Starting phenix.real_space_refine on Thu Feb 15 00:33:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dps_27641/02_2024/8dps_27641.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dps_27641/02_2024/8dps_27641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dps_27641/02_2024/8dps_27641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dps_27641/02_2024/8dps_27641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dps_27641/02_2024/8dps_27641.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dps_27641/02_2024/8dps_27641.pdb" } resolution = 3.47 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= 1.000 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 36 5.16 5 C 6752 2.51 5 N 1826 2.21 5 O 1996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "C TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "F TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 175": "OE1" <-> "OE2" Residue "F PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 288": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10610 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2382 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 280} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1262 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 150} Chain: "C" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1566 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 25, 'TRANS': 174} Chain breaks: 1 Chain: "D" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2382 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 280} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1262 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 150} Chain: "F" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1566 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 25, 'TRANS': 174} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.03, per 1000 atoms: 0.57 Number of scatterers: 10610 At special positions: 0 Unit cell: (148.03, 129.69, 90.39, 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 36 16.00 O 1996 8.00 N 1826 7.00 C 6752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 32 " distance=2.03 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 81 " distance=2.04 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 160 " distance=2.05 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 32 " distance=2.04 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 81 " distance=2.04 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 160 " distance=2.05 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 108 " distance=2.04 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 158 " 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 Atom "HETATM10499 O5 NAG I 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM10432 O5 NAG G 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM10580 O5 NAG A 402 .*. O " rejected from bonding due to valence issues. Atom "HETATM10608 O5 NAG D 402 .*. O " rejected from bonding due to valence issues. Atom "HETATM10566 O5 NAG A 401 .*. O " rejected from bonding due to valence issues. Atom "HETATM10594 O5 NAG D 401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 135 " " NAG D 401 " - " ASN D 21 " " NAG D 402 " - " ASN D 135 " " NAG G 1 " - " ASN A 61 " " NAG H 1 " - " ASN C 172 " " NAG I 1 " - " ASN D 61 " " NAG J 1 " - " ASN F 172 " Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 1.8 seconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 24 sheets defined 24.5% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.866A pdb=" N ALA A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 43 removed outlier: 3.856A pdb=" N SER B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.572A pdb=" N LEU B 64 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY B 65 " --> pdb=" O GLY B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 65' Processing helix chain 'B' and resid 68 through 94 removed outlier: 3.746A pdb=" N VAL B 72 " --> pdb=" O GLN B 68 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 4.394A pdb=" N THR B 100 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 126 Processing helix chain 'B' and resid 145 through 157 Processing helix chain 'B' and resid 159 through 178 removed outlier: 3.738A pdb=" N ASP B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 193 through 196 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.865A pdb=" N ALA D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 43 removed outlier: 3.855A pdb=" N SER E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.571A pdb=" N LEU E 64 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY E 65 " --> pdb=" O