Starting phenix.real_space_refine on Tue Feb 13 14:34:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jnc_22404/02_2024/7jnc_22404.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jnc_22404/02_2024/7jnc_22404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jnc_22404/02_2024/7jnc_22404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jnc_22404/02_2024/7jnc_22404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jnc_22404/02_2024/7jnc_22404.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jnc_22404/02_2024/7jnc_22404.pdb" } resolution = 3.73 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= 0.005 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 24 5.16 5 C 4287 2.51 5 N 1080 2.21 5 O 1182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 107": "OE1" <-> "OE2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C ARG 259": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6573 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2121 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 13, 'TRANS': 273} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2121 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 13, 'TRANS': 273} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "C" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2121 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 13, 'TRANS': 273} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 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 Chain: "E" 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: "F" 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 3.99, per 1000 atoms: 0.61 Number of scatterers: 6573 At special positions: 0 Unit cell: (84.132, 82.08, 126.198, 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 24 16.00 O 1182 8.00 N 1080 7.00 C 4287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 149 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG D 1 " - " ASN A 155 " " NAG E 1 " - " ASN B 155 " " NAG F 1 " - " ASN C 155 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.5 seconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1662 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 37.0% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 53 through 96 removed outlier: 4.215A pdb=" N PHE A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.777A pdb=" N ASN A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 339 removed outlier: 3.920A pdb=" N THR A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 308 " --> pdb=" O TRP A 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 96 removed outlier: 4.443A pdb=" N ALA B 60 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.777A pdb=" N ASN B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 339 removed outlier: 3.920A pdb=" N THR B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 308 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 96 removed outlier: 4.442A pdb=" N ALA C 60 " --> pdb=" O ARG C 56 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 215 through 226 Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.777A pdb=" N ASN C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 339 removed outlier: 3.920A pdb=" N THR C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 308 " --> pdb=" O TRP C 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.519A pdb=" N LEU B 244 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 258 removed outlier: 5.519A pdb=" N LEU A 244 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 removed outlier: 4.023A pdb=" N ASP A 200 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 199 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 232 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 131 removed outlier: 6.383A pdb=" N GLN A 186 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS A 128 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 184 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS A 130 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 182 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE A 282 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 241 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 261 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 157 removed outlier: 3.550A pdb=" N TYR A 156 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 101 removed outlier: 5.520A pdb=" N LEU C 244 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.023A pdb=" N ASP B 200 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 199 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 232 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 131 removed outlier: 6.383A pdb=" N GLN B 186 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS B 128 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B 184 