Starting phenix.real_space_refine on Sat Mar 16 00:59:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byi_16326/03_2024/8byi_16326_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byi_16326/03_2024/8byi_16326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byi_16326/03_2024/8byi_16326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byi_16326/03_2024/8byi_16326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byi_16326/03_2024/8byi_16326_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byi_16326/03_2024/8byi_16326_trim_updated.pdb" } resolution = 4.1 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: 5 Type Number sf(0) Gaussians S 85 5.16 5 Na 2 4.78 5 C 8550 2.51 5 N 2075 2.21 5 O 2319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13031 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2548 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2548 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2548 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2548 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2548 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' NA': 1, 'CPS': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CPS': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' NA': 1, 'CPS': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CPS': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CPS': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.96, per 1000 atoms: 0.53 Number of scatterers: 13031 At special positions: 0 Unit cell: (91.494, 91.494, 121.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 Na 2 11.00 O 2319 8.00 N 2075 7.00 C 8550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 167 " " NAG B 501 " - " ASN B 167 " " NAG C 501 " - " ASN C 167 " " NAG D 501 " - " ASN D 167 " " NAG E 502 " - " ASN E 167 " Time building additional restraints: 4.99 Conformation dependent library (CDL) restraints added in 2.0 seconds 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 25 sheets defined 30.9% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 221 through 225 removed outlier: 4.273A pdb=" N PHE A 225 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 249 through 270 Processing helix chain 'A' and resid 280 through 301 Processing helix chain 'A' and resid 417 through 442 Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 221 through 225 removed outlier: 4.272A pdb=" N PHE B 225 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 249 through 270 Processing helix chain 'B' and resid 280 through 301 Processing helix chain 'B' and resid 417 through 442 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 221 through 225 removed outlier: 4.273A pdb=" N PHE C 225 " --> pdb=" O GLN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 241 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 249 through 270 Processing helix chain 'C' and resid 280 through 301 Processing helix chain 'C' and resid 417 through 442 Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 221 through 225 removed outlier: 4.272A pdb=" N PHE D 225 " --> pdb=" O GLN D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 249 through 270 Processing helix chain 'D' and resid 280 through 301 Processing helix chain 'D' and resid 417 through 442 Processing helix chain 'E' and resid 13 through 21 Processing helix chain 'E' and resid 221 through 225 removed outlier: 4.273A pdb=" N PHE E 225 " --> pdb=" O GLN E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 241 Proline residue: E 240 - end of helix Processing helix chain 'E' and resid 249 through 270 Processing helix chain 'E' and resid 280 through 301 Processing helix chain 'E' and resid 417 through 442 Processing sheet with id= A, first strand: chain 'A' and resid 166 through 169 removed outlier: 7.083A pdb=" N VAL A 39 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR A 169 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL A 41 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 131 through 137 removed outlier: 3.620A pdb=" N ALA A 132 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN A 63 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL A 50 " --> pdb=" O ASN A 63 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= D, first strand: chain 'A' and resid 149 through 156 Processing sheet with id= E, first strand: chain 'A' and resid 193 through 197 Processing sheet with id= F, first strand: chain 'B' and resid 166 through 169 removed outlier: 7.083A pdb=" N VAL B 39 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR B 169 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 41 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 131 through 137 removed outlier: 3.621A pdb=" N ALA B 132 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN B 63 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL B 50 " --> pdb=" O ASN B 63 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= I, first strand: chain 'B' and resid 149 through 156 Processing sheet with