 (p0) REVERT: B 36 LYS cc_start: 0.9008 (tptt) cc_final: 0.8559 (tttt) REVERT: B 111 TYR cc_start: 0.8484 (m-10) cc_final: 0.8086 (m-10) REVERT: B 212 LYS cc_start: 0.7810 (mttp) cc_final: 0.7290 (mttp) REVERT: B 326 ASN cc_start: 0.6802 (p0) cc_final: 0.6074 (p0) REVERT: B 333 LEU cc_start: 0.8645 (pp) cc_final: 0.8409 (pp) REVERT: B 337 GLU cc_start: 0.8117 (pm20) cc_final: 0.7916 (pm20) REVERT: C 36 LYS cc_start: 0.9141 (tptt) cc_final: 0.8717 (tttt) REVERT: C 212 LYS cc_start: 0.7990 (mttp) cc_final: 0.7397 (mttp) REVERT: C 213 TYR cc_start: 0.8805 (t80) cc_final: 0.8528 (t80) REVERT: C 326 ASN cc_start: 0.6510 (p0) cc_final: 0.5835 (p0) REVERT: C 327 ASP cc_start: 0.8621 (m-30) cc_final: 0.8409 (m-30) REVERT: D 36 LYS cc_start: 0.9147 (tptt) cc_final: 0.8703 (tttt) REVERT: D 75 ARG cc_start: 0.8638 (mmm160) cc_final: 0.8226 (mmt180) REVERT: D 83 TYR cc_start: 0.8634 (t80) cc_final: 0.8088 (t80) REVERT: D 111 TYR cc_start: 0.8502 (m-10) cc_final: 0.8025 (m-10) REVERT: D 212 LYS cc_start: 0.7873 (mttp) cc_final: 0.7378 (mttp) REVERT: D 276 LEU cc_start: 0.9194 (mt) cc_final: 0.8932 (mt) REVERT: D 326 ASN cc_start: 0.6657 (p0) cc_final: 0.5887 (p0) REVERT: E 36 LYS cc_start: 0.9114 (tptt) cc_final: 0.8642 (tttm) REVERT: E 276 LEU cc_start: 0.9288 (mt) cc_final: 0.9085 (mt) REVERT: E 327 ASP cc_start: 0.8596 (m-30) cc_final: 0.8354 (m-30) REVERT: F 36 LYS cc_start: 0.9174 (tptt) cc_final: 0.8627 (tttt) REVERT: F 75 ARG cc_start: 0.8693 (mmm160) cc_final: 0.8305 (mmt180) REVERT: F 248 ILE cc_start: 0.9004 (pt) cc_final: 0.8794 (tp) REVERT: F 276 LEU cc_start: 0.9210 (mt) cc_final: 0.9004 (mt) REVERT: G 36 LYS cc_start: 0.9089 (tptt) cc_final: 0.8705 (tttt) REVERT: G 75 ARG cc_start: 0.8495 (mmm160) cc_final: 0.8180 (mmt180) REVERT: G 111 TYR cc_start: 0.8685 (m-10) cc_final: 0.8226 (m-10) REVERT: G 326 ASN cc_start: 0.6980 (p0) cc_final: 0.6156 (p0) REVERT: G 334 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.7778 (t80) outliers start: 27 outliers final: 25 residues processed: 309 average time/residue: 0.2647 time to fit residues: 111.0361 Evaluate side-chains 309 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 283 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12040 Z= 0.361 Angle : 0.696 8.220 16422 Z= 0.335 Chirality : 0.042 0.129 1995 Planarity : 0.004 0.035 1953 Dihedral : 4.041 15.255 1554 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.17 % Allowed : 23.05 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1407 helix: 1.64 (0.17), residues: 1008 sheet: -2.13 (0.52), residues: 84 loop : -2.94 (0.26), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 74 HIS 0.001 0.001 HIS E 106 PHE 0.027 0.001 PHE G 126 TYR 0.021 0.002 TYR B 293 ARG 0.005 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 272 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9138 (tptt) cc_final: 0.8730 (tttt) REVERT: A 75 ARG cc_start: 0.8683 (mmm160) cc_final: 0.8482 (mmt180) REVERT: A 326 ASN cc_start: 0.6946 (p0) cc_final: 0.6231 (p0) REVERT: B 36 LYS cc_start: 0.9014 (tptt) cc_final: 0.8561 (tttt) REVERT: B 