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS B 130 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 182 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B 282 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B 241 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 261 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 157 removed outlier: 3.550A pdb=" N TYR B 156 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 118 through 119 removed outlier: 4.023A pdb=" N ASP C 200 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 199 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 232 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 124 through 131 removed outlier: 6.383A pdb=" N GLN C 186 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS C 128 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE C 184 " --> pdb=" O CYS C 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS C 130 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 182 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE C 282 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 241 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 261 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 157 removed outlier: 3.550A pdb=" N TYR C 156 " --> pdb=" O LYS C 166 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 1035 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: 1.78 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2049 1.35 - 1.47: 1758 1.47 - 1.58: 2892 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 6735 Sorted by residual: bond pdb=" N LYS B 319 " pdb=" CA LYS B 319 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.52e+00 bond pdb=" N LYS C 319 " pdb=" CA LYS C 319 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.31e+00 bond pdb=" N LYS A 319 " pdb=" CA LYS A 319 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.20e-02 6.94e+03 5.22e+00 bond pdb=" N PHE A 318 " pdb=" CA PHE A 318 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.92e+00 bond pdb=" N PHE B 318 " pdb=" CA PHE B 318 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.87e+00 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.74: 198 106.74 - 113.58: 3767 113.58 - 120.42: 2437 120.42 - 127.26: 2724 127.26 - 134.10: 69 Bond angle restraints: 9195 Sorted by residual: angle pdb=" CA LYS B 319 " pdb=" C LYS B 319 " pdb=" O LYS B 319 " ideal model delta sigma weight residual 120.90 118.00 2.90 1.07e+00 8.73e-01 7.36e+00 angle pdb=" CA LYS A 319 " pdb=" C LYS A 319 " pdb=" O LYS A 319 " ideal model delta sigma weight residual 120.90 118.00 2.90 1.07e+00 8.73e-01 7.35e+00 angle pdb=" CA LYS C 319 " pdb=" C LYS C 319 " pdb=" O LYS C 319 " ideal model delta sigma weight residual 120.90 118.03 2.87 1.07e+00 8.73e-01 7.19e+00 angle pdb=" O PHE B 318 " pdb=" C PHE B 318 " pdb=" N LYS B 319 " ideal model delta sigma weight residual 122.03 124.55 -2.52 1.04e+00 9.25e-01 5.87e+00 angle pdb=" O PHE C 318 " pdb=" C PHE C 318 " pdb=" N LYS C 319 " ideal model delta sigma weight residual 122.03 124.50 -2.47 1.04e+00 9.25e-01 5.64e+00 ... (remaining 9190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 3763 16.08 - 32.16: 299 32.16 - 48.24: 66 48.24 - 64.32: 30 64.32 - 80.39: 3 Dihedral angle restraints: 4161 sinusoidal: 1611 harmonic: 2550 Sorted by residual: dihedral pdb=" CB CYS C 128 " pdb=" SG CYS C 128 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 41.20 51.80 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 41.23 51.77 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CB CYS B 128 " pdb=" SG CYS B 128 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 41.24 51.76 1 1.00e+01 1.00e-02 3.66e+01 ... (remaining 4158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 837 0.047 - 0.094: 224 0.094 - 0.140: 40 0.140 - 0.187: 3 0.187 - 0.234: 3 Chirality restraints: 1107 Sorted by residual: chirality pdb=" CA PHE A 318 " pdb=" N PHE A 318 " pdb=" C PHE A 318 " pdb=" CB PHE A 318 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA PHE B 318 " pdb=" N PHE B 318 " pdb=" C PHE B 318 " pdb=" CB PHE B 318 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PHE C 318 " pdb=" N PHE C 318 " pdb=" C PHE C 318 " pdb=" CB PHE C 318 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1104 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 232 " -0.014 2.00e-02 2.50e+03 1.02e-02 1.82e+00 pdb=" CG PHE A 232 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 232 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 232 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 232 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 232 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 232 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 232 " 0.014 2.00e-02 2.50e+03 1.02e-02 1.81e+00 pdb=" CG PHE B 232 