Starting phenix.real_space_refine on Wed Feb 14 07:11:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxh_33503/02_2024/7xxh_33503_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxh_33503/02_2024/7xxh_33503.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxh_33503/02_2024/7xxh_33503_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxh_33503/02_2024/7xxh_33503_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxh_33503/02_2024/7xxh_33503_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxh_33503/02_2024/7xxh_33503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxh_33503/02_2024/7xxh_33503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxh_33503/02_2024/7xxh_33503_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxh_33503/02_2024/7xxh_33503_updated.pdb" } resolution = 2.9 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 62 5.16 5 C 5654 2.51 5 N 1501 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "H GLU 46": "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: 8847 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2326 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 10, 'TRANS': 290} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1808 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2537 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "G" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 416 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1731 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'6AD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.14, per 1000 atoms: 0.58 Number of scatterers: 8847 At special positions: 0 Unit cell: (122.265, 111.815, 109.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 2 15.00 O 1628 8.00 N 1501 7.00 C 5654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 42 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 13 sheets defined 33.6% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'R' and resid 49 through 78 Proline residue: R 55 - end of helix Processing helix chain 'R' and resid 85 through 110 Proline residue: R 105 - end of helix Processing helix chain 'R' and resid 121 through 154 Processing helix chain 'R' and resid 156 through 159 No H-bonds generated for 'chain 'R' and resid 156 through 159' Processing helix chain 'R' and resid 165 through 189 Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 211 through 245 removed outlier: 4.201A pdb=" N VAL R 228 " --> pdb=" O ALA R 224 " (cutoff:3.500A) Proline residue: R 229 - end of helix Processing helix chain 'R' and resid 256 through 289 removed outlier: 3.854A pdb=" N SER R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE R 274 " --> pdb=" O ALA R 270 " (cutoff:3.500A) Proline residue: R 275 - end of helix removed outlier: 3.670A pdb=" N LEU R 288 " --> pdb=" O LEU R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 325 Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 332 through 339 Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.123A pdb=" N ARG A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 211 through 214 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.533A pdb=" N GLU A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 removed outlier: 3.619A pdb=" N LEU A 310 " --> pdb=" O MET A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 349 removed outlier: 3.862A pdb=" N VAL A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.332A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'R' and resid 191 through 194 removed outlier: 3.536A pdb=" N GLY R 191 " --> pdb=" O TYR R 203 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.258A pdb=" N VAL A 263 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N HIS A 321 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 265 " --> pdb=" O HIS A 321 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 268 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER A 219 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE A 194 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU A 36 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ARG A 196 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 38 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL A 198 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY A 40 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.004A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.707A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.537A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.752A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 250 through 254 removed outlier: 3.835A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 243 " --> pdb=" O ARG B 251 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= I, first strand: chain 'B' and resid 317 through 320 removed outlier: 4.101A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.642A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 92 through 97 removed outlier: 3.681A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 155 through 159 Processing sheet with id= M, first strand: chain 'H' and resid 226 through 231 removed outlier: 6.466A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 