212 LYS cc_start: 0.8000 (mttp) cc_final: 0.7449 (mttp) REVERT: B 326 ASN cc_start: 0.7101 (p0) cc_final: 0.6378 (p0) REVERT: C 36 LYS cc_start: 0.9134 (tptt) cc_final: 0.8744 (tttt) REVERT: C 75 ARG cc_start: 0.8674 (mmm160) cc_final: 0.8464 (mmt180) REVERT: C 126 PHE cc_start: 0.8979 (t80) cc_final: 0.8700 (t80) REVERT: C 212 LYS cc_start: 0.8085 (mttp) cc_final: 0.7464 (mttp) REVERT: C 275 LEU cc_start: 0.9159 (tt) cc_final: 0.8711 (tp) REVERT: C 276 LEU cc_start: 0.9255 (mt) cc_final: 0.8795 (mp) REVERT: D 36 LYS cc_start: 0.9121 (tptt) cc_final: 0.8700 (tttt) REVERT: D 75 ARG cc_start: 0.8683 (mmm160) cc_final: 0.8261 (mmt180) REVERT: D 326 ASN cc_start: 0.7149 (p0) cc_final: 0.6323 (p0) REVERT: E 36 LYS cc_start: 0.9079 (tptt) cc_final: 0.8651 (tttt) REVERT: E 326 ASN cc_start: 0.6766 (p0) cc_final: 0.6062 (p0) REVERT: E 327 ASP cc_start: 0.8654 (m-30) cc_final: 0.8293 (m-30) REVERT: F 36 LYS cc_start: 0.9168 (tptt) cc_final: 0.8655 (tttt) REVERT: F 75 ARG cc_start: 0.8725 (mmm160) cc_final: 0.8363 (mmt180) REVERT: F 276 LEU cc_start: 0.9311 (mt) cc_final: 0.9094 (mt) REVERT: F 326 ASN cc_start: 0.7094 (p0) cc_final: 0.6347 (p0) REVERT: G 36 LYS cc_start: 0.9052 (tptt) cc_final: 0.8616 (tttt) REVERT: G 75 ARG cc_start: 0.8645 (mmm160) cc_final: 0.8354 (mmt180) REVERT: G 334 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7948 (t80) outliers start: 42 outliers final: 32 residues processed: 295 average time/residue: 0.2834 time to fit residues: 112.7663 Evaluate side-chains 283 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 250 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12040 Z= 0.192 Angle : 0.614 7.488 16422 Z= 0.293 Chirality : 0.039 0.127 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.758 12.658 1554 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.80 % Allowed : 23.73 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1407 helix: 1.88 (0.17), residues: 1008 sheet: -2.23 (0.49), residues: 84 loop : -2.72 (0.26), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS E 106 PHE 0.025 0.001 PHE G 126 TYR 0.017 0.001 TYR B 293 ARG 0.006 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 285 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9143 (tptt) cc_final: 0.8769 (tttt) REVERT: A 75 ARG cc_start: 0.8632 (mmm160) cc_final: 0.8420 (mmt180) REVERT: A 111 TYR cc_start: 0.8538 (m-10) cc_final: 0.8125 (m-10) REVERT: A 326 ASN cc_start: 0.6879 (p0) cc_final: 0.6208 (p0) REVERT: B 36 LYS cc_start: 0.9015 (tptt) cc_final: 0.8556 (tttt) REVERT: B 75 ARG cc_start: 0.8663 (mmm160) cc_final: 0.8383 (mmt180) REVERT: B 111 TYR cc_start: 0.8609 (m-10) cc_final: 0.8175 (m-10) REVERT: B 212 LYS cc_start: 0.8005 (mttp) cc_final: 0.7469 (mttp) REVERT: B 326 ASN cc_start: 0.6882 (p0) cc_final: 0.6147 (p0) REVERT: C 36 LYS cc_start: 0.9125 (tptt) cc_final: 0.8790 (tttt) REVERT: C 75 ARG cc_start: 0.8644 (mmm160) cc_final: 0.8379 (mmt180) REVERT: C 212 LYS cc_start: 0.8058 (mttp) cc_final: 0.7488 (mttp) REVERT: C 326 ASN cc_start: 0.6701 (p0) cc_final: 0.6002 (p0) REVERT: D 36 LYS cc_start: 