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 232 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 232 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 232 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 232 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 232 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 232 " 0.014 2.00e-02 2.50e+03 1.01e-02 1.79e+00 pdb=" CG PHE C 232 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE C 232 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 232 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 232 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 232 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 232 " 0.006 2.00e-02 2.50e+03 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1760 2.80 - 3.32: 6510 3.32 - 3.85: 10764 3.85 - 4.37: 12187 4.37 - 4.90: 21104 Nonbonded interactions: 52325 Sorted by model distance: nonbonded pdb=" O PRO A 174 " pdb=" NE1 TRP A 287 " model vdw 2.269 2.520 nonbonded pdb=" O PRO C 174 " pdb=" NE1 TRP C 287 " model vdw 2.269 2.520 nonbonded pdb=" O PRO B 174 " pdb=" NE1 TRP B 287 " model vdw 2.270 2.520 nonbonded pdb=" CG ARG A 259 " pdb=" OE2 GLU B 261 " model vdw 2.295 3.440 nonbonded pdb=" CG ARG B 259 " pdb=" OE2 GLU C 261 " model vdw 2.301 3.440 ... (remaining 52320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 2.000 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.620 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6735 Z= 0.321 Angle : 0.682 5.468 9195 Z= 0.372 Chirality : 0.045 0.234 1107 Planarity : 0.003 0.028 1152 Dihedral : 13.562 80.394 2490 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.52 % Allowed : 6.74 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.24), residues: 855 helix: -1.00 (0.24), residues: 291 sheet: -3.58 (0.25), residues: 255 loop : -3.22 (0.30), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 230 HIS 0.001 0.000 HIS C 98 PHE 0.022 0.002 PHE A 232 TYR 0.015 0.002 TYR A 267 ARG 0.002 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 220 time to evaluate : 0.745 Fit side-chains REVERT: A 131 HIS cc_start: 0.8117 (m-70) cc_final: 0.7282 (m-70) REVERT: A 220 MET cc_start: 0.6991 (tpp) cc_final: 0.6719 (tpp) REVERT: A 286 GLU cc_start: 0.7176 (pt0) cc_final: 0.6612 (pt0) REVERT: B 286 GLU cc_start: 0.7102 (pt0) cc_final: 0.6692 (pt0) outliers start: 3 outliers final: 0 residues processed: 220 average time/residue: 0.2010 time to fit residues: 56.7915 Evaluate side-chains 163 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 293 GLN B 186 GLN B 293 GLN C 98 HIS C 186 GLN C 293 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6735 Z= 0.301 Angle : 0.683 7.035 9195 Z= 0.347 Chirality : 0.047 0.194 1107 Planarity : 0.004 0.029 1152 Dihedral : 8.834 59.936 1233 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.66 % Allowed : 20.73 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.27), residues: 855 helix: 0.36 (0.28), residues: 297 sheet: -3.01 (0.26), residues: 303 loop : -2.24 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 304 HIS 0.002 0.001 HIS C 98 PHE 0.029 0.002 PHE B 232 TYR 0.015 0.002 TYR A 201 ARG 0.003 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 0.990 Fit side-chains REVERT: A 220 MET cc_start: 0.7105 (tpp) cc_final: 0.6855 (tpp) REVERT: A 286 GLU cc_start: 0.7465 (pt0) cc_final: 0.7226 (pt0) REVERT: A 304 TRP cc_start: 0.7604 (m100) cc_final: 0.7170 (m100) REVERT: A 318 PHE cc_start: 0.6824 (m-10) cc_final: 0.6617 (m-10) REVERT: B 152 GLN cc_start: 0.6850 (mp10) cc_final: 0.6621 (mp10) REVERT: B 153 ARG cc_start: 0.7694 (mtp-110) cc_final: 0.6912 (mtm180) REVERT: B 188 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.6904 (ttm170) REVERT: B 318 PHE cc_start: 0.6990 (m-10) cc_final: 0.6718 (m-10) REVERT: C 304 TRP cc_start: 0.7909 (m100) cc_final: 0.7399 (m100) REVERT: C 315 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6071 (mp) outliers start: 27 outliers final: 17 residues processed: 183 average time/residue: 0.2364 time to fit residues: 58.8520 Evaluate side-chains 165 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 293 GLN C 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6735 Z= 0.214 Angle : 0.577 5.926 9195 Z= 0.289 Chirality : 0.043 0.210 1107 Planarity : 0.003 0.030 1152 Dihedral : 7.847 59.934 1233 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 7.94 % Allowed : 18.65 % Favored : 73.40 % 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: -1.73 (0.28), residues: 855 helix: 1.16 (0.28), residues: 297 sheet: -2.72 (0.27), residues: 285 loop : -1.70 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 304 HIS 0.001 0.000 HIS A 98 PHE 0.021 0.001 PHE B 232 TYR 0.024 0.002 TYR B 267 ARG 0.005 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 160 time to evaluate : 0.722 Fit side-chains REVERT: A 220 MET cc_start: 0.7217 (tpp) cc_final: 0.6938 (tpp) REVERT: A 238 THR cc_start: 0.8974 (t) cc_final: 0.8762 (p) REVERT: A 259 ARG cc_start: 0.8206 (mtm180) cc_final: 0.7871 (mtp-110) REVERT: A 286 GLU cc_start: 0.7630 (pt0) cc_final: 0.7318 (pt0) REVERT: A 304 TRP cc_start: 0.7633 (m100) cc_final: 0.7322 (m100) REVERT: A 309 LEU cc_start: 0.7720 (tp) cc_final: 0.7237 (tp) REVERT: A 318 PHE cc_start: 0.6884 (m-10) cc_final: 0.6607 (m-10) REVERT: B 318 PHE cc_start: 0.7038 (m-10) cc_final: 0.6788 (m-10) REVERT: C 188 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7597 (ttm-80) REVERT: C 259 ARG cc_start: 0.8434 (mtp85) cc_final: 0.7890 (mtp-110) REVERT: C 304 TRP cc_start: 0.7941 (m100) cc_final: 0.7380 (m100) outliers start: 46 outliers final: 24 residues processed: 188 average time/residue: 0.1997 time to fit residues: 48.6921 Evaluate side-chains 179 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS C 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6735 Z= 0.220 Angle : 0.562 5.714 9195 Z= 0.284 Chirality : 0.042 0.156 1107 Planarity : 0.003 0.028 1152 Dihedral : 7.663 59.653 1233 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.60 % Allowed : 20.03 % Favored : 72.37 % 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: -1.58 (0.28), residues: 855 helix: 1.11 (0.27), residues: 312 sheet: -2.59 (0.27), residues: 285 loop : -1.61 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 304 HIS 0.002 0.000 HIS B 130 PHE 0.022 0.001 PHE B 232 TYR 0.019 0.001 TYR B 267 ARG 0.002 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 160 time to evaluate : 0.803 Fit side-chains REVERT: A 182 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8960 (pp) REVERT: A 259 ARG cc_start: 0.8142 (mtm180) cc_final: 0.7895 (mtp-110) REVERT: A 286 GLU cc_start: 0.7553 (pt0) cc_final: 0.7269 (pt0) REVERT: A 304 TRP cc_start: 0.7630 (m100) cc_final: 0.7310 (m100) REVERT: A 318 PHE cc_start: 0.6837 (m-10) cc_final: 0.6559 (m-10) REVERT: B 94 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6554 (tm-30) REVERT: C 111 TYR cc_start: 0.8715 (m-80) cc_final: 0.8495 (m-80) REVERT: C 259 ARG cc_start: 0.8333 (mtp85) cc_final: 0.7818 (mtp-110) REVERT: C 304 TRP cc_start: 0.7904 (m100) cc_final: 0.7301 (m100) outliers start: 44 outliers final: 24 residues processed: 188 average time/residue: 0.1946 time to fit residues: 47.3517 Evaluate side-chains 184 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6735 Z= 0.271 Angle : 0.603 8.425 9195 Z= 0.303 Chirality : 0.043 0.164 1107 Planarity : 0.004 0.029 1152 Dihedral : 7.404 57.300 1233 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 8.64 % Allowed : 21.76 % Favored : 69.60 % 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: -1.41 (0.28), residues: 855 helix: 1.17 (0.27), residues: 312 sheet: -2.48 (0.29), residues: 255 loop : -1.61 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 230 HIS 0.002 0.001 HIS A 131 PHE 0.030 0.002 PHE B 219 TYR 0.018 0.002 TYR C 227 ARG 0.005 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 0.736 Fit side-chains REVERT: A 75 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6570 (mm) REVERT: A 259 ARG cc_start: 0.8069 (mtm180) cc_final: 0.7811 (mtp-110) REVERT: A 304 TRP cc_start: 0.7762 (m100) cc_final: 0.7394 (m100) REVERT: A 318 PHE cc_start: 0.6738 (m-10) cc_final: 0.6445 (m-10) REVERT: B 124 GLN cc_start: 0.6577 (pm20) cc_final: 0.6354 (pp30) REVERT: B 250 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5683 (pt0) REVERT: C 75 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6775 (mm) REVERT: C 94 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6786 (tm-30) REVERT: C 111 TYR cc_start: 0.8792 (m-80) cc_final: 0.8568 (m-80) REVERT: C 182 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8864 (pp) REVERT: C 250 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5865 (pt0) REVERT: C 259 ARG cc_start: 0.8278 (mtp85) cc_final: 0.8044 (mtp85) outliers start: 50 outliers final: 35 residues processed: 185 average time/residue: 0.2109 time to fit residues: 49.6617 Evaluate side-chains 186 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 146 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6735 Z= 0.277 Angle : 0.595 6.906 9195 Z= 0.301 Chirality : 0.044 0.177 1107 Planarity : 0.004 0.030 1152 Dihedral : 7.079 53.873 1233 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 9.50 % Allowed : 23.14 % Favored : 67.36 % 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: -1.38 (0.28), residues: 855 helix: 1.27 (0.27), residues: 312 sheet: -2.47 (0.29), residues: 255 loop : -1.68 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.001 0.001 HIS A 98 PHE 0.026 0.002 PHE B 232 TYR 0.015 0.002 TYR B 267 ARG 0.004 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 149 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 