id= J, first strand: chain 'B' and resid 193 through 197 Processing sheet with id= K, first strand: chain 'C' and resid 166 through 169 removed outlier: 7.084A pdb=" N VAL C 39 " --> pdb=" O ASN C 167 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR C 169 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 41 " --> pdb=" O THR C 169 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 131 through 137 removed outlier: 3.620A pdb=" N ALA C 132 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN C 63 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL C 50 " --> pdb=" O ASN C 63 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= N, first strand: chain 'C' and resid 149 through 156 Processing sheet with id= O, first strand: chain 'C' and resid 193 through 197 Processing sheet with id= P, first strand: chain 'D' and resid 166 through 169 removed outlier: 7.083A pdb=" N VAL D 39 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR D 169 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL D 41 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 131 through 137 removed outlier: 3.620A pdb=" N ALA D 132 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN D 63 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL D 50 " --> pdb=" O ASN D 63 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 87 through 90 Processing sheet with id= S, first strand: chain 'D' and resid 149 through 156 Processing sheet with id= T, first strand: chain 'D' and resid 193 through 197 Processing sheet with id= U, first strand: chain 'E' and resid 166 through 169 removed outlier: 7.082A pdb=" N VAL E 39 " --> pdb=" O ASN E 167 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR E 169 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL E 41 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 131 through 137 removed outlier: 3.621A pdb=" N ALA E 132 " --> pdb=" O GLY E 64 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN E 63 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL E 50 " --> pdb=" O ASN E 63 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 87 through 90 Processing sheet with id= X, first strand: chain 'E' and resid 149 through 156 Processing sheet with id= Y, first strand: chain 'E' and resid 193 through 197 560 hydrogen bonds defined for protein. 1575 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: 3.68 Time building geometry restraints manager: 5.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1975 1.32 - 1.45: 3753 1.45 - 1.58: 7407 1.58 - 1.71: 80 1.71 - 1.84: 145 Bond restraints: 13360 Sorted by residual: bond pdb=" C20 CPS D 502 " pdb=" C9 CPS D 502 " ideal model delta sigma weight residual 1.536 1.381 0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C20 CPS B 502 " pdb=" C9 CPS B 502 " ideal model delta sigma weight residual 1.536 1.381 0.155 2.00e-02 2.50e+03 6.01e+01 bond pdb=" C20 CPS E 501 " pdb=" C9 CPS E 501 " ideal model delta sigma weight residual 1.536 1.381 0.155 2.00e-02 2.50e+03 5.97e+01 bond pdb=" C20 CPS A 502 " pdb=" C9 CPS A 502 " ideal model delta sigma weight residual 1.536 1.382 0.154 2.00e-02 2.50e+03 5.93e+01 bond pdb=" C20 CPS C 502 " pdb=" C9 CPS C 502 " ideal model delta sigma weight residual 1.536 1.382 0.154 2.00e-02 2.50e+03 5.90e+01 ... (remaining 13355 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.53: 436 106.53 - 113.40: 7533 113.40 - 120.26: 4470 120.26 - 127.13: 5700 127.13 - 134.00: 171 Bond angle restraints: 18310 Sorted by residual: angle pdb=" O1S CPS A 502 " pdb=" S CPS A 502 " pdb=" O3S CPS A 502 " ideal model delta sigma weight residual 113.37 101.14 12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O1S CPS D 502 " pdb=" S CPS D 502 " pdb=" O3S CPS D 502 " ideal model delta sigma weight residual 113.37 101.15 12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O1S CPS B 502 " pdb=" S CPS B 502 " pdb=" O3S CPS B 502 " ideal model delta sigma weight residual 113.37 101.16 12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O1S CPS E 501 " pdb=" S CPS E 501 " pdb=" O3S CPS E 501 " ideal model delta sigma weight residual 113.37 101.21 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O1S CPS C 502 " pdb=" S CPS C 502 " pdb=" O3S CPS C 502 " ideal model delta sigma weight residual 113.37 101.22 12.15 3.00e+00 1.11e-01 1.64e+01 ... (remaining 18305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.11: 7810 19.11 - 38.23: 245 38.23 - 57.34: 70 57.34 - 76.46: 10 76.46 - 95.57: 30 Dihedral angle restraints: 8165 sinusoidal: 3410 harmonic: 4755 Sorted by residual: dihedral pdb=" CA PHE A 145 " pdb=" C PHE A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta harmonic sigma weight residual 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE B 145 " pdb=" C PHE B 145 " pdb=" N PRO B 146 " pdb=" CA PRO B 146 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA PHE E 145 " pdb=" C PHE E 145 " pdb=" N PRO E 146 " pdb=" CA PRO E 146 " ideal model delta harmonic sigma weight residual 