0.9130 (tptt) cc_final: 0.8722 (tttt) REVERT: D 75 ARG cc_start: 0.8644 (mmm160) cc_final: 0.8194 (mmt180) REVERT: D 83 TYR cc_start: 0.8687 (t80) cc_final: 0.8014 (t80) REVERT: D 111 TYR cc_start: 0.8595 (m-10) cc_final: 0.8122 (m-10) REVERT: D 212 LYS cc_start: 0.7957 (mttp) cc_final: 0.7394 (mttp) REVERT: D 301 GLN cc_start: 0.7843 (pp30) cc_final: 0.7612 (pp30) REVERT: D 326 ASN cc_start: 0.6917 (p0) cc_final: 0.6085 (p0) REVERT: E 36 LYS cc_start: 0.9064 (tptt) cc_final: 0.8613 (tttt) REVERT: E 326 ASN cc_start: 0.6692 (p0) cc_final: 0.6020 (p0) REVERT: E 327 ASP cc_start: 0.8539 (m-30) cc_final: 0.8267 (m-30) REVERT: F 36 LYS cc_start: 0.9150 (tptt) cc_final: 0.8635 (tttt) REVERT: F 75 ARG cc_start: 0.8646 (mmm160) cc_final: 0.8261 (mmt180) REVERT: F 276 LEU cc_start: 0.9261 (mt) cc_final: 0.9033 (mt) REVERT: F 301 GLN cc_start: 0.7946 (pp30) cc_final: 0.7721 (pp30) REVERT: F 326 ASN cc_start: 0.6974 (p0) cc_final: 0.6203 (p0) REVERT: G 36 LYS cc_start: 0.9097 (tptt) cc_final: 0.8689 (tttt) REVERT: G 75 ARG cc_start: 0.8619 (mmm160) cc_final: 0.8329 (mmt180) REVERT: G 111 TYR cc_start: 0.8709 (m-10) cc_final: 0.8239 (m-10) REVERT: G 212 LYS cc_start: 0.7816 (mttp) cc_final: 0.7500 (mttp) REVERT: G 301 GLN cc_start: 0.7906 (pp30) cc_final: 0.7625 (pp30) REVERT: G 326 ASN cc_start: 0.7145 (OUTLIER) cc_final: 0.6715 (p0) REVERT: G 334 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7890 (t80) outliers start: 37 outliers final: 32 residues processed: 301 average time/residue: 0.2729 time to fit residues: 110.7981 Evaluate side-chains 300 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 266 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 98 optimal weight: 0.0970 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 134 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12040 Z= 0.189 Angle : 0.606 7.116 16422 Z= 0.289 Chirality : 0.039 0.129 1995 Planarity : 0.004 0.035 1953 Dihedral : 3.638 11.741 1554 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.25 % Allowed : 24.41 % Favored : 72.34 % 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: 1.16 (0.23), residues: 1407 helix: 1.98 (0.17), residues: 1008 sheet: -2.08 (0.50), residues: 84 loop : -2.54 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 85 HIS 0.001 0.000 HIS E 106 PHE 0.023 0.001 PHE G 126 TYR 0.024 0.001 TYR B 293 ARG 0.006 0.001 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 281 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9131 (tptt) cc_final: 0.8756 (tttt) REVERT: A 75 ARG cc_start: 0.8665 (mmm160) cc_final: 0.8456 (mmt180) REVERT: A 326 ASN cc_start: 0.6879 (p0) cc_final: 0.6212 (p0) REVERT: B 36 LYS cc_start: 0.8973 (tptt) cc_final: 0.8532 (tttt) REVERT: B 75 ARG cc_start: 0.8665 (mmm160) cc_final: 0.8374 (mmt180) REVERT: B 111 TYR cc_start: 0.8571 (m-10) cc_final: 0.8184 (m-10) REVERT: B 212 LYS cc_start: 0.8005 (mttp) cc_final: 0.7473 (mttp) REVERT: B 326 ASN cc_start: 0.6755 (p0) cc_final: 0.6048 (p0) REVERT: C 36 LYS cc_start: 0.9120 (tptt) cc_final: 0.8778 (tttt) REVERT: C 75 ARG cc_start: 0.8682 (mmm160) cc_final: 0.8423 (mmt180) REVERT: C 212 LYS cc_start: 0.8013 (mttp) cc_final: 0.7446 (mttp) REVERT: C 248 ILE cc_start: 0.9133 (pt) cc_final: 0.8748 (tp) REVERT: C 326 ASN cc_start: 0.6676 (p0) cc_final: 0.6031 (p0) REVERT: D 36 LYS cc_start: 0.9123 (tptt) cc_final: 0.8724 (tttt) REVERT: D 75 ARG cc_start: 0.8730 (mmm160) cc_final: 0.8323 (mmt180) REVERT: D 111 TYR cc_start: 0.8602 (m-10) cc_final: 0.8075 (m-10) REVERT: D 212 LYS cc_start: 0.8013 (mttp) cc_final: 0.7420 (mttp) REVERT: D 326 ASN cc_start: 0.6775 (p0) cc_final: 0.6010 (p0) REVERT: E 36 LYS cc_start: 0.9045 (tptt) cc_final: 0.8624 (tttt) REVERT: E 268 ILE cc_start: 0.9225 (mm) cc_final: 0.8991 (mm) REVERT: E 326 ASN cc_start: 0.6738 (p0) cc_final: 0.6079 (p0) REVERT: F 36 LYS cc_start: 0.9135 (tptt) cc_final: 0.8634 (tttt) REVERT: F 75 ARG cc_start: 0.8657 (mmm160) cc_final: 0.8232 (mmt180) REVERT: F 276 LEU cc_start: 0.9230 (mt) cc_final: 0.8999 (mt) REVERT: F 301 GLN cc_start: 0.7881 (pp30) cc_final: 0.7612 (pp30) REVERT: F 326 ASN cc_start: 0.6986 (p0) cc_final: 0.6223 (p0) REVERT: G 36 LYS cc_start: 0.9084 (tptt) cc_final: 0.8683 (tttt) REVERT: G 75 ARG cc_start: 0.8617 (mmm160) cc_final: 0.8329 (mmt180) REVERT: G 111 TYR cc_start: 0.8705 (m-10) cc_final: 0.8211 (m-10) REVERT: G 301 GLN cc_start: 0.7909 (pp30) cc_final: 0.7598 (pp30) REVERT: G 326 ASN cc_start: 0.7145 (OUTLIER) cc_final: 0.6795 (p0) REVERT: G 334 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7972 (t80) outliers start: 43 outliers final: 36 residues processed: 302 average time/residue: 0.2748 time to fit residues: 111.8048 Evaluate side-chains 301 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 263 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12040 Z= 0.177 Angle : 0.608 7.251 16422 Z= 0.289 Chirality : 0.038 0.128 1995 Planarity : 0.004 0.035 1953 Dihedral : 3.557 11.676 1554 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.48 % Allowed : 25.09 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.23), residues: 1407 helix: 2.04 (0.17), residues: 1008 sheet: -1.87 (0.51), residues: 84 loop : -2.37 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 85 HIS 0.001 0.000 HIS E 106 PHE 0.024 0.001 PHE C 126 TYR 0.025 0.001 TYR B 293 ARG 0.007 0.001 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 283 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9110 (tptt) cc_final: 0.8718 (tttt) REVERT: A 75 ARG cc_start: 0.8664 (mmm160) cc_final: 0.8460 (mmt180) REVERT: A 111 TYR cc_start: 0.8454 (m-10) cc_final: 0.8234 (m-10) REVERT: A 326 ASN cc_start: 0.6636 (p0) cc_final: 0.5981 (p0) REVERT: B 36 LYS cc_start: 0.8971 (tptt) cc_final: 0.8534 (tttt) REVERT: B 75 ARG cc_start: 0.8640 (mmm160) cc_final: 0.8373 (mmt180) REVERT: B 111 TYR cc_start: 0.8571 (m-10) cc_final: 0.8178 (m-10) REVERT: B 212 LYS cc_start: 0.7995 (mttp) cc_final: 0.7455 (mttp) REVERT: B 255 ASN cc_start: 0.8986 (p0) cc_final: 0.8746 (p0) REVERT: B 326 ASN cc_start: 0.6688 (p0) cc_final: 0.6035 (p0) REVERT: C 36 LYS cc_start: 0.9096 (tptt) cc_final: 0.8759 (tttt) REVERT: C 75 ARG cc_start: 