75 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6623 (mm) REVERT: A 221 GLN cc_start: 0.7023 (mt0) cc_final: 0.6806 (mt0) REVERT: A 250 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5848 (pt0) REVERT: A 304 TRP cc_start: 0.7810 (m100) cc_final: 0.7485 (m100) REVERT: A 318 PHE cc_start: 0.6737 (m-10) cc_final: 0.6412 (m-10) REVERT: B 165 VAL cc_start: 0.7375 (OUTLIER) cc_final: 0.7156 (m) REVERT: B 188 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7516 (ttm-80) REVERT: B 250 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5678 (pt0) REVERT: B 259 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7712 (mtp-110) REVERT: C 75 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6706 (mm) REVERT: C 94 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6881 (tm-30) REVERT: C 111 TYR cc_start: 0.8798 (m-80) cc_final: 0.8578 (m-80) REVERT: C 156 TYR cc_start: 0.8517 (p90) cc_final: 0.8259 (p90) REVERT: C 182 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8825 (pp) REVERT: C 241 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7420 (mtmm) outliers start: 55 outliers final: 42 residues processed: 190 average time/residue: 0.2263 time to fit residues: 54.4558 Evaluate side-chains 192 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 143 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.0670 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6735 Z= 0.180 Angle : 0.560 6.619 9195 Z= 0.282 Chirality : 0.042 0.164 1107 Planarity : 0.003 0.030 1152 Dihedral : 6.556 52.119 1233 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 7.43 % Allowed : 25.22 % Favored : 67.36 % 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: -1.28 (0.28), residues: 855 helix: 1.41 (0.27), residues: 312 sheet: -2.50 (0.28), residues: 273 loop : -1.51 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 230 HIS 0.001 0.000 HIS A 130 PHE 0.018 0.001 PHE B 232 TYR 0.030 0.002 TYR A 156 ARG 0.003 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6642 (mm) REVERT: A 156 TYR cc_start: 0.8123 (p90) cc_final: 0.7753 (p90) REVERT: A 250 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5824 (pt0) REVERT: A 304 TRP cc_start: 0.7765 (m100) cc_final: 0.7408 (m100) REVERT: A 318 PHE cc_start: 0.6663 (m-10) cc_final: 0.6404 (m-10) REVERT: B 165 VAL cc_start: 0.7380 (OUTLIER) cc_final: 0.7176 (m) REVERT: B 249 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.5670 (pp20) REVERT: B 250 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5447 (mt-10) REVERT: B 259 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7633 (mtp-110) REVERT: C 75 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6714 (mm) REVERT: C 94 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6849 (tm-30) REVERT: C 152 GLN cc_start: 0.7136 (tm-30) cc_final: 0.6901 (mp10) REVERT: C 182 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8841 (pp) REVERT: C 188 ARG cc_start: 0.7357 (ttm-80) cc_final: 0.5500 (ttt-90) REVERT: C 241 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7435 (mtmm) outliers start: 43 outliers final: 29 residues processed: 174 average time/residue: 0.2537 time to fit residues: 56.0729 Evaluate side-chains 175 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 138 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 73 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.6052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6735 Z= 0.324 Angle : 0.626 6.702 9195 Z= 0.322 Chirality : 0.044 0.169 1107 Planarity : 0.004 0.031 1152 Dihedral : 6.527 53.688 1233 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 8.64 % Allowed : 24.53 % Favored : 66.84 % 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: -1.37 (0.28), residues: 855 helix: 1.35 (0.27), residues: 312 sheet: -2.54 (0.28), residues: 261 loop : -1.66 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 304 HIS 0.002 0.001 HIS B 98 PHE 0.044 0.002 PHE C 219 TYR 0.026 0.002 TYR A 156 ARG 0.003 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 141 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 75 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6646 (mm) REVERT: A 221 GLN cc_start: 0.7457 (mt0) cc_final: 0.7167 (mt0) REVERT: A 250 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5759 (pt0) REVERT: A 304 TRP cc_start: 0.7875 (m100) cc_final: 0.7227 (m100) REVERT: A 318 PHE cc_start: 0.6777 (m-10) cc_final: 0.6508 (m-10) REVERT: B 153 ARG cc_start: 0.8264 (mmm160) cc_final: 0.7996 (mmm160) REVERT: B 165 VAL cc_start: 0.7289 (OUTLIER) cc_final: 0.7059 (m) REVERT: B 188 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7800 (ttm-80) REVERT: B 249 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5702 (pp20) REVERT: B 250 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5139 (mt-10) REVERT: B 259 