180.00 154.54 25.46 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 8162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.700: 2175 0.700 - 1.400: 0 1.400 - 2.099: 10 2.099 - 2.799: 0 2.799 - 3.499: 5 Chirality restraints: 2190 Sorted by residual: chirality pdb=" C18 CPS D 502 " pdb=" C17 CPS D 502 " pdb=" C19 CPS D 502 " pdb=" C6 CPS D 502 " both_signs ideal model delta sigma weight residual False 2.51 -0.99 3.50 2.00e-01 2.50e+01 3.06e+02 chirality pdb=" C18 CPS B 502 " pdb=" C17 CPS B 502 " pdb=" C19 CPS B 502 " pdb=" C6 CPS B 502 " both_signs ideal model delta sigma weight residual False 2.51 -0.99 3.50 2.00e-01 2.50e+01 3.06e+02 chirality pdb=" C18 CPS C 502 " pdb=" C17 CPS C 502 " pdb=" C19 CPS C 502 " pdb=" C6 CPS C 502 " both_signs ideal model delta sigma weight residual False 2.51 -0.99 3.49 2.00e-01 2.50e+01 3.05e+02 ... (remaining 2187 not shown) Planarity restraints: 2205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 145 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO E 146 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 146 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 146 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 145 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO B 146 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 145 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO D 146 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " 0.021 5.00e-02 4.00e+02 ... (remaining 2202 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 202 2.69 - 3.24: 13008 3.24 - 3.79: 20039 3.79 - 4.35: 25630 4.35 - 4.90: 43075 Nonbonded interactions: 101954 Sorted by model distance: nonbonded pdb=" O HOH A 602 " pdb=" O HOH E 601 " model vdw 2.132 2.440 nonbonded pdb=" O HOH D 601 " pdb=" O HOH E 601 " model vdw 2.137 2.440 nonbonded pdb=" O HOH A 602 " pdb=" O HOH D 601 " model vdw 2.137 2.440 nonbonded pdb=" O HOH A 601 " pdb=" O HOH E 602 " model vdw 2.143 2.440 nonbonded pdb=" O HOH C 601 " pdb=" O HOH D 601 " model vdw 2.199 2.440 ... (remaining 101949 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' and resid 11 through 443) selection = (chain 'B' and resid 11 through 443) selection = (chain 'C' and resid 11 through 443) selection = (chain 'D' and resid 11 through 443) selection = (chain 'E' and resid 11 through 443) } 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.290 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 34.480 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.060 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.009 0.155 13360 Z= 0.573 Angle : 0.725 12.228 18310 Z= 0.290 Chirality : 0.207 3.499 2190 Planarity : 0.003 0.036 2200 Dihedral : 12.071 95.575 5080 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % 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: 1.89 (0.22), residues: 1580 helix: 4.12 (0.21), residues: 490 sheet: 0.87 (0.29), residues: 365 loop : -0.63 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 70 HIS 0.007 0.001 HIS E 442 PHE 0.008 0.001 PHE B 289 TYR 0.007 0.001 TYR C 67 ARG 0.001 0.000 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 1.363 Fit side-chains REVERT: A 19 LYS cc_start: 0.8238 (tptp) cc_final: 0.7680 (tmmt) REVERT: A 57 GLU cc_start: 0.7772 (tp30) cc_final: 0.7434 (tp30) REVERT: A 82 TYR cc_start: 0.8317 (m-80) cc_final: 0.8051 (m-80) REVERT: A 170 LEU cc_start: 0.8407 (mt) cc_final: 0.8108 (mm) REVERT: A 178 TYR cc_start: 0.6642 (p90) cc_final: 0.6426 (p90) REVERT: A 234 PHE cc_start: 0.7650 (t80) cc_final: 0.7446 (t80) REVERT: A 237 LEU cc_start: 0.7829 (mt) cc_final: 0.7612 (tp) REVERT: A 279 PRO cc_start: 0.7666 (Cg_endo) cc_final: 0.7403 (Cg_exo) REVERT: A 288 VAL cc_start: 0.8943 (p) cc_final: 0.8694 (p) REVERT: B 11 MET cc_start: 0.6578 (ptp) cc_final: 0.6337 (ptm) REVERT: B 16 ARG cc_start: 0.7336 (ttp-170) cc_final: 0.7023 (ttp80) REVERT: B 34 ASN cc_start: 0.7303 (m-40) cc_final: 0.7082 (m-40) REVERT: B 46 THR cc_start: 0.9261 (m) cc_final: 0.8901 (p) REVERT: B 56 LYS cc_start: 0.8238 (mtmt) cc_final: 0.7920 (mttm) REVERT: B 86 LYS cc_start: 0.7987 (tppt) cc_final: 0.7753 (mmtt) REVERT: B 170 LEU cc_start: 0.8348 (mt) cc_final: 0.8084 (mm) REVERT: B 234 PHE cc_start: 0.7632 (t80) cc_final: 0.7258 (t80) REVERT: B 279 PRO cc_start: 0.7691 (Cg_endo) cc_final: 0.7359 (Cg_exo) REVERT: B 288 VAL cc_start: 0.8937 (p) cc_final: 0.8665 (p) REVERT: C 19 LYS cc_start: 0.8328 (tptp) cc_final: 0.7732 (tmmt) REVERT: C 46 THR cc_start: 0.9133 (m) cc_final: 0.8920 (p) REVERT: C 56 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7841 (mttm) REVERT: C 82 TYR cc_start: 0.8397 (m-80) cc_final: 0.7957 (m-80) REVERT: C 226 ILE cc_start: 0.7894 (mt) cc_final: 0.7495 (mm) REVERT: D 11 MET cc_start: 0.6353 (ptp) cc_final: 0.6124 (ptm) REVERT: D 16 ARG cc_start: 0.7447 (ttp-170) cc_final: 0.7211 (ttp80) REVERT: D 19 LYS cc_start: 0.8269 (tptp) cc_final: 0.7588 (tmmt) REVERT: D 46 THR cc_start: 0.9246 (m) cc_final: 0.9036 (p) REVERT: D 56 