0.8655 (mmm160) cc_final: 0.8405 (mmt180) REVERT: C 212 LYS cc_start: 0.8011 (mttp) cc_final: 0.7450 (mttp) REVERT: C 213 TYR cc_start: 0.8808 (t80) cc_final: 0.8406 (t80) REVERT: C 248 ILE cc_start: 0.9023 (pt) cc_final: 0.8787 (tp) REVERT: C 326 ASN cc_start: 0.6754 (p0) cc_final: 0.6109 (p0) REVERT: D 36 LYS cc_start: 0.9112 (tptt) cc_final: 0.8719 (tttt) REVERT: D 75 ARG cc_start: 0.8679 (mmm160) cc_final: 0.8227 (mmt180) REVERT: D 111 TYR cc_start: 0.8616 (m-10) cc_final: 0.8174 (m-10) REVERT: D 212 LYS cc_start: 0.8002 (mttp) cc_final: 0.7525 (mttp) REVERT: D 276 LEU cc_start: 0.9206 (mt) cc_final: 0.8950 (mt) REVERT: D 301 GLN cc_start: 0.7875 (pp30) cc_final: 0.7481 (pp30) REVERT: D 326 ASN cc_start: 0.6672 (p0) cc_final: 0.5891 (p0) REVERT: E 36 LYS cc_start: 0.9055 (tptt) cc_final: 0.8615 (tttt) REVERT: E 126 PHE cc_start: 0.8957 (t80) cc_final: 0.8625 (t80) REVERT: E 326 ASN cc_start: 0.6684 (p0) cc_final: 0.6012 (p0) REVERT: F 36 LYS cc_start: 0.9126 (tptt) cc_final: 0.8626 (tttt) REVERT: F 75 ARG cc_start: 0.8686 (mmm160) cc_final: 0.8159 (mmt180) REVERT: F 248 ILE cc_start: 0.9035 (pt) cc_final: 0.8759 (tp) REVERT: F 276 LEU cc_start: 0.9214 (mt) cc_final: 0.9013 (mt) REVERT: F 326 ASN cc_start: 0.7017 (p0) cc_final: 0.6286 (p0) REVERT: G 36 LYS cc_start: 0.9075 (tptt) cc_final: 0.8669 (tttt) REVERT: G 75 ARG cc_start: 0.8673 (mmm160) cc_final: 0.8369 (mmt180) REVERT: G 81 ASP cc_start: 0.7598 (m-30) cc_final: 0.6999 (m-30) REVERT: G 111 TYR cc_start: 0.8697 (m-10) cc_final: 0.8233 (m-10) REVERT: G 301 GLN cc_start: 0.7938 (pp30) cc_final: 0.7534 (pp30) REVERT: G 326 ASN cc_start: 0.7163 (OUTLIER) cc_final: 0.6778 (p0) REVERT: G 334 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7966 (t80) outliers start: 46 outliers final: 41 residues processed: 301 average time/residue: 0.2877 time to fit residues: 115.8582 Evaluate side-chains 317 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 274 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12040 Z= 0.228 Angle : 0.631 7.675 16422 Z= 0.301 Chirality : 0.039 0.130 1995 Planarity : 0.004 0.034 1953 Dihedral : 3.642 11.622 1554 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.48 % Allowed : 25.47 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.23), residues: 1407 helix: 1.97 (0.17), residues: 1008 sheet: -1.78 (0.52), residues: 84 loop : -2.29 (0.28), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 85 HIS 0.001 0.000 HIS E 106 PHE 0.026 0.001 PHE G 126 TYR 0.026 0.001 TYR B 293 ARG 0.007 0.001 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 266 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9121 (tptt) cc_final: 0.8733 (tttt) REVERT: A 111 TYR cc_start: 0.8567 (m-10) cc_final: 0.8069 (m-10) REVERT: A 326 ASN cc_start: 0.6798 (p0) cc_final: 0.6151 (p0) REVERT: B 36 LYS cc_start: 0.8964 (tptt) cc_final: 0.8536 (tttt) REVERT: B 75 ARG cc_start: 0.8649 (mmm160) cc_final: 0.8440 (mmt180) REVERT: B 111 TYR cc_start: 0.8601 (m-10) cc_final: 0.8200 (m-10) REVERT: B 212 LYS cc_start: 0.8013 (mttp) cc_final: 0.7468 (mttp) REVERT: B 255 