Starting phenix.real_space_refine on Sun Dec 29 10:52:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v6a_31740/12_2024/7v6a_31740.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v6a_31740/12_2024/7v6a_31740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v6a_31740/12_2024/7v6a_31740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v6a_31740/12_2024/7v6a_31740.map" model { file = "/net/cci-nas-00/data/ceres_data/7v6a_31740/12_2024/7v6a_31740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v6a_31740/12_2024/7v6a_31740.cif" } resolution = 3.6 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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2132 atoms to isotropic. 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 65 5.16 5 C 5497 2.51 5 N 1460 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8584 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2562 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2168 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'5XI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.40, per 1000 atoms: 0.63 Number of scatterers: 8584 At special positions: 0 Unit cell: (94.2936, 123.414, 123.414, 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 65 16.00 O 1562 8.00 N 1460 7.00 C 5497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.27 Conformation dependent library (CDL) restraints added in 1.0 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 35.9% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.087A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.887A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 removed outlier: 4.124A pdb=" N ARG A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.558A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 55 Processing helix chain 'R' and resid 55 through 60 Processing helix chain 'R' and resid 65 through 67 No H-bonds generated for 'chain 'R' and resid 65 through 67' Processing helix chain 'R' and resid 68 through 91 removed outlier: 5.378A pdb=" N MET R 86 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ASN R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'R' and resid 101 through 136 removed outlier: 4.149A pdb=" N TYR R 113 " --> pdb=" O LEU R 109 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN R 117 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 144 Processing helix chain 'R' and resid 145 through 165 Processing helix chain 'R' and resid 165 through 176 removed outlier: 4.291A pdb=" N LEU R 169 " --> pdb=" O ALA R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 204 removed outlier: 3.929A pdb=" N THR R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA R 202 " --> pdb=" O GLY R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 222 Processing helix chain 'R' and resid 392 through 413 removed outlier: 3.654A pdb=" N LEU R 406 " --> pdb=" O ILE R 402 " (cutoff:3.500A) Processing helix chain 'R' and resid 415 through 420 Processing helix chain 'R' and resid 431 through 441 Processing helix chain 'R' and resid 443 through 455 Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 457 through 463 Processing helix chain 'R' and resid 465 through 470 removed outlier: 3.823A pdb=" N CYS R 470 " --> pdb=" O HIS R 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.503A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 226 removed outlier: 7.147A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.731A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.435A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.084A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.796A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.881A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.648A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.322A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.513A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU S 81 " --> pdb=" O LEU S 20 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU S 79 " --> pdb=" O CYS S 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.691A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 143 through 146 removed outlier: 3.599A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 174 through 177 removed outlier: 6.782A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1050 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: 2.58 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2252 1.33 - 1.45: 1739 1.45 - 1.57: 4685 1.57 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 8770 Sorted by residual: bond pdb=" C19 5XI R 601 " pdb=" N4 5XI R 601 " ideal model delta sigma weight residual 1.351 1.479 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C19 5XI R 601 " pdb=" O3 5XI R 601 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C8 5XI R 601 " pdb=" N1 5XI R 601 " ideal model delta sigma weight residual 1.439 1.480 -0.041 2.00e-02 2.50e+03 4.22e+00 bond pdb=" C9 5XI R 601 " pdb=" N2 5XI R 601 " ideal model delta sigma weight residual 1.452 1.493 -0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" CA THR B 181 " pdb=" CB THR B 181 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.35e-02 5.49e+03 3.35e+00 ... (remaining 8765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 11425 1.54 - 3.08: 407 3.08 - 4.62: 70 4.62 - 6.16: 16 6.16 - 7.70: 5 Bond angle restraints: 11923 Sorted by residual: angle pdb=" N VAL R 418 " pdb=" CA VAL R 418 " pdb=" C VAL R 418 " ideal model delta sigma weight residual 112.96 108.07 4.89 1.00e+00 1.00e+00 2.39e+01 angle pdb=" CA TRP R 435 " pdb=" CB TRP R 435 " pdb=" CG TRP R 435 " ideal model delta sigma weight residual 113.60 119.04 -5.44 1.90e+00 2.77e-01 8.20e+00 angle pdb=" N TRP R 435 " pdb=" CA TRP R 435 " pdb=" C TRP R 435 " ideal model delta sigma weight residual 111.33 107.91 3.42 1.21e+00 6.83e-01 8.00e+00 angle pdb=" N ASP B 246 " pdb=" CA ASP B 246 " pdb=" C ASP B 246 " ideal model delta