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7793 (mttp) REVERT: D 57 GLU cc_start: 0.8007 (tp30) cc_final: 0.7687 (tp30) REVERT: D 61 THR cc_start: 0.7846 (p) cc_final: 0.7632 (p) REVERT: D 170 LEU cc_start: 0.8377 (mt) cc_final: 0.8156 (mm) REVERT: D 279 PRO cc_start: 0.7566 (Cg_endo) cc_final: 0.7144 (Cg_exo) REVERT: E 13 ASP cc_start: 0.8017 (p0) cc_final: 0.7784 (m-30) REVERT: E 19 LYS cc_start: 0.8356 (tptp) cc_final: 0.7774 (tmmt) REVERT: E 56 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7940 (mttm) REVERT: E 82 TYR cc_start: 0.8344 (m-80) cc_final: 0.8035 (m-80) REVERT: E 86 LYS cc_start: 0.7981 (tppt) cc_final: 0.7752 (mmtt) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.2618 time to fit residues: 164.4858 Evaluate side-chains 300 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.0970 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 0.0070 chunk 64 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 HIS B 186 GLN B 295 ASN C 68 HIS ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13360 Z= 0.192 Angle : 0.554 8.548 18310 Z= 0.278 Chirality : 0.044 0.171 2190 Planarity : 0.004 0.042 2200 Dihedral : 7.139 63.135 2260 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % 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: 1.03 (0.21), residues: 1580 helix: 2.38 (0.22), residues: 515 sheet: 0.63 (0.26), residues: 420 loop : -0.67 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 65 HIS 0.007 0.002 HIS A 442 PHE 0.022 0.002 PHE D 289 TYR 0.018 0.001 TYR E 284 ARG 0.004 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 358 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8207 (tptp) cc_final: 0.7713 (tmmt) REVERT: A 234 PHE cc_start: 0.7434 (t80) cc_final: 0.7233 (t80) REVERT: B 16 ARG cc_start: 0.7273 (ttp-170) cc_final: 0.6904 (ttp80) REVERT: B 56 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7884 (mmtt) REVERT: B 184 GLU cc_start: 0.7333 (pt0) cc_final: 0.6551 (mt-10) REVERT: B 234 PHE cc_start: 0.7313 (t80) cc_final: 0.6975 (t80) REVERT: C 13 ASP cc_start: 0.7875 (p0) cc_final: 0.7403 (m-30) REVERT: C 19 LYS cc_start: 0.8369 (tptp) cc_final: 0.7803 (tmmt) REVERT: C 52 ASP cc_start: 0.7947 (t0) cc_final: 0.7712 (t0) REVERT: C 57 GLU cc_start: 0.7525 (tp30) cc_final: 0.7180 (tp30) REVERT: C 165 SER cc_start: 0.7555 (t) cc_final: 0.7235 (p) REVERT: C 226 ILE cc_start: 0.8033 (mt) cc_final: 0.7361 (mm) REVERT: D 19 LYS cc_start: 0.8308 (tptp) cc_final: 0.7684 (tmmt) REVERT: D 56 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7854 (mmtt) REVERT: D 108 GLU cc_start: 0.7527 (pt0) cc_final: 0.7301 (pm20) REVERT: D 178 TYR cc_start: 0.6191 (p90) cc_final: 0.5827 (p90) REVERT: D 227 MET cc_start: 0.8334 (ttp) cc_final: 0.6675 (tpt) REVERT: E 13 ASP cc_start: 0.7959 (p0) cc_final: 0.7750 (m-30) REVERT: E 19 LYS cc_start: 0.8403 (tptp) cc_final: 0.7765 (tmmt) REVERT: E 56 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7963 (mmtt) REVERT: E 204 ASN cc_start: 0.7867 (t0) cc_final: 0.7492 (p0) REVERT: E 227 MET cc_start: 0.8038 (ttp) cc_final: 0.6813 (tpt) REVERT: E 271 MET cc_start: 0.7821 (tpt) cc_final: 0.7469 (tpp) outliers start: 1 outliers final: 1 residues processed: 358 average time/residue: 0.2336 time to fit residues: 121.4439 Evaluate side-chains 269 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 157 optimal weight: 0.0030 chunk 129 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 overall best weight: 2.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 186 GLN B 186 GLN C 186 GLN C 295 ASN D 68 HIS D 186 GLN D 295 ASN E 68 HIS E 186 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13360 Z= 0.265 Angle : 0.568 6.347 18310 Z= 0.297 Chirality : 0.046 0.160 2190 Planarity : 0.004 0.038 2200 Dihedral : 6.149 55.754 2260 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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 (0.22), residues: 1580 helix: 2.18 (0.22), residues: 490 sheet: 0.37 (0.26), residues: 420 loop : -0.55 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 65 HIS 0.007 0.002 HIS B 68 PHE 0.019 0.002 PHE E 234 TYR 0.014 0.001 TYR E 284 ARG 0.003 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7185 (ttp80) REVERT: A 19 LYS cc_start: 0.8243 (tptp) cc_final: 0.7741 (tmmt) REVERT: A 52 ASP cc_start: 0.8103 (t0) cc_final: 0.7846 (t0) REVERT: A 279 PRO cc_start: 0.7327 (Cg_exo) cc_final: 0.7120 (Cg_endo) REVERT: B 16 ARG cc_start: 0.7334 (ttp-170) cc_final: 0.7003 (ttp80) REVERT: B 19 LYS cc_start: 0.8307 (tptp) cc_final: 0.7718 (tmmt) REVERT: B 56 LYS cc_start: 0.8305 (mtmt) cc_final: 0.8080 (mmtt) REVERT: B 184 GLU cc_start: 0.7392 (pt0) cc_final: 0.6561 (mt-10) REVERT: B 234 PHE cc_start: 0.7580 (t80) cc_final: 0.7113 (t80) REVERT: C 16 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.7975 (ttp-170) REVERT: C 19 LYS cc_start: 0.8450 (tptp) cc_final: 0.7855 (tmmt) REVERT: C 52 ASP cc_start: 0.8093 (t0) cc_final: 0.7859 (t0) REVERT: D 19 LYS cc_start: 0.8341 (tptp) cc_final: 