GLY E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 65' Processing helix chain 'E' and resid 68 through 94 removed outlier: 3.746A pdb=" N VAL E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG E 92 " --> pdb=" O GLN E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 102 removed outlier: 4.393A pdb=" N THR E 100 " --> pdb=" O SER E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 126 Processing helix chain 'E' and resid 145 through 157 Processing helix chain 'E' and resid 159 through 178 removed outlier: 3.738A pdb=" N ASP E 165 " --> pdb=" O HIS E 161 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 6.718A pdb=" N ALA A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 5.622A pdb=" N ASN A 92 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 83 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 161 removed outlier: 4.190A pdb=" N ASP A 125 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASN A 109 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LYS A 199 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL A 114 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'A' and resid 204 through 210 removed outlier: 5.680A pdb=" N ASN A 205 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR A 223 " --> pdb=" O ASN A 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 99 Processing sheet with id=AA9, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB1, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 200 through 206 removed outlier: 4.137A pdb=" N LEU C 202 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER C 217 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL C 204 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG C 215 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 247 through 249 Processing sheet with id=AB4, first strand: chain 'D' and resid 7 through 10 removed outlier: 6.717A pdb=" N ALA D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 15 through 17 removed outlier: 5.621A pdb=" N ASN D 92 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE D 83 " --> pdb=" O ASN D 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161 removed outlier: 4.191A pdb=" N ASP D 125 " --> pdb=" O ASN D 109 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASN D 109 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS D 199 " --> pdb=" O CYS D 112 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL D 114 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AB8, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AB9, first strand: chain 'D' and resid 204 through 210 removed outlier: 5.681A pdb=" N ASN D 205 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR D 223 " --> pdb=" O ASN D 205 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 248 through 249 Processing sheet with id=AC2, first strand: chain 'F' and resid 95 through 99 Processing sheet with id=AC3, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AC4, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AC5, first strand: chain 'F' and resid 200 through 206 removed outlier: 4.138A pdb=" N LEU F 202 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER F 217 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL F 204 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG F 215 " --> pdb=" O VAL F 204 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 247 through 249 492 hydrogen bonds defined for protein. 1266 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: 3.10 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3405 1.35 - 1.48: 2940 1.48 - 1.61: 4513 1.61 - 1.75: 2 1.75 - 1.88: 44 Bond restraints: 10904 Sorted by residual: bond pdb=" CB TRP A 142 " pdb=" CG TRP A 142 " ideal model delta sigma weight residual 1.498 1.404 0.094 3.10e-02 1.04e+03 9.10e+00 bond pdb=" CB TRP D 142 " pdb=" CG TRP D 142 " ideal model delta sigma weight residual 1.498 1.405 0.093 3.10e-02 1.04e+03 9.08e+00 bond pdb=" CB CYS A 160 " pdb=" SG CYS A 160 " ideal model delta sigma weight residual 1.808 1.879 -0.071 3.30e-02 9.18e+02 4.69e+00 bond pdb=" CB CYS D 160 " pdb=" SG CYS D 160 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.54e+00 bond pdb=" CG LEU C 186 " pdb=" CD2 LEU C 186 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.41e+00 ... (remaining 10899 not shown) Histogram of bond angle deviations from ideal: 99.45 - 107.33: 795 107.33 - 115.22: 6382 115.22 - 123.11: 6651 123.11 - 131.00: 995 131.00 - 138.89: 79 Bond angle restraints: 14902 Sorted by residual: angle pdb=" C ALA D 148 " pdb=" N ASP D 149 " pdb=" CA ASP D 149 " ideal model delta sigma weight residual 120.94 132.46 -11.52 1.57e+00 4.06e-01 5.38e+01 