ASN cc_start: 0.8994 (p0) cc_final: 0.8733 (p0) REVERT: B 326 ASN cc_start: 0.6870 (p0) cc_final: 0.6217 (p0) REVERT: C 36 LYS cc_start: 0.9099 (tptt) cc_final: 0.8766 (tttt) REVERT: C 75 ARG cc_start: 0.8669 (mmm160) cc_final: 0.8423 (mmt180) REVERT: C 212 LYS cc_start: 0.7969 (mttp) cc_final: 0.7415 (mttp) REVERT: C 326 ASN cc_start: 0.6934 (p0) cc_final: 0.6289 (p0) REVERT: D 36 LYS cc_start: 0.9113 (tptt) cc_final: 0.8719 (tttt) REVERT: D 75 ARG cc_start: 0.8681 (mmm160) cc_final: 0.8237 (mmt180) REVERT: D 212 LYS cc_start: 0.8079 (mttp) cc_final: 0.7586 (mttp) REVERT: D 301 GLN cc_start: 0.8022 (pp30) cc_final: 0.7609 (pp30) REVERT: D 326 ASN cc_start: 0.6798 (p0) cc_final: 0.5997 (p0) REVERT: E 36 LYS cc_start: 0.9053 (tptt) cc_final: 0.8631 (tttt) REVERT: E 326 ASN cc_start: 0.6761 (p0) cc_final: 0.6061 (p0) REVERT: F 36 LYS cc_start: 0.9132 (tptt) cc_final: 0.8645 (tttt) REVERT: F 75 ARG cc_start: 0.8695 (mmm160) cc_final: 0.8266 (mmt180) REVERT: F 248 ILE cc_start: 0.9086 (pt) cc_final: 0.8814 (tp) REVERT: F 276 LEU cc_start: 0.9234 (mt) cc_final: 0.9011 (mt) REVERT: F 326 ASN cc_start: 0.7071 (p0) cc_final: 0.6358 (p0) REVERT: G 36 LYS cc_start: 0.9057 (tptt) cc_final: 0.8652 (tttt) REVERT: G 75 ARG cc_start: 0.8639 (mmm160) cc_final: 0.8308 (mmt180) REVERT: G 81 ASP cc_start: 0.7691 (m-30) cc_final: 0.7173 (m-30) REVERT: G 111 TYR cc_start: 0.8717 (m-10) cc_final: 0.8230 (m-10) REVERT: G 301 GLN cc_start: 0.7868 (pp30) cc_final: 0.7456 (pp30) REVERT: G 326 ASN cc_start: 0.7085 (OUTLIER) cc_final: 0.6670 (p0) REVERT: G 334 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8027 (t80) outliers start: 46 outliers final: 41 residues processed: 288 average time/residue: 0.2849 time to fit residues: 109.7983 Evaluate side-chains 304 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 261 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 128 optimal weight: 0.0270 chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12040 Z= 0.167 Angle : 0.609 7.435 16422 Z= 0.290 Chirality : 0.038 0.128 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.472 10.846 1554 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.48 % Allowed : 25.32 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.23), residues: 1407 helix: 2.10 (0.17), residues: 1008 sheet: -1.72 (0.52), residues: 84 loop : -2.14 (0.28), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 85 HIS 0.001 0.000 HIS E 106 PHE 0.026 0.001 PHE C 126 TYR 0.026 0.001 TYR B 293 ARG 0.006 0.001 ARG E 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 293 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9101 (tptt) cc_final: 0.8727 (tttt) REVERT: A 111 TYR cc_start: 0.8479 (m-10) cc_final: 0.8077 (m-10) REVERT: A 326 ASN cc_start: 0.6587 (p0) cc_final: 0.5879 (p0) REVERT: B 36 LYS cc_start: 0.8930 (tptt) cc_final: 0.8549 (tttt) REVERT: B 75 ARG cc_start: 0.8630 (mmm160) cc_final: 0.8405 (mmt180) REVERT: B 111 TYR cc_start: 0.8561 (m-10) cc_final: 0.8173 (m-10) REVERT: B 255 ASN cc_start: 0.9033 (p0) cc_final: 0.8822 (p0) REVERT: B 326 ASN cc_start: 0.6549 (p0) cc_final: 0.5923 (p0) REVERT: C 36 LYS cc_start: 0.9087 (tptt) cc_final: 0.8756 (tttt) REVERT: C 75 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8393 (mmt180) REVERT: C 212 LYS cc_start: 0.7970 (mttp) cc_final: 0.7414 (mttp) REVERT: C 326 ASN cc_start: 0.6777 (p0) cc_final: 0.6163 (p0) REVERT: D 36 LYS cc_start: 0.9090 (tptt) cc_final: 0.8715 (tttt) REVERT: D 75 ARG cc_start: 0.8679 (mmm160) cc_final: 0.8126 (mmt180) REVERT: D 212 LYS cc_start: 0.8010 (mttp) cc_final: 0.7521 (mttp) REVERT: D 276 LEU cc_start: 0.9185 (mt) cc_final: 0.8950 (mt) REVERT: D 301 GLN cc_start: 0.8005 (pp30) cc_final: 0.7538 (pp30) REVERT: D 326 ASN cc_start: 0.6629 (p0) cc_final: 0.5867 (p0) REVERT: E 36 LYS cc_start: 0.9032 (tptt) cc_final: 0.8647 (tttt) REVERT: E 81 ASP cc_start: 0.7670 (m-30) cc_final: 0.7088 (m-30) REVERT: E 126 PHE cc_start: 0.8905 (t80) cc_final: 0.8648 (t80) REVERT: E 276 LEU cc_start: 0.9222 (mt) cc_final: 0.8953 (mt) REVERT: E 326 ASN cc_start: 0.6690 (p0) cc_final: 0.6018 (p0) REVERT: F 36 LYS cc_start: 0.9095 (tptt) cc_final: 0.8667 (tttt) REVERT: F 75 ARG cc_start: 0.8663 (mmm160) cc_final: 0.8206 (mmt180) REVERT: F 111 TYR cc_start: 0.8617 (m-10) cc_final: 0.7814 (m-10) REVERT: F 248 ILE cc_start: 0.9028 (pt) cc_final: 0.8769 (tp) REVERT: F 326 ASN cc_start: 0.6962 (p0) cc_final: 0.6239 (p0) REVERT: G 36 LYS cc_start: 0.9052 (tptt) cc_final: 0.8655 (tttt) REVERT: G 75 ARG cc_start: 0.8604 (mmm160) cc_final: 0.8245 (mmt180) REVERT: G 81 ASP cc_start: 0.7519 (m-30) cc_final: 0.7107 (m-30) REVERT: G 111 TYR cc_start: 0.8683 (m-10) cc_final: 0.8194 (m-10) REVERT: G 301 GLN cc_start: 0.7774 (pp30) cc_final: 0.7427 (pp30) REVERT: G 326 ASN cc_start: 0.7017 (OUTLIER) cc_final: 0.6666 (p0) REVERT: G 334 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.7998 (t80) outliers start: 46 outliers final: 40 residues processed: 312 average time/residue: 0.2721 time to fit residues: 114.4752 Evaluate side-chains 322 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 280 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 97 optimal weight: 0.0370 chunk 6 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.089655 restraints weight = 19559.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.091957 restraints weight = 10471.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.093276 restraints weight = 7378.010| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12040 Z= 0.166 Angle : 0.610 7.280 16422 Z= 0.290 Chirality : 0.038 0.129 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.405 10.588 1554 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.17 % Allowed : 25.55 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1407 helix: 2.15 (0.17), residues: 994 sheet: -1.54 (0.52), residues: 84 loop : -2.09 (0.28), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 85 HIS 0.001 0.000 HIS E 106 PHE 0.031 0.001 PHE G 126 TYR 0.027 0.001 TYR B 293 ARG 0.006 0.000 ARG E 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2560.34 seconds wall clock time: 47 minutes 50.65 seconds (2870.65 seconds total)