0.7741 (tmmt) REVERT: D 56 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7949 (mmtt) REVERT: D 178 TYR cc_start: 0.6274 (p90) cc_final: 0.5955 (p90) REVERT: D 435 ILE cc_start: 0.6720 (mm) cc_final: 0.6013 (mm) REVERT: E 19 LYS cc_start: 0.8416 (tptp) cc_final: 0.7837 (tmmt) REVERT: E 56 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8135 (mmtt) REVERT: E 57 GLU cc_start: 0.7880 (tp30) cc_final: 0.7630 (tp30) REVERT: E 184 GLU cc_start: 0.7322 (pt0) cc_final: 0.6574 (mt-10) REVERT: E 227 MET cc_start: 0.8043 (ttp) cc_final: 0.6753 (tpt) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.2205 time to fit residues: 100.1257 Evaluate side-chains 251 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 16 optimal weight: 0.0270 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 154 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 295 ASN B 186 GLN B 295 ASN D 186 GLN D 295 ASN E 186 GLN E 295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13360 Z= 0.139 Angle : 0.499 5.191 18310 Z= 0.260 Chirality : 0.043 0.165 2190 Planarity : 0.004 0.044 2200 Dihedral : 5.590 57.888 2260 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.22 % Allowed : 2.59 % Favored : 97.19 % 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: 0.47 (0.21), residues: 1580 helix: 1.75 (0.23), residues: 515 sheet: 0.28 (0.25), residues: 420 loop : -0.82 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 70 HIS 0.007 0.002 HIS C 68 PHE 0.026 0.001 PHE C 428 TYR 0.015 0.001 TYR B 443 ARG 0.002 0.000 ARG E 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 312 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7644 (ttp-170) cc_final: 0.7212 (ttp80) REVERT: A 19 LYS cc_start: 0.8219 (tptp) cc_final: 0.7666 (tmmt) REVERT: A 56 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8044 (mmtt) REVERT: A 279 PRO cc_start: 0.7127 (Cg_exo) cc_final: 0.6870 (Cg_endo) REVERT: A 297 LEU cc_start: 0.9059 (tt) cc_final: 0.8386 (mt) REVERT: B 16 ARG cc_start: 0.7272 (ttp-170) cc_final: 0.6888 (ttp80) REVERT: B 17 LEU cc_start: 0.7535 (tt) cc_final: 0.7234 (tt) REVERT: B 184 GLU cc_start: 0.7444 (pt0) cc_final: 0.6537 (mt-10) REVERT: B 234 PHE cc_start: 0.7502 (t80) cc_final: 0.7044 (t80) REVERT: C 19 LYS cc_start: 0.8435 (tptp) cc_final: 0.7818 (tmmt) REVERT: C 52 ASP cc_start: 0.8026 (t0) cc_final: 0.7804 (t0) REVERT: C 56 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8343 (mmtt) REVERT: C 179 MET cc_start: 0.6426 (ttt) cc_final: 0.6149 (ttt) REVERT: C 227 MET cc_start: 0.8516 (ttp) cc_final: 0.6322 (tpt) REVERT: D 17 LEU cc_start: 0.7428 (tt) cc_final: 0.7202 (tt) REVERT: D 19 LYS cc_start: 0.8305 (tptp) cc_final: 0.7636 (tmmt) REVERT: D 178 TYR cc_start: 0.6066 (p90) cc_final: 0.5674 (p90) REVERT: D 179 MET cc_start: 0.6424 (ttt) cc_final: 0.5954 (ttm) REVERT: D 435 ILE cc_start: 0.6718 (mm) cc_final: 0.6388 (mt) REVERT: E 16 ARG cc_start: 0.7464 (ttp-170) cc_final: 0.7228 (ttp80) REVERT: E 17 LEU cc_start: 0.7599 (tt) cc_final: 0.7385 (tt) REVERT: E 19 LYS cc_start: 0.8359 (tptp) cc_final: 0.7754 (tmmt) REVERT: E 57 GLU cc_start: 0.7905 (tp30) cc_final: 0.7635 (tp30) REVERT: E 184 GLU cc_start: 0.7241 (pt0) cc_final: 0.6473 (mt-10) REVERT: E 227 MET cc_start: 0.8048 (ttp) cc_final: 0.6804 (tpt) REVERT: E 234 PHE cc_start: 0.7492 (t80) cc_final: 0.7132 (t80) outliers start: 3 outliers final: 3 residues processed: 312 average time/residue: 0.2183 time to fit residues: 102.1690 Evaluate side-chains 253 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 250 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 0.0000 chunk 39 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 186 GLN C 295 ASN D 186 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13360 Z= 0.292 Angle : 0.596 7.007 18310 Z= 0.310 Chirality : 0.046 0.155 2190 Planarity : 0.005 0.042 2200 Dihedral : 6.066 59.991 2260 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.07 % Allowed : 4.82 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.34 (0.21), residues: 1580 helix: 1.82 (0.23), residues: 485 sheet: 0.00 (0.27), residues: 395 loop : -0.75 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 128 HIS 0.010 0.003 HIS B 68 PHE 0.021 0.002 PHE D 234 TYR 0.014 0.002 TYR C 82 ARG 0.003 0.000 ARG D 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.7261 (ttp80) REVERT: A 19 LYS cc_start: 0.8324 (tptp) cc_final: 0.7806 (tmmt) REVERT: A 56 LYS cc_start: 0.8406 (mtmt) cc_final: 0.8169 (mmmt) REVERT: A 153 THR cc_start: 0.8579 (p) cc_final: 0.8310 (t) REVERT: A 252 TYR cc_start: 0.8393 (t80) cc_final: 0.7987 (t80) REVERT: A 254 ILE cc_start: 0.8583 (mm) cc_final: 0.8372 (mm) REVERT: A 279 PRO cc_start: 0.7316 (Cg_exo) cc_final: 0.7047 (Cg_endo) REVERT: A 297 LEU cc_start: 0.9068 (tt) cc_final: 0.8376 (mt) REVERT: B 16 ARG cc_start: 0.7398 (ttp-170) cc_final: 0.7019 (ttp80) REVERT: B 19 LYS cc_start: 0.8335 (tptp) cc_final: 0.7760 (tmmt) REVERT: B 56 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8074 (mmmt) REVERT: B 234 PHE cc_start: 0.7732 (t80) cc_final: 0.7280 (t80) REVERT: C 16 ARG cc_start: 0.8270 (ttp-110) cc_final: 0.8040 (ttp-170) REVERT: C 19 LYS cc_start: 0.8455 (tptp) cc_final: 0.7851 (tmmt) REVERT: C 56 LYS cc_start: 0.8635 (mmtt) cc_final: 0.8372 (mmtt) REVERT: C 184 GLU cc_start: 0.7429 (pt0) cc_final: 0.6918 (mt-10) REVERT: D 19 LYS cc_start: 0.8342 (tptp) cc_final: 0.7712 (tmmt) REVERT: D 56 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8372 (mmtt) REVERT: D 73 PHE cc_start: 0.7871 (p90) cc_final: 0.7667 (p90) REVERT: D 178 TYR cc_start: 0.6092 (p90) cc_final: 0.5606 (p90) REVERT: D 179 MET cc_start: 0.6189 (ttt) cc_final: 0.5761 (ttm) REVERT: E 19 LYS cc_start: 0.8420 (tptp) cc_final: 0.7859 (tmmt) REVERT: E 184 GLU cc_start: 0.7681 (pt0) cc_final: 0.6695 (mm-30) REVERT: E 227 MET cc_start: 0.8267 (ttp) cc_final: 0.6546 (tpp) outliers start: 1 outliers final: 1 residues processed: 315 average time/residue: 0.2193 time to fit residues: 102.7278 Evaluate side-chains 247 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 186 GLN D 186 GLN D 295 ASN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13360 Z= 0.408 Angle : 0.664 7.118 18310 Z= 0.350 Chirality : 0.048 0.162 2190 Planarity : 0.005 0.045 2200 Dihedral : 6.475 52.005 2260 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1580 helix: 1.13 (0.22), residues: 500 sheet: -0.22 (0.28), residues: 355 loop : -0.98 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 65 HIS 0.011 0.003 HIS C 68 PHE 0.019 0.002 PHE C 73 TYR 0.030 0.002 TYR D 284 ARG 0.005 0.001 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 317 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.7346 (ttp80) REVERT: A 19 LYS cc_start: 0.8410 (tptp) cc_final: 0.7903 (tmmt) REVERT: A 57 GLU cc_start: 0.7774 (tp30) cc_final: 0.7542 (tp30) REVERT: A 153 THR cc_start: 0.8655 (p) cc_final: 0.8389 (t) REVERT: A 252 TYR cc_start: 0.8530 (t80) cc_final: 0.8211 (t80) REVERT: A 254 ILE cc_start: 0.8664 (mm) cc_final: 0.8461 (mm) REVERT: A 279 PRO cc_start: 0.7270 (Cg_exo) cc_final: 0.7033 (Cg_endo) REVERT: B 19 LYS cc_start: 0.8334 (tptp) cc_final: 0.7873 (tmmt) REVERT: B 131 HIS cc_start: 0.8298 (t70) cc_final: 0.8014 (t-170) REVERT: B 234 PHE cc_start: 0.7837 (t80) cc_final: 0.7343 (t80) REVERT: C 16 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8174 (ttp-170) REVERT: C 19 LYS cc_start: 0.8517 (tptp) cc_final: 0.7893 (tmmt) REVERT: C 56 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8298 (mmtt) REVERT: C 184 GLU cc_start: 0.7632 (pt0) cc_final: 0.7157 (mt-10) REVERT: D 19 LYS cc_start: 0.8374 (tptp) cc_final: 0.7774 (tmmt) REVERT: D 57 GLU cc_start: 0.7808 (tp30) cc_final: 0.7513 (tp30) REVERT: D 131 HIS cc_start: 0.8235 (t70) cc_final: 0.7976 (t70) REVERT: D 268 SER cc_start: 0.7963 (t) cc_final: 0.7690 (t) REVERT: D 435 ILE cc_start: 0.6796 (mm) cc_final: 0.6107 (mm) REVERT: E 16 ARG cc_start: 0.7668 (ttp-170) cc_final: 0.7322 (ttp80) REVERT: E 19 LYS cc_start: 0.8452 (tptp) cc_final: 0.7938 (tmmt) REVERT: E 56 LYS cc_start: 0.8753 (mmtp) cc_final: 0.8543 (mmtt) REVERT: E 184 GLU cc_start: 0.7768 (pt0) cc_final: 0.6998 (mm-30) REVERT: E 227 MET cc_start: 0.8491 (ttp) cc_final: 0.6714 (tpp) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.2292 time to fit residues: 107.3022 Evaluate side-chains 257 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 186 GLN C 295 ASN D 186 GLN D 295 ASN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13360 Z= 0.358 Angle : 0.645 6.628 18310 Z= 0.337 Chirality : 0.047 0.155 2190 Planarity : 0.005 0.044 2200 Dihedral : 6.585 52.274 2260 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.07 % Allowed : 1.73 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1580 helix: 1.38 (0.22), residues: 475 sheet: -0.38 (0.28), residues: 350 loop : -1.05 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 128 HIS 0.011 0.003 HIS C 68 PHE 0.016 0.002 PHE B 73 TYR 0.018 0.002 TYR D 284 ARG 0.002 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 302 time to evaluate : 1.463 Fit side-chains REVERT: A 16 ARG cc_start: 0.7909 (ttp-170) cc_final: 0.7355 (ttp80) REVERT: A 19 LYS cc_start: 0.8407 (tptp) cc_final: 0.7911 (tmmt) REVERT: A 57 GLU cc_start: 0.7789 (tp30) cc_final: 0.7565 (tp30) REVERT: A 178 TYR cc_start: 0.6642 (p90) cc_final: 0.6284 (p90) REVERT: A 227 MET cc_start: 0.8506 (ttp) cc_final: 0.6416 (tpp) REVERT: A 279 PRO cc_start: 0.7385 (Cg_exo) cc_final: 0.7148 (Cg_endo) REVERT: B 16 ARG cc_start: 0.7515 (ttp-170) cc_final: 0.7087 (ttp80) REVERT: B 19 LYS cc_start: 0.8389 (tptp) cc_final: 0.7900 (tmmt) REVERT: B 131 HIS cc_start: 0.8196 (t70) cc_final: 0.7914 (t-170) REVERT: B 179 MET cc_start: 0.6445 (ttt) cc_final: 0.5285 (ptp) REVERT: B 227 MET cc_start: 0.6747 (tpt) cc_final: 0.6378 (tpp) REVERT: B 234 PHE cc_start: 0.7797 (t80) cc_final: 0.7262 (t80) REVERT: C 16 ARG cc_start: 0.8377 (ttp-110) cc_final: 0.8091 (ttp-170) REVERT: C 19 LYS cc_start: 0.8533 (tptp) cc_final: 0.7907 (tmmt) REVERT: C 56 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8261 (mmtt) REVERT: C 179 MET cc_start: 0.6199 (ttt) cc_final: 0.5915 (ttt) REVERT: C 184 GLU cc_start: 0.7633 (pt0) cc_final: 0.7170 (mt-10) REVERT: D 19 LYS cc_start: 0.8395 (tptp) cc_final: 0.7769 (tmmt) REVERT: D 57 GLU cc_start: 0.7821 (tp30) cc_final: 0.7498 (tp30) REVERT: D 131 HIS cc_start: 0.8128 (t70) cc_final: 0.7901 (t70) REVERT: D 435 ILE cc_start: 0.6952 (mm) cc_final: 0.5998 (mm) REVERT: E 16 ARG cc_start: 0.7683 (ttp-170) cc_final: 0.7408 (ttp80) REVERT: E 19 LYS cc_start: 0.8434 (tptp) cc_final: 0.7904 (tmmt) REVERT: E 56 LYS cc_start: 0.8722 (mmtp) cc_final: 0.8394 (mmtt) REVERT: E 184 GLU cc_start: 0.7931 (pt0) cc_final: 0.7152 (mt-10) REVERT: E 227 MET cc_start: 0.8608 (ttp) cc_final: 0.6996 (tpp) outliers start: 1 outliers final: 1 residues processed: 302 average time/residue: 0.2222 time to fit residues: 99.7804 Evaluate side-chains 255 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 295 ASN B 186 GLN D 186 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13360 Z= 0.290 Angle : 0.611 7.687 18310 Z= 0.317 Chirality : 0.046 0.146 2190 Planarity : 0.005 0.047 2200 Dihedral : 6.439 52.684 2260 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -0.29 (0.21), residues: 1580 helix: 1.43 (0.23), residues: 475 sheet: -0.44 (0.28), residues: 350 loop : -1.12 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 159 HIS 0.008 0.003 HIS E 68 PHE 0.019 0.002 PHE A 289 TYR 0.018 0.002 TYR A 284 ARG 0.002 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.367 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7329 (ttp80) REVERT: A 19 LYS cc_start: 0.8412 (tptp) cc_final: 0.7880 (tmmt) REVERT: A 57 GLU cc_start: 0.7695 (tp30) cc_final: 0.7490 (tp30) REVERT: A 153 THR cc_start: 0.8695 (p) cc_final: 0.8430 (t) REVERT: A 279 PRO cc_start: 0.7393 (Cg_exo) cc_final: 0.7157 (Cg_endo) REVERT: B 16 ARG cc_start: 0.7547 (ttp-170) cc_final: 0.7111 (ttp80) REVERT: B 19 LYS cc_start: 0.8353 (tptp) cc_final: 0.7867 (tmmt) REVERT: B 131 HIS cc_start: 0.8118 (t70) cc_final: 0.7825 (t70) REVERT: B 179 MET cc_start: 0.6350 (ttt) cc_final: 0.5268 (ptp) REVERT: B 227 MET cc_start: 0.6726 (tpt) cc_final: 0.6298 (tpp) REVERT: C 19 LYS cc_start: 0.8513 (tptp) cc_final: 0.7919 (tmmt) REVERT: C 21 ILE cc_start: 0.9060 (tt) cc_final: 0.8851 (tt) REVERT: C 56 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8354 (mmtt) REVERT: C 184 GLU cc_start: 0.7720 (pt0) cc_final: 0.7178 (mt-10) REVERT: D 19 LYS cc_start: 0.8404 (tptp) cc_final: 0.7777 (tmmt) REVERT: D 57 GLU cc_start: 0.7765 (tp30) cc_final: 0.7401 (tp30) REVERT: D 131 HIS cc_start: 0.8090 (t70) cc_final: 0.7823 (t70) REVERT: D 184 GLU cc_start: 0.7270 (pt0) cc_final: 0.6837 (mt-10) REVERT: D 435 ILE cc_start: 0.6891 (mm) cc_final: 0.6001 (mm) REVERT: E 16 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7357 (ttp80) REVERT: E 19 LYS cc_start: 0.8433 (tptp) cc_final: 0.7921 (tmmt) REVERT: E 56 LYS cc_start: 0.8708 (mmtp) cc_final: 0.8374 (mmtt) REVERT: E 179 MET cc_start: 0.6413 (ttt) cc_final: 0.5286 (ptp) REVERT: E 184 GLU cc_start: 0.7912 (pt0) cc_final: 0.7156 (mt-10) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2200 time to fit residues: 95.7255 Evaluate side-chains 237 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 112 optimal weight: 0.0170 chunk 44 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 186 GLN B 295 ASN C 295 ASN D 63 ASN D 186 GLN D 295 ASN E 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13360 Z= 0.186 Angle : 0.559 7.280 18310 Z= 0.288 Chirality : 0.044 0.142 2190 Planarity : 0.005 0.046 2200 Dihedral : 6.159 54.038 2260 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.14 % Allowed : 0.94 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.62 % 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: -0.13 (0.21), residues: 1580 helix: 1.64 (0.24), residues: 475 sheet: -0.32 (0.28), residues: 350 loop : -1.10 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 65 HIS 0.005 0.002 HIS C 442 PHE 0.027 0.002 PHE C 289 TYR 0.015 0.001 TYR C 443 ARG 0.002 0.000 ARG E 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 300 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7261 (ttp80) REVERT: A 19 LYS cc_start: 0.8364 (tptp) cc_final: 0.7830 (tmmt) REVERT: A 33 GLN cc_start: 0.6969 (tt0) cc_final: 0.6623 (mt0) REVERT: A 153 THR cc_start: 0.8605 (p) cc_final: 0.8322 (t) REVERT: A 178 TYR cc_start: 0.6377 (p90) cc_final: 0.6093 (p90) REVERT: A 271 MET cc_start: 0.8166 (tpt) cc_final: 0.7755 (tpt) REVERT: A 279 PRO cc_start: 0.7330 (Cg_exo) cc_final: 0.7066 (Cg_endo) REVERT: A 435 ILE cc_start: 0.6663 (mm) cc_final: 0.6164 (mt) REVERT: B 16 ARG cc_start: 0.7484 (ttp-170) cc_final: 0.7065 (ttp80) REVERT: B 19 LYS cc_start: 0.8283 (tptp) cc_final: 0.7751 (tmmt) REVERT: B 56 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8033 (mmtp) REVERT: B 179 MET cc_start: 0.6226 (ttt) cc_final: 0.5241 (ptp) REVERT: B 227 