angle pdb=" C ALA A 148 " pdb=" N ASP A 149 " pdb=" CA ASP A 149 " ideal model delta sigma weight residual 120.94 132.42 -11.48 1.57e+00 4.06e-01 5.34e+01 angle pdb=" CA CYS A 150 " pdb=" CB CYS A 150 " pdb=" SG CYS A 150 " ideal model delta sigma weight residual 114.40 129.32 -14.92 2.30e+00 1.89e-01 4.21e+01 angle pdb=" CA CYS D 150 " pdb=" CB CYS D 150 " pdb=" SG CYS D 150 " ideal model delta sigma weight residual 114.40 129.31 -14.91 2.30e+00 1.89e-01 4.20e+01 angle pdb=" CA LEU E 173 " pdb=" CB LEU E 173 " pdb=" CG LEU E 173 " ideal model delta sigma weight residual 116.30 138.89 -22.59 3.50e+00 8.16e-02 4.16e+01 ... (remaining 14897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.09: 6180 19.09 - 38.18: 450 38.18 - 57.28: 76 57.28 - 76.37: 40 76.37 - 95.46: 10 Dihedral angle restraints: 6756 sinusoidal: 2892 harmonic: 3864 Sorted by residual: dihedral pdb=" CB CYS A 6 " pdb=" SG CYS A 6 " pdb=" SG CYS A 32 " pdb=" CB CYS A 32 " ideal model delta sinusoidal sigma weight residual 93.00 44.57 48.43 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS D 6 " pdb=" SG CYS D 6 " pdb=" SG CYS D 32 " pdb=" CB CYS D 32 " ideal model delta sinusoidal sigma weight residual 93.00 44.60 48.40 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" C PHE A 147 " pdb=" N PHE A 147 " pdb=" CA PHE A 147 " pdb=" CB PHE A 147 " ideal model delta harmonic sigma weight residual -122.60 -135.89 13.29 0 2.50e+00 1.60e-01 2.83e+01 ... (remaining 6753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 1674 0.179 - 0.359: 20 0.359 - 0.538: 10 0.538 - 0.717: 0 0.717 - 0.897: 4 Chirality restraints: 1708 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 172 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.45e+01 ... (remaining 1705 not shown) Planarity restraints: 1894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.240 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" CG ASN A 61 " -0.097 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.494 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.403 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 61 " 0.240 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" CG ASN D 61 " -0.098 2.00e-02 2.50e+03 pdb=" OD1 ASN D 61 " -0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN D 61 " -0.494 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.402 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 172 " -0.109 2.00e-02 2.50e+03 1.31e-01 2.15e+02 pdb=" CG ASN C 172 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C 172 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 172 " 0.218 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.158 2.00e-02 2.50e+03 ... (remaining 1891 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 211 2.63 - 3.20: 9855 3.20 - 3.77: 16271 3.77 - 4.33: 21793 4.33 - 4.90: 36372 Nonbonded interactions: 84502 Sorted by model distance: nonbonded pdb=" O THR A 144 " pdb=" ND1 HIS A 145 " model vdw 2.063 2.520 nonbonded pdb=" O THR D 144 " pdb=" ND1 HIS D 145 " model vdw 2.064 2.520 nonbonded pdb=" OG1 THR A 58 " pdb=" OG SER A 66 " model vdw 2.087 2.440 nonbonded pdb=" OG1 THR D 58 " pdb=" OG SER D 66 " model vdw 2.088 2.440 nonbonded pdb=" OG SER A 261 " pdb=" OG SER C 247 " model vdw 2.114 2.440 ... (remaining 84497 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 3.500 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 30.620 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 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 : 0.008 0.094 10904 Z= 0.490 Angle : 1.401 22.586 14902 Z= 0.742 Chirality : 0.081 0.897 1708 Planarity : 0.006 0.050 1886 Dihedral : 14.649 95.461 4216 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 0.52 % Allowed : 2.35 % Favored : 97.13 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 3.70 % 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: -0.57 (0.21), residues: 1308 helix: 1.10 (0.29), residues: 238 sheet: 0.22 (0.23), residues: 420 loop : -1.37 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 45 HIS 0.008 0.002 HIS A 49 PHE 0.047 0.004 PHE F 230 TYR 0.021 0.004 TYR C 89 ARG 0.023 0.002 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7598 (t0) REVERT: C 99 GLN cc_start: 0.5717 (pm20) cc_final: 0.5500 (pm20) REVERT: C 105 ASN cc_start: 0.7783 (p0) cc_final: 0.7477 (p0) REVERT: C 125 SER cc_start: 0.8145 (t) cc_final: 0.7579 (m) REVERT: D 62 ARG cc_start: 0.7243 (mtp-110) cc_final: 0.7022 (ptp-110) REVERT: D 109 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7560 (t0) REVERT: F 99 GLN cc_start: 0.5867 (pm20) cc_final: 0.5590 (pm20) REVERT: F 256 GLU cc_start: 0.6659 (tp30) cc_final: 0.6332 (tp30) outliers