3.82 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: 2837 1.35 - 1.48: 2367 1.48 - 1.60: 3740 1.60 - 1.72: 4 1.72 - 1.85: 92 Bond restraints: 9040 Sorted by residual: bond pdb=" C3' 6AD R 501 " pdb=" C4' 6AD R 501 " ideal model delta sigma weight residual 1.267 1.577 -0.310 2.00e-02 2.50e+03 2.41e+02 bond pdb=" C4' 6AD R 501 " pdb=" O4' 6AD R 501 " ideal model delta sigma weight residual 1.558 1.312 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C2' 6AD R 501 " pdb=" C3' 6AD R 501 " ideal model delta sigma weight residual 1.657 1.520 0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C2' 6AD R 501 " pdb=" O2' 6AD R 501 " ideal model delta sigma weight residual 1.460 1.362 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C1' 6AD R 501 " pdb=" C2' 6AD R 501 " ideal model delta sigma weight residual 1.272 1.349 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 9035 not shown) Histogram of bond angle deviations from ideal: 96.38 - 103.90: 99 103.90 - 111.43: 4024 111.43 - 118.95: 3170 118.95 - 126.48: 4871 126.48 - 134.00: 129 Bond angle restraints: 12293 Sorted by residual: angle pdb=" N1 6AD R 501 " pdb=" C2 6AD R 501 " pdb=" S1 6AD R 501 " ideal model delta sigma weight residual 86.15 119.67 -33.52 3.00e+00 1.11e-01 1.25e+02 angle pdb=" N3 6AD R 501 " pdb=" C2 6AD R 501 " pdb=" S1 6AD R 501 " ideal model delta sigma weight residual 152.34 119.02 33.32 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C2' 6AD R 501 " pdb=" C1' 6AD R 501 " pdb=" N9 6AD R 501 " ideal model delta sigma weight residual 110.13 126.84 -16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" N1 6AD R 501 " pdb=" C6 6AD R 501 " pdb=" N6 6AD R 501 " ideal model delta sigma weight residual 104.75 120.96 -16.21 3.00e+00 1.11e-01 2.92e+01 angle pdb=" C1' 6AD R 501 " pdb=" N9 6AD R 501 " pdb=" C8 6AD R 501 " ideal model delta sigma weight residual 111.17 127.04 -15.87 3.00e+00 1.11e-01 2.80e+01 ... (remaining 12288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 4864 16.86 - 33.71: 356 33.71 - 50.57: 71 50.57 - 67.43: 6 67.43 - 84.29: 13 Dihedral angle restraints: 5310 sinusoidal: 1943 harmonic: 3367 Sorted by residual: dihedral pdb=" CB CYS R 42 " pdb=" SG CYS R 42 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual -86.00 -163.56 77.56 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.24 40.76 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CA PHE R 78 " pdb=" C PHE R 78 " pdb=" N HIS R 79 " pdb=" CA HIS R 79 " ideal model delta harmonic sigma weight residual -180.00 -162.84 -17.16 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1130 0.045 - 0.090: 224 0.090 - 0.135: 60 0.135 - 0.181: 1 0.181 - 0.226: 2 Chirality restraints: 1417 Sorted by residual: chirality pdb=" C3' 6AD R 501 " pdb=" C2' 6AD R 501 " pdb=" C4' 6AD R 501 " pdb=" O3' 6AD R 501 " both_signs ideal model delta sigma weight residual False -2.45 -2.67 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C2' 6AD R 501 " pdb=" C1' 6AD R 501 " pdb=" C3' 6AD R 501 " pdb=" O2' 6AD R 501 " both_signs ideal model delta sigma weight residual False -2.44 -2.23 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA PHE R 78 " pdb=" N PHE R 78 " pdb=" C PHE R 78 " pdb=" CB PHE R 78 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1414 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 74 " 0.016 2.00e-02 2.50e+03 1.71e-02 7.27e+00 pdb=" CG TRP R 74 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP R 74 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP R 74 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 74 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 74 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 74 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 74 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 74 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 74 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 58 " -0.015 2.00e-02 2.50e+03 1.40e-02 3.91e+00 pdb=" CG TYR R 58 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR R 58 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR R 58 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR R 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 58 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR R 58 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 58 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 186 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A 187 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " 0.020 5.00e-02 4.00e+02 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2780 2.83 - 3.35: 8403 3.35 - 3.86: 15024 3.86 - 4.38: 16941 4.38 - 4.90: 29684 Nonbonded interactions: 72832 Sorted by model distance: nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.309 2.440 nonbonded pdb=" OH TYR A 319 " pdb=" OD1 ASP A 340 " model vdw 2.314 2.440 nonbonded pdb=" O ILE H 138 " pdb=" OG1 THR H 238 " model vdw 2.320 2.440 nonbonded pdb=" O TYR R 324 " pdb=" ND2 ASN A 351 " model vdw 2.320 2.520 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.322 2.440 ... (remaining 72827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.710 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: 4.080 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.030 Find NCS groups from input model: 0.300 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:14.