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7672 (mtp-110) REVERT: C 75 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6762 (mm) REVERT: C 182 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8841 (pp) REVERT: C 188 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.5474 (ttt-90) REVERT: C 259 ARG cc_start: 0.7940 (mtp85) cc_final: 0.7311 (mtt90) outliers start: 50 outliers final: 39 residues processed: 174 average time/residue: 0.2205 time to fit residues: 48.4792 Evaluate side-chains 180 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 134 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 310 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.0050 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6735 Z= 0.195 Angle : 0.561 5.973 9195 Z= 0.287 Chirality : 0.042 0.145 1107 Planarity : 0.003 0.032 1152 Dihedral : 6.019 51.881 1233 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 7.08 % Allowed : 26.77 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.28), residues: 855 helix: 1.63 (0.27), residues: 312 sheet: -2.59 (0.27), residues: 279 loop : -1.38 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 304 HIS 0.001 0.000 HIS A 131 PHE 0.029 0.001 PHE C 219 TYR 0.024 0.002 TYR C 156 ARG 0.002 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 GLN cc_start: 0.7343 (mt0) cc_final: 0.7080 (mt0) REVERT: A 304 TRP cc_start: 0.7864 (m100) cc_final: 0.7218 (m100) REVERT: A 318 PHE cc_start: 0.6663 (m-10) cc_final: 0.6441 (m-10) REVERT: B 153 ARG cc_start: 0.8260 (mmm160) cc_final: 0.8003 (mmm160) REVERT: B 188 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7734 (ttm-80) REVERT: B 221 GLN cc_start: 0.7666 (mt0) cc_final: 0.7439 (mt0) REVERT: B 249 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5848 (pp20) REVERT: C 94 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6807 (tm-30) REVERT: C 188 ARG cc_start: 0.7372 (ttm-80) cc_final: 0.5253 (ttt-90) REVERT: C 259 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7405 (mtt90) outliers start: 41 outliers final: 32 residues processed: 170 average time/residue: 0.2506 time to fit residues: 54.2637 Evaluate side-chains 166 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 311 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6735 Z= 0.212 Angle : 0.581 6.114 9195 Z= 0.297 Chirality : 0.044 0.229 1107 Planarity : 0.004 0.031 1152 Dihedral : 5.911 52.722 1233 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.39 % Allowed : 27.98 % Favored : 65.63 % 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: -1.10 (0.28), residues: 855 helix: 1.71 (0.27), residues: 312 sheet: -2.60 (0.27), residues: 279 loop : -1.32 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 230 HIS 0.001 0.000 HIS B 98 PHE 0.029 0.002 PHE C 219 TYR 0.028 0.002 TYR C 156 ARG 0.003 0.000 ARG A 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 221 GLN cc_start: 0.7531 (mt0) cc_final: 0.7283 (mt0) REVERT: A 304 TRP cc_start: 0.7851 (m100) cc_final: 0.7220 (m100) REVERT: A 318 PHE cc_start: 0.6670 (m-10) cc_final: 0.6470 (m-10) REVERT: B 157 THR cc_start: 0.7441 (p) cc_final: 0.7239 (p) REVERT: B 188 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7756 (ttm-80) REVERT: B 221 GLN cc_start: 0.7696 (mt0) cc_final: 0.7420 (mt0) REVERT: B 249 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5797 (pp20) REVERT: C 94 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6783 (tm-30) REVERT: C 259 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7420 (mtt90) outliers start: 37 outliers final: 29 residues processed: 164 average time/residue: 0.2420 time to fit residues: 50.3808 Evaluate side-chains 166 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 311 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.161563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.141524 restraints weight = 8950.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141750 restraints weight = 8402.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141750 restraints weight = 8077.117| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.6484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6735 Z= 0.196 Angle : 0.598 9.820 9195 Z= 0.297 Chirality : 0.044 0.275 1107 Planarity : 0.004 0.031 1152 Dihedral : 5.995 52.595 1233 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.87 % Allowed : 27.98 % Favored : 66.15 % 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: -0.93 (0.28), residues: 855 helix: 1.81 (0.27), residues: 312 sheet: -2.42 (0.28), residues: 261 loop : -1.42 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 304 HIS 0.001 0.000 HIS B 98 PHE 0.029 0.002 PHE C 219 TYR 0.021 0.001 TYR B 267 ARG 0.002 0.000 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1887.22 seconds wall clock time: 35 minutes 2.02 seconds (2102.02 seconds total)