start: 6 outliers final: 0 residues processed: 177 average time/residue: 0.2274 time to fit residues: 57.5840 Evaluate side-chains 124 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain D residue 109 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 56 GLN C 114 GLN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10904 Z= 0.247 Angle : 0.832 14.262 14902 Z= 0.401 Chirality : 0.048 0.240 1708 Planarity : 0.005 0.040 1886 Dihedral : 8.362 58.426 1736 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.04 % Allowed : 9.04 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.17 (0.22), residues: 1308 helix: 0.93 (0.31), residues: 264 sheet: 0.38 (0.23), residues: 418 loop : -0.34 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 222 HIS 0.004 0.001 HIS B 154 PHE 0.025 0.002 PHE F 106 TYR 0.024 0.002 TYR D 239 ARG 0.005 0.000 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TYR cc_start: 0.6036 (t80) cc_final: 0.5765 (t80) REVERT: C 125 SER cc_start: 0.8171 (t) cc_final: 0.7645 (m) REVERT: C 151 ASP cc_start: 0.5180 (OUTLIER) cc_final: 0.4736 (m-30) REVERT: D 33 MET cc_start: 0.6744 (tmm) cc_final: 0.6479 (tmm) REVERT: D 191 ASN cc_start: 0.7641 (t0) cc_final: 0.7317 (t0) REVERT: F 99 GLN cc_start: 0.5761 (pm20) cc_final: 0.5502 (pm20) REVERT: F 256 GLU cc_start: 0.6574 (tp30) cc_final: 0.6157 (tp30) outliers start: 12 outliers final: 7 residues processed: 177 average time/residue: 0.2241 time to fit residues: 56.5765 Evaluate side-chains 135 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 0.0670 chunk 80 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 chunk 117 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN ** F 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10904 Z= 0.229 Angle : 0.722 10.373 14902 Z= 0.351 Chirality : 0.047 0.265 1708 Planarity : 0.005 0.042 1886 Dihedral : 6.667 58.043 1732 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.52 % Allowed : 11.74 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.34 (0.23), residues: 1308 helix: 0.91 (0.32), residues: 264 sheet: 0.40 (0.23), residues: 420 loop : -0.08 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 222 HIS 0.003 0.001 HIS F 161 PHE 0.024 0.002 PHE C 106 TYR 0.020 0.002 TYR D 239 ARG 0.006 0.000 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7128 (tmm) cc_final: 0.6914 (tmm) REVERT: B 42 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7650 (mtpp) REVERT: C 114 GLN cc_start: 0.7950 (mt0) cc_final: 0.6440 (pp30) REVERT: D 296 SER cc_start: 0.6913 (m) cc_final: 0.6638 (p) REVERT: F 99 GLN cc_start: 0.5772 (pm20) cc_final: 0.5421 (pm20) outliers start: 29 outliers final: 15 residues processed: 167 average time/residue: 0.2279 time to fit residues: 53.7020 Evaluate side-chains 138 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 0.1980 chunk 88 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10904 Z= 0.214 Angle : 0.670 9.776 14902 Z= 0.326 Chirality : 0.046 0.258 1708 Planarity : 0.004 0.040 1886 Dihedral : 6.189 57.033 1732 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.87 % Allowed : 12.43 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.37 (0.24), residues: 1308 helix: 0.98 (0.33), residues: 264 sheet: 0.24 (0.24), residues: 422 loop : 0.07 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 222 HIS 0.004 0.001 HIS C 229 PHE 0.022 0.002 PHE C 106 TYR 0.017 0.002 TYR D 239 ARG 0.006 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7099 (tmm) cc_final: 0.6856 (tmm) REVERT: B 56 THR cc_start: 0.7465 (OUTLIER) cc_final: 0.7260 (t) REVERT: C 114 GLN cc_start: 0.7929 (mt0) cc_final: 0.6382 (pp30) REVERT: C 193 ILE cc_start: 0.7892 (tp) cc_final: 0.7657 (tt) REVERT: C 256 GLU cc_start: 0.6312 (tp30) cc_final: 0.5877 (tp30) REVERT: D 296 SER cc_start: 0.7058 (m) cc_final: 0.6745 (p) REVERT: E 42 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7688 (mtpp) REVERT: E 56 THR cc_start: 0.7542 (OUTLIER) cc_final: 0.7266 (t) REVERT: F 99 GLN cc_start: 0.5781 (pm20) cc_final: 0.5345 (pm20) REVERT: F 188 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8181 (t) REVERT: F 256 GLU cc_start: 0.6368 (tp30) cc_final: 0.5998 (tp30) outliers start: 33 outliers final: 21 residues processed: 174 average time/residue: 0.2155 time to fit residues: 54.2662 Evaluate side-chains 146 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10904 Z= 0.334 Angle : 0.755 12.645 14902 Z= 0.366 Chirality : 0.049 0.275 1708 Planarity : 0.005 0.043 1886 Dihedral : 6.603 57.449 1732 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.09 % Allowed : 14.43 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.03 (0.24), residues: 