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 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 0.310 9040 Z= 0.389 Angle : 0.710 33.525 12293 Z= 0.304 Chirality : 0.039 0.226 1417 Planarity : 0.003 0.036 1546 Dihedral : 12.561 84.285 3132 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.67 % 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: 0.23 (0.26), residues: 1142 helix: 2.08 (0.26), residues: 401 sheet: -0.41 (0.36), residues: 240 loop : -1.17 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP R 74 HIS 0.004 0.001 HIS R 79 PHE 0.014 0.001 PHE R 78 TYR 0.035 0.001 TYR R 58 ARG 0.004 0.000 ARG R 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 0.836 Fit side-chains REVERT: R 73 ILE cc_start: 0.7457 (mm) cc_final: 0.7234 (mm) REVERT: H 231 GLN cc_start: 0.4856 (pp30) cc_final: 0.4501 (pp30) outliers start: 1 outliers final: 2 residues processed: 181 average time/residue: 1.0914 time to fit residues: 211.7459 Evaluate side-chains 141 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 291 GLN Chi-restraints excluded: chain B residue 18 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 ASN R 291 GLN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 110 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 340 ASN H 231 GLN H 232 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9040 Z= 0.270 Angle : 0.641 19.559 12293 Z= 0.322 Chirality : 0.044 0.165 1417 Planarity : 0.004 0.037 1546 Dihedral : 5.994 80.818 1273 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.28 % Allowed : 12.35 % Favored : 84.37 % 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: -0.12 (0.25), residues: 1142 helix: 1.69 (0.26), residues: 408 sheet: -0.89 (0.31), residues: 277 loop : -1.15 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.007 0.002 HIS A 212 PHE 0.014 0.002 PHE B 234 TYR 0.023 0.002 TYR H 235 ARG 0.006 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 0.924 Fit side-chains REVERT: R 90 MET cc_start: 0.7639 (mtt) cc_final: 0.7373 (mmt) REVERT: G 46 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7630 (mppt) REVERT: H 180 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7331 (mpt-90) outliers start: 30 outliers final: 11 residues processed: 171 average time/residue: 1.0637 time to fit residues: 195.0587 Evaluate side-chains 144 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 180 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 85 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN B 266 HIS B 340 ASN ** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN H 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 9040 Z= 0.463 Angle : 0.738 18.780 12293 Z= 0.376 Chirality : 0.048 0.181 1417 Planarity : 0.005 0.045 1546 Dihedral : 6.406 78.701 1268 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.14 % Allowed : 17.70 % Favored : 77.16 % 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: -0.54 (0.25), residues: 1142 helix: 0.98 (0.25), residues: 407 sheet: -0.78 (0.31), residues: 269 loop : -1.23 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP H 36 HIS 0.011 0.002 HIS A 212 PHE 0.021 0.003 PHE R 131 TYR 0.033 0.002 TYR H 235 ARG 0.009 0.001 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 158 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: R 104 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6321 (mm) REVERT: R 285 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6809 (tpp-160) REVERT: B 46 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6770 (mmp80) REVERT: B 228 ASP cc_start: 0.7761 (t0) cc_final: 0.7553 (t0) REVERT: B 269 ILE cc_start: 0.7804 (tp) cc_final: 0.7353 (mt) REVERT: B 322 ASP cc_start: 0.6694 (OUTLIER) cc_final: 0.6245 (m-30) REVERT: G 46 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7719 (mppt) REVERT: H 192 MET cc_start: 0.5820 (OUTLIER) cc_final: 0.5606 (tpt) outliers start: 47 outliers final: 23 residues processed: 184 average time/residue: 1.0921 time to fit residues: 215.4990 Evaluate side-chains 164 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 132 HIS Chi-restraints excluded: chain R residue 176 TRP Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 285 ARG Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 0.0470 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 239 ASN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9040 Z= 0.204 Angle : 0.595 18.632 12293 Z= 0.297 Chirality : 0.042 0.168 1417 Planarity : 0.004 0.045 1546 Dihedral : 6.060 81.154 1268 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.81 % Allowed : 20.55 % Favored : 74.64 % 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: -0.23 (0.25), residues: 1142 helix: 1.35 (0.26), residues: 406 sheet: -0.60 (0.32), residues: 256 loop : -1.16 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 176 HIS 0.006 0.001 HIS R 79 PHE 0.016 0.001 PHE B 151 TYR 0.031 0.002 TYR H 235 ARG 0.004 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 