MET cc_start: 0.6785 (tpt) cc_final: 0.6395 (tpp) REVERT: C 19 LYS cc_start: 0.8487 (tptp) cc_final: 0.7873 (tmmt) REVERT: C 82 TYR cc_start: 0.8310 (m-80) cc_final: 0.7896 (m-80) REVERT: C 153 THR cc_start: 0.8479 (p) cc_final: 0.8274 (t) REVERT: C 184 GLU cc_start: 0.7653 (pt0) cc_final: 0.7099 (mt-10) REVERT: D 19 LYS cc_start: 0.8348 (tptp) cc_final: 0.7716 (tmmt) REVERT: D 153 THR cc_start: 0.8650 (p) cc_final: 0.8352 (t) REVERT: D 178 TYR cc_start: 0.6145 (p90) cc_final: 0.5723 (p90) REVERT: D 184 GLU cc_start: 0.7193 (pt0) cc_final: 0.6787 (mt-10) REVERT: D 435 ILE cc_start: 0.6839 (mm) cc_final: 0.5949 (mm) REVERT: E 16 ARG cc_start: 0.7600 (ttp-170) cc_final: 0.7240 (ttp80) REVERT: E 19 LYS cc_start: 0.8395 (tptp) cc_final: 0.7845 (tmmt) REVERT: E 56 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8366 (mmtt) REVERT: E 184 GLU cc_start: 0.7784 (pt0) cc_final: 0.7086 (mt-10) REVERT: E 227 MET cc_start: 0.8595 (ttp) cc_final: 0.6664 (tpp) outliers start: 2 outliers final: 2 residues processed: 300 average time/residue: 0.2151 time to fit residues: 96.6285 Evaluate side-chains 247 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 245 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 146 optimal weight: 0.0070 chunk 126 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 98 optimal weight: 0.0070 chunk 77 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 overall best weight: 1.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 63 ASN B 186 GLN D 63 ASN D 186 GLN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13360 Z= 0.197 Angle : 0.570 10.324 18310 Z= 0.291 Chirality : 0.044 0.139 2190 Planarity : 0.005 0.046 2200 Dihedral : 6.179 55.174 2260 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -0.10 (0.21), residues: 1580 helix: 1.64 (0.24), residues: 475 sheet: -0.28 (0.28), residues: 350 loop : -1.07 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 65 HIS 0.005 0.002 HIS A 442 PHE 0.027 0.002 PHE C 289 TYR 0.016 0.001 TYR D 284 ARG 0.002 0.000 ARG E 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8368 (tptp) cc_final: 0.7862 (tmmt) REVERT: A 33 GLN cc_start: 0.7033 (tt0) cc_final: 0.6654 (mt0) REVERT: A 153 THR cc_start: 0.8575 (p) cc_final: 0.8297 (t) REVERT: A 271 MET cc_start: 0.8163 (tpt) cc_final: 0.7768 (tpt) REVERT: A 279 PRO cc_start: 0.7290 (Cg_exo) cc_final: 0.7038 (Cg_endo) REVERT: A 435 ILE cc_start: 0.6581 (mm) cc_final: 0.6190 (tp) REVERT: B 16 ARG cc_start: 0.7486 (ttp-170) cc_final: 0.7069 (ttp80) REVERT: B 19 LYS cc_start: 0.8295 (tptp) cc_final: 0.7755 (tmmt) REVERT: B 56 LYS cc_start: 0.8703 (mmmt) cc_final: 0.7939 (mmtt) REVERT: B 179 MET cc_start: 0.6287 (ttt) cc_final: 0.5280 (ptp) REVERT: B 227 MET cc_start: 0.6742 (tpt) cc_final: 0.6351 (tpp) REVERT: C 19 LYS cc_start: 0.8489 (tptp) cc_final: 0.7881 (tmmt) REVERT: C 56 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8368 (mmtt) REVERT: C 153 THR cc_start: 0.8445 (p) cc_final: 0.8237 (t) REVERT: C 184 GLU cc_start: 0.7678 (pt0) cc_final: 0.7107 (mt-10) REVERT: D 19 LYS cc_start: 0.8367 (tptp) cc_final: 0.7752 (tmmt) REVERT: D 153 THR cc_start: 0.8628 (p) cc_final: 0.8348 (t) REVERT: D 178 TYR cc_start: 0.6095 (p90) cc_final: 0.5673 (p90) REVERT: D 184 GLU cc_start: 0.7147 (pt0) cc_final: 0.6661 (mt-10) REVERT: D 435 ILE cc_start: 0.6869 (mm) cc_final: 0.5966 (mm) REVERT: E 16 ARG cc_start: 0.7656 (ttp-170) cc_final: 0.7279 (ttp80) REVERT: E 19 LYS cc_start: 0.8393 (tptp) cc_final: 0.7855 (tmmt) REVERT: E 56 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8297 (mmtt) REVERT: E 179 MET cc_start: 0.6237 (ttt) cc_final: 0.5051 (ptp) REVERT: E 184 GLU cc_start: 0.7780 (pt0) cc_final: 0.7079 (mt-10) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2175 time to fit residues: 96.3944 Evaluate side-chains 246 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.0010 chunk 38 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 63 ASN B 186 GLN D 63 ASN D 186 GLN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.146768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.120897 restraints weight = 17187.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.121915 restraints weight = 13532.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.122896 restraints weight = 11977.521| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13360 Z= 0.204 Angle : 0.569 9.167 18310 Z= 0.292 Chirality : 0.044 0.139 2190 Planarity : 0.005 0.046 2200 Dihedral : 6.227 55.474 2260 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.15 % 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: -0.32 (0.21), residues: 1580 helix: 1.26 (0.23), residues: 500 sheet: -0.31 (0.28), residues: 350 loop : -1.19 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.005 0.002 HIS D 442 PHE 0.027 0.002 PHE B 73 TYR 0.019 0.001 TYR A 284 ARG 0.002 0.000 ARG E 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2692.66 seconds wall clock time: 49 minutes 24.97 seconds (2964.97 seconds total)