1308 helix: 0.75 (0.33), residues: 264 sheet: -0.03 (0.24), residues: 422 loop : -0.12 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 222 HIS 0.005 0.001 HIS E 49 PHE 0.025 0.003 PHE F 106 TYR 0.016 0.002 TYR D 239 ARG 0.005 0.001 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 138 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7281 (tmm) cc_final: 0.6949 (tmm) REVERT: A 62 ARG cc_start: 0.7174 (mtp-110) cc_final: 0.6967 (ttp-110) REVERT: A 96 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7250 (pt) REVERT: B 56 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7338 (t) REVERT: C 114 GLN cc_start: 0.8255 (mt0) cc_final: 0.6739 (pp30) REVERT: C 193 ILE cc_start: 0.7967 (tp) cc_final: 0.7758 (tt) REVERT: C 256 GLU cc_start: 0.6505 (tp30) cc_final: 0.5946 (tp30) REVERT: D 96 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7207 (pt) REVERT: E 42 LYS cc_start: 0.7822 (mtpp) cc_final: 0.7600 (mtpp) REVERT: E 56 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7476 (t) REVERT: F 256 GLU cc_start: 0.6308 (tp30) cc_final: 0.6073 (tp30) outliers start: 47 outliers final: 35 residues processed: 177 average time/residue: 0.2031 time to fit residues: 52.6208 Evaluate side-chains 166 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 125 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10904 Z= 0.196 Angle : 0.668 11.578 14902 Z= 0.323 Chirality : 0.046 0.263 1708 Planarity : 0.004 0.039 1886 Dihedral : 6.257 57.388 1732 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.04 % Allowed : 15.91 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.15 (0.24), residues: 1308 helix: 0.86 (0.34), residues: 264 sheet: -0.01 (0.24), residues: 422 loop : 0.00 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 222 HIS 0.003 0.001 HIS F 229 PHE 0.027 0.002 PHE C 230 TYR 0.015 0.001 TYR D 239 ARG 0.004 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7336 (tmm) cc_final: 0.6966 (tmm) REVERT: A 62 ARG cc_start: 0.7262 (mtp-110) cc_final: 0.7017 (ttp-110) REVERT: B 29 LEU cc_start: 0.8495 (tt) cc_final: 0.7975 (tt) REVERT: B 56 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7357 (t) REVERT: B 162 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7219 (mp) REVERT: C 114 GLN cc_start: 0.8166 (mt0) cc_final: 0.7507 (mt0) REVERT: C 188 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8167 (t) REVERT: C 193 ILE cc_start: 0.7761 (tp) cc_final: 0.7531 (tt) REVERT: C 256 GLU cc_start: 0.6346 (tp30) cc_final: 0.5788 (tp30) REVERT: D 62 ARG cc_start: 0.7489 (mtp-110) cc_final: 0.7070 (ttm-80) REVERT: E 42 LYS cc_start: 0.7679 (mtpp) cc_final: 0.7463 (mtpp) REVERT: E 56 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7388 (t) REVERT: F 215 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7197 (ttt90) outliers start: 35 outliers final: 26 residues processed: 173 average time/residue: 0.2224 time to fit residues: 55.0449 Evaluate side-chains 158 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10904 Z= 0.209 Angle : 0.677 11.320 14902 Z= 0.328 Chirality : 0.046 0.260 1708 Planarity : 0.005 0.039 1886 Dihedral : 6.251 56.661 1732 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.30 % Allowed : 17.30 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.19 (0.24), residues: 1308 helix: 0.98 (0.34), residues: 258 sheet: -0.04 (0.24), residues: 422 loop : 0.03 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 291 HIS 0.003 0.001 HIS F 229 PHE 0.032 0.002 PHE F 230 TYR 0.015 0.002 TYR D 239 ARG 0.006 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7338 (mtp-110) cc_final: 0.6898 (ttm-80) REVERT: B 29 LEU cc_start: 0.8603 (tt) cc_final: 0.8103 (tt) REVERT: C 193 ILE cc_start: 0.7788 (tp) cc_final: 0.7584 (tt) REVERT: C 256 GLU cc_start: 0.6362 (tp30) cc_final: 0.5803 (tp30) REVERT: D 33 MET cc_start: 0.7151 (tmm) cc_final: 0.6763 (tmm) REVERT: D 62 ARG cc_start: 0.7606 (mtp-110) cc_final: 0.7326 (ttm-80) REVERT: E 56 THR cc_start: 0.7670 (OUTLIER) cc_final: 0.7402 (t) REVERT: F 215 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7204 (ttt90) outliers start: 38 outliers final: 29 residues processed: 169 average time/residue: 0.2185 time to fit residues: 52.9316 Evaluate side-chains 158 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS B 50 ASN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10904 Z= 0.227 Angle : 0.701 12.258 14902 Z= 0.339 Chirality : 0.048 0.382 1708 Planarity : 0.005 0.039 1886 Dihedral : 6.196 56.686 1732 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.96 % Allowed : 17.65 % Favored : 79.39 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.70 % 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: 