1.111 Fit side-chains REVERT: R 54 LEU cc_start: 0.4556 (OUTLIER) cc_final: 0.4275 (tt) REVERT: R 80 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.6101 (mmm) REVERT: R 90 MET cc_start: 0.7548 (mtt) cc_final: 0.7248 (mmt) REVERT: R 104 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6133 (mm) REVERT: R 285 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6832 (tpp-160) REVERT: A 185 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: A 252 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7511 (mm) REVERT: A 275 ASP cc_start: 0.6700 (OUTLIER) cc_final: 0.6384 (m-30) REVERT: B 46 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6660 (mmt90) REVERT: B 269 ILE cc_start: 0.7655 (tp) cc_final: 0.7097 (mt) REVERT: G 46 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7612 (mppt) REVERT: H 180 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6722 (mpt-90) outliers start: 44 outliers final: 16 residues processed: 170 average time/residue: 1.0138 time to fit residues: 185.7609 Evaluate side-chains 156 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 285 ARG Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 180 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.0030 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN B 110 ASN B 175 GLN B 237 ASN B 266 HIS B 340 ASN ** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9040 Z= 0.251 Angle : 0.609 18.358 12293 Z= 0.304 Chirality : 0.042 0.168 1417 Planarity : 0.004 0.045 1546 Dihedral : 6.035 82.441 1268 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 6.56 % Allowed : 20.22 % Favored : 73.22 % 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: -0.25 (0.25), residues: 1142 helix: 1.33 (0.26), residues: 409 sheet: -0.61 (0.32), residues: 256 loop : -1.19 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.005 0.001 HIS R 79 PHE 0.015 0.002 PHE B 151 TYR 0.032 0.002 TYR H 235 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 144 time to evaluate : 0.978 Fit side-chains REVERT: R 54 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4430 (tt) REVERT: R 104 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.6142 (mm) REVERT: R 285 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6784 (tpp-160) REVERT: A 185 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: A 252 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7544 (mm) REVERT: A 275 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6383 (m-30) REVERT: B 19 ARG cc_start: 0.7439 (ttp-110) cc_final: 0.7080 (tmm-80) REVERT: B 46 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6698 (mmt90) REVERT: B 228 ASP cc_start: 0.7625 (t0) cc_final: 0.7226 (t0) REVERT: B 234 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.7578 (m-80) REVERT: B 269 ILE cc_start: 0.7715 (tp) cc_final: 0.7117 (mt) REVERT: B 322 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6241 (m-30) REVERT: G 46 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7545 (mppt) REVERT: H 180 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6782 (mpt-90) outliers start: 60 outliers final: 27 residues processed: 178 average time/residue: 0.9990 time to fit residues: 191.6830 Evaluate side-chains 175 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 138 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 132 HIS Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 167 ASN Chi-restraints excluded: chain R residue 175 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 250 ASP Chi-restraints excluded: chain R residue 285 ARG Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 180 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 0.0020 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN B 175 GLN B 266 HIS B 340 ASN ** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9040 Z= 0.285 Angle : 0.628 19.418 12293 Z= 0.314 Chirality : 0.043 0.172 1417 Planarity : 0.004 0.045 1546 Dihedral : 6.107 82.298 1268 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 7.10 % Allowed : 20.87 % Favored : 72.02 % 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: -0.32 (0.25), residues: 1142 helix: 1.30 (0.26), residues: 403 sheet: -0.65 (0.32), residues: 260 loop : -1.23 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.006 0.001 HIS A 212 PHE 0.018 0.002 PHE A 49 TYR 0.034 0.002 TYR H 235 ARG 0.004 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 143 time to evaluate : 0.953 Fit side-chains REVERT: R 90 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7289 (mmt) REVERT: R 104 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.6148 (mm) REVERT: R 165 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6937 (mmtt) REVERT: R 285 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6812 (tpp-160) REVERT: A 252 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7482 (mm) REVERT: A 275 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.6413 (m-30) REVERT: B 46 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6698 (mmt90) REVERT: B 52 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7594 (ptp-110) REVERT: B 228 ASP cc_start: 0.7659 (t0) cc_final: 0.7194 (t0) REVERT: B 234 