0.15 (0.24), residues: 1308 helix: 0.95 (0.34), residues: 258 sheet: -0.06 (0.24), residues: 418 loop : 0.00 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 222 HIS 0.003 0.001 HIS C 229 PHE 0.034 0.002 PHE C 230 TYR 0.014 0.002 TYR D 239 ARG 0.006 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7100 (tmm) cc_final: 0.6803 (tmm) REVERT: A 62 ARG cc_start: 0.7417 (mtp-110) cc_final: 0.7149 (ttm-80) REVERT: B 29 LEU cc_start: 0.8616 (tt) cc_final: 0.8168 (tt) REVERT: C 256 GLU cc_start: 0.6370 (tp30) cc_final: 0.5788 (tp30) REVERT: D 62 ARG cc_start: 0.7578 (mtp-110) cc_final: 0.7304 (ttm-80) REVERT: E 56 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7406 (t) REVERT: F 215 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7286 (ttt90) outliers start: 34 outliers final: 28 residues processed: 167 average time/residue: 0.2265 time to fit residues: 53.6633 Evaluate side-chains 162 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10904 Z= 0.222 Angle : 0.697 11.227 14902 Z= 0.335 Chirality : 0.047 0.278 1708 Planarity : 0.005 0.039 1886 Dihedral : 6.427 56.654 1732 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.87 % Allowed : 17.91 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.13 (0.24), residues: 1308 helix: 0.96 (0.34), residues: 258 sheet: -0.14 (0.24), residues: 414 loop : 0.02 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 222 HIS 0.002 0.001 HIS C 229 PHE 0.035 0.002 PHE C 230 TYR 0.015 0.002 TYR C 122 ARG 0.006 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7176 (tmm) cc_final: 0.6868 (tmm) REVERT: A 62 ARG cc_start: 0.7361 (mtp-110) cc_final: 0.7119 (ttm-80) REVERT: B 29 LEU cc_start: 0.8435 (tt) cc_final: 0.7984 (tt) REVERT: C 256 GLU cc_start: 0.6357 (tp30) cc_final: 0.5766 (tp30) REVERT: D 33 MET cc_start: 0.7143 (tmm) cc_final: 0.6760 (tmm) REVERT: D 62 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.7281 (ttm-80) REVERT: E 56 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7415 (t) REVERT: F 215 ARG cc_start: 0.7523 (ttp80) cc_final: 0.7270 (ttt90) outliers start: 33 outliers final: 27 residues processed: 165 average time/residue: 0.2412 time to fit residues: 57.3761 Evaluate side-chains 160 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS C 114 GLN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10904 Z= 0.258 Angle : 0.710 11.108 14902 Z= 0.342 Chirality : 0.046 0.266 1708 Planarity : 0.005 0.039 1886 Dihedral : 6.404 56.508 1732 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.52 % Allowed : 18.96 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.05 (0.24), residues: 1308 helix: 1.08 (0.35), residues: 246 sheet: -0.31 (0.24), residues: 420 loop : 0.02 (0.27), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 222 HIS 0.003 0.001 HIS E 49 PHE 0.032 0.002 PHE F 230 TYR 0.019 0.002 TYR F 122 ARG 0.007 0.000 ARG A 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7178 (tmm) cc_final: 0.6837 (tmm) REVERT: A 62 ARG cc_start: 0.7402 (mtp-110) cc_final: 0.7167 (ttm-80) REVERT: B 29 LEU cc_start: 0.8463 (tt) cc_final: 0.8030 (tt) REVERT: B 123 MET cc_start: 0.6259 (mmp) cc_final: 0.5536 (mmt) REVERT: C 256 GLU cc_start: 0.6404 (tp30) cc_final: 0.5841 (tp30) REVERT: D 33 MET cc_start: 0.7122 (tmm) cc_final: 0.6715 (tmm) REVERT: D 62 ARG cc_start: 0.7622 (mtp-110) cc_final: 0.7363 (ttm-80) REVERT: E 56 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7440 (t) REVERT: F 215 ARG cc_start: 0.7488 (ttp80) cc_final: 0.7089 (ttt90) outliers start: 29 outliers final: 27 residues processed: 159 average time/residue: 0.2313 time to fit residues: 52.8816 Evaluate side-chains 160 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.0040 chunk 90 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.171658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.147176 restraints weight = 14383.190| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.49 r_work: 0.3826 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10904 Z= 0.194 Angle : 0.669 10.250 14902 Z= 0.322 Chirality : 0.044 0.257 1708 Planarity : 0.004 0.037 1886 Dihedral : 6.026 56.892 1732 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.70 % Allowed : 19.13 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.14 (0.24), residues: 1308 helix: 1.19 (0.35), residues: 246 sheet: -0.25 (0.24), residues: 418 loop : 0.05 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 222 HIS 0.002 0.001 HIS E 161 PHE 0.031 0.002 PHE F 230 TYR 0.015 0.001 TYR F 122 ARG 0.007 0.000 ARG A 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2365.24 seconds wall clock time: 44 minutes 2.75 seconds (2642.75 seconds total)