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: B 322 ASP cc_start: 0.6710 (OUTLIER) cc_final: 0.6254 (m-30) REVERT: G 46 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7569 (mppt) REVERT: H 180 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6943 (mpt-90) outliers start: 65 outliers final: 31 residues processed: 185 average time/residue: 1.0100 time to fit residues: 201.5626 Evaluate side-chains 175 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 133 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 90 MET Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 132 HIS Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 165 LYS Chi-restraints excluded: chain R residue 167 ASN Chi-restraints excluded: chain R residue 175 VAL Chi-restraints excluded: chain R residue 176 TRP Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 285 ARG Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 180 ARG Chi-restraints excluded: chain H residue 231 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9040 Z= 0.199 Angle : 0.594 18.722 12293 Z= 0.296 Chirality : 0.042 0.173 1417 Planarity : 0.004 0.044 1546 Dihedral : 5.998 82.975 1268 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 6.23 % Allowed : 22.08 % Favored : 71.69 % 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: -0.20 (0.26), residues: 1142 helix: 1.41 (0.26), residues: 403 sheet: -0.61 (0.32), residues: 261 loop : -1.17 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 79 PHE 0.015 0.001 PHE A 49 TYR 0.035 0.001 TYR H 235 ARG 0.003 0.000 ARG R 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 138 time to evaluate : 1.021 Fit side-chains REVERT: R 54 LEU cc_start: 0.4817 (OUTLIER) cc_final: 0.4534 (tt) REVERT: R 90 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7398 (mmt) REVERT: R 104 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.6185 (mm) REVERT: R 165 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6797 (mmtt) REVERT: R 285 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6616 (tpp-160) REVERT: A 185 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: A 275 ASP cc_start: 0.6686 (OUTLIER) cc_final: 0.6381 (m-30) REVERT: B 46 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6643 (mmt90) REVERT: B 228 ASP cc_start: 0.7563 (t0) cc_final: 0.7094 (t0) REVERT: B 234 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: G 46 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7567 (mppt) REVERT: H 180 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6924 (mpt-90) REVERT: H 231 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.6340 (pp30) outliers start: 57 outliers final: 27 residues processed: 176 average time/residue: 1.0510 time to fit residues: 200.2984 Evaluate side-chains 169 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 90 MET Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 132 HIS Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 165 LYS Chi-restraints excluded: chain R residue 175 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 285 ARG Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 180 ARG Chi-restraints excluded: chain H residue 231 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN B 340 ASN ** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9040 Z= 0.202 Angle : 0.602 18.845 12293 Z= 0.298 Chirality : 0.042 0.169 1417 Planarity : 0.004 0.043 1546 Dihedral : 5.952 83.021 1268 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.92 % Allowed : 23.72 % Favored : 71.37 % 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: -0.17 (0.26), residues: 1142 helix: 1.42 (0.26), residues: 403 sheet: -0.59 (0.32), residues: 261 loop : -1.12 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 79 PHE 0.023 0.001 PHE A 49 TYR 0.034 0.001 TYR H 235 ARG 0.003 0.000 ARG R 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 135 time to evaluate : 1.017 Fit side-chains REVERT: R 54 LEU cc_start: 0.4824 (OUTLIER) cc_final: 0.4547 (tt) REVERT: R 90 MET cc_start: 0.7607 (mtt) cc_final: 0.7384 (mmt) REVERT: R 104 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6236 (mm) REVERT: R 285 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6607 (tpp-160) REVERT: A 185 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: A 275 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6359 (m-30) REVERT: B 46 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6645 (mmt90) REVERT: B 228 ASP cc_start: 0.7562 (t0) cc_final: 0.7092 (t0) REVERT: B 234 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: G 46 LYS cc_start: 0.8018 (mtpt) cc_final: 0.7564 (mppt) REVERT: H 180 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6918 (mpt-90) REVERT: H 231 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.6397 (pp30) outliers start: 45 outliers final: 25 residues processed: 166 average time/residue: 0.9948 time to fit residues: 178.3665 Evaluate side-chains 162 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 175 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 285 ARG Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 180 ARG Chi-restraints excluded: chain H residue 231 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN B 340 ASN ** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9040 Z= 0.241 Angle : 0.620 19.037 12293 Z= 0.308 Chirality : 0.043 0.176 1417 Planarity : 0.004 0.043 1546 Dihedral : 5.985 82.692 1268 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.01 % Allowed : 23.17 % Favored : 70.82 % 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: -0.20 (0.26), residues: 1142 helix: 1.36 (0.26), residues: 404 sheet: -0.61 (0.32), residues: 261 loop : -1.12 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.005 0.001 HIS A 212 PHE 0.022 0.002 PHE A 49 TYR 0.036 0.002 TYR H 235 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 129 time to evaluate : 1.077 Fit side-chains REVERT: R 54 LEU cc_start: 0.4916 (OUTLIER) cc_final: 0.4625 (tt) REVERT: R 80 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5730 (mmm) REVERT: R 104 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6222 (mm) REVERT: R 165 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6870 (mmtt) REVERT: R 285 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6621 (tpp-160) REVERT: A 185 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: A 275 ASP cc_start: 0.6693 (OUTLIER) cc_final: 0.6385 (m-30) REVERT: B 46 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6656 (mmt90) REVERT: B 228 ASP cc_start: 0.7573 (t0) cc_final: 0.7110 (t0) REVERT: B 234 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: B 322 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.6177 (m-30) REVERT: G 46 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7580 (mppt) REVERT: H 180 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6814 (mpt-90) outliers start: 55 outliers final: 28 residues processed: 168 average time/residue: 0.9922 time to fit residues: 181.4631 Evaluate side-chains 167 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 132 HIS Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 165 LYS Chi-restraints excluded: chain R residue 175 VAL Chi-restraints excluded: chain R residue 176 TRP Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 285 ARG Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 180 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 0.0040 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9040 Z= 0.182 Angle : 0.605 18.942 12293 Z= 0.297 Chirality : 0.042 0.182 1417 Planarity : 0.004 0.041 1546 Dihedral : 5.875 82.991 1268 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.93 % Allowed : 24.92 % Favored : 71.15 % 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: -0.08 (0.26), residues: 1142 helix: 1.45 (0.26), residues: 406 sheet: -0.53 (0.32), residues: 259 loop : -1.05 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.004 0.001 HIS R 79 PHE 0.021 0.001 PHE A 49 TYR 0.033 0.001 TYR H 235 ARG 0.003 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 1.077 Fit side-chains REVERT: R 54 LEU cc_start: 0.4735 (OUTLIER) cc_final: 0.4468 (tt) REVERT: R 104 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.6160 (mm) REVERT: R 285 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6578 (tpp-160) REVERT: A 275 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6370 (m-30) REVERT: A 297 GLN cc_start: 0.7360 (tm-30) cc_final: 0.7106 (tm130) REVERT: B 52 ARG cc_start: 0.7689 (ptp-110) cc_final: 0.7393 (ptp-110) REVERT: B 228 ASP cc_start: 0.7552 (t0) cc_final: 0.7108 (t0) REVERT: B 234 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: G 46 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7587 (mppt) REVERT: H 180 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6825 (mpt-90) outliers start: 36 outliers final: 20 residues processed: 164 average time/residue: 1.0131 time to fit residues: 179.6997 Evaluate side-chains 155 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 175 VAL Chi-restraints excluded: chain R residue 176 TRP Chi-restraints excluded: chain R residue 285 ARG Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 180 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0000 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 64 optimal weight: 0.0050 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** H 167 HIS ** 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 = 0.4315 r_free = 0.4315 target = 0.180904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.141327 restraints weight = 9444.888| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.00 r_work: 0.3754 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9040 Z= 0.167 Angle : 0.599 19.094 12293 Z= 0.292 Chirality : 0.041 0.170 1417 Planarity : 0.004 0.041 1546 Dihedral : 5.780 83.376 1268 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.17 % Allowed : 26.23 % Favored : 70.60 % 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: -0.02 (0.26), residues: 1142 helix: 1.48 (0.27), residues: 406 sheet: -0.53 (0.32), residues: 252 loop : -0.98 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 332 HIS 0.003 0.001 HIS R 79 PHE 0.029 0.001 PHE A 49 TYR 0.030 0.001 TYR H 235 ARG 0.003 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4433.37 seconds wall clock time: 78 minutes 55.01 seconds (4735.01 seconds total)