sigma weight residual 113.38 110.13 3.25 1.23e+00 6.61e-01 6.96e+00 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 122.19 118.54 3.65 1.41e+00 5.03e-01 6.71e+00 ... (remaining 11918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4695 17.90 - 35.80: 373 35.80 - 53.70: 78 53.70 - 71.60: 11 71.60 - 89.49: 10 Dihedral angle restraints: 5167 sinusoidal: 1908 harmonic: 3259 Sorted by residual: dihedral pdb=" CB CYS R 426 " pdb=" SG CYS R 426 " pdb=" SG CYS R 429 " pdb=" CB CYS R 429 " ideal model delta sinusoidal sigma weight residual 93.00 136.93 -43.93 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CA VAL R 434 " pdb=" C VAL R 434 " pdb=" N TRP R 435 " pdb=" CA TRP R 435 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA MET S 93 " pdb=" C MET S 93 " pdb=" N TYR S 94 " pdb=" CA TYR S 94 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1222 0.069 - 0.137: 156 0.137 - 0.206: 7 0.206 - 0.274: 0 0.274 - 0.343: 2 Chirality restraints: 1387 Sorted by residual: chirality pdb=" C9 5XI R 601 " pdb=" C10 5XI R 601 " pdb=" C13 5XI R 601 " pdb=" N2 5XI R 601 " both_signs ideal model delta sigma weight residual False -2.30 -2.65 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C14 5XI R 601 " pdb=" C15 5XI R 601 " pdb=" C18 5XI R 601 " pdb=" N3 5XI R 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.62 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB ILE R 93 " pdb=" CA ILE R 93 " pdb=" CG1 ILE R 93 " pdb=" CG2 ILE R 93 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.34e-01 ... (remaining 1384 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 414 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO R 415 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO R 415 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 415 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO S 41 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 201 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C ILE R 201 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE R 201 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA R 202 " -0.011 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 182 2.67 - 3.23: 8623 3.23 - 3.79: 13522 3.79 - 4.34: 17889 4.34 - 4.90: 29286 Nonbonded interactions: 69502 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.113 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.163 3.040 nonbonded pdb=" OH TYR R 439 " pdb=" OH TYR R 443 " model vdw 2.179 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O SER B 160 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.210 3.040 ... (remaining 69497 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.840 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 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 : 0.004 0.128 8770 Z= 0.254 Angle : 0.706 7.697 11923 Z= 0.397 Chirality : 0.045 0.343 1387 Planarity : 0.004 0.056 1488 Dihedral : 14.081 89.494 3057 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.88 (0.25), residues: 1104 helix: 0.44 (0.27), residues: 398 sheet: -2.68 (0.30), residues: 230 loop : -1.90 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.029 0.002 PHE B 235 TYR 0.020 0.002 TYR S 103 ARG 0.008 0.001 ARG S 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.876 Fit side-chains REVERT: A 14 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 210 LYS cc_start: 0.7389 (tptt) cc_final: 0.6844 (mmtm) REVERT: A 252 SER cc_start: 0.7474 (p) cc_final: 0.7193 (p) REVERT: A 255 ASN cc_start: 0.6919 (m-40) cc_final: 0.6498 (m-40) REVERT: A 337 ASP cc_start: 0.6790 (t70) cc_final: 0.6584 (t70) REVERT: A 345 LYS cc_start: 0.8149 (tptt) cc_final: 0.7755 (tptt) REVERT: A 353 LEU cc_start: 0.8697 (tp) cc_final: 0.8402 (tp) REVERT: B 110 ASN cc_start: 0.8503 (m110) cc_final: 0.8224 (m110) REVERT: B 125 ASN cc_start: 0.8332 (t0) cc_final: 0.8092 (t0) REVERT: B 161 SER cc_start: 0.8108 (p) cc_final: 0.7846 (p) REVERT: B 228 ASP cc_start: 0.6713 (p0) cc_final: 0.6192 (p0) REVERT: B 239 ASN cc_start: 0.7808 (m110) cc_final: 0.7451 (m-40) REVERT: B 279 SER cc_start: 0.7990 (t) cc_final: 0.7480 (p) REVERT: B 294 CYS cc_start: 0.7277 (t) cc_final: 0.7024 (t) REVERT: B 297 TRP cc_start: 0.8425 (m100) cc_final: 0.8143 (m100) REVERT: C 15 LEU cc_start: 0.8064 (tt) cc_final: 0.7775 (tt) REVERT: S 45 LEU cc_start: 0.7481 (mp) cc_final: 0.7278 (mt) REVERT: S 128 MET cc_start: 0.7325 (mtp) cc_final: 0.6859 (mtp) REVERT: S 179 ARG cc_start: 0.7552 (tpp-160) cc_final: 0.7326 (tpp-160) REVERT: S 214 VAL cc_start: 0.8351 (t) cc_final: 0.8150 (p) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2507 time to fit residues: 89.2962 Evaluate side-chains 240 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 331 ASN B 88 ASN B 110 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8770 Z= 0.242 Angle : 0.618 10.715 11923 Z= 0.325 Chirality : 0.043 0.196 1387 Planarity : 0.004 0.055 1488 Dihedral : 6.179 58.417 1242 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.56 % Allowed : 12.36 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.69 (0.25), residues: 1104 helix: 0.58 (0.27), residues: 392 sheet: -2.25 (0.32), residues: 218 loop : -1.96 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.006 0.001 HIS S 35 PHE 0.013 0.002 PHE B 234 TYR 0.012 0.002 TYR S 223 ARG 0.005 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.924 Fit side-chains REVERT: A 14 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6883 (tm-30) REVERT: A 210 LYS cc_start: 0.7655 (tptt) cc_final: 0.7418 (tptt) REVERT: A 211 TRP cc_start: 0.7765 (p-90) cc_final: 0.7215 (p-90) REVERT: A 252 SER cc_start: 0.7499 (p) cc_final: 0.7168 (p) REVERT: A 255 ASN cc_start: 0.7113 (m-40) cc_final: 0.6751 (m110) REVERT: A 337 ASP cc_start: 0.6945 (t70) cc_final: 0.6721 (t70) REVERT: A 351 CYS cc_start: 0.7225 (m) cc_final: 0.6735 (m) REVERT: B 105 TYR cc_start: 0.8104 (t80) cc_final: 0.7882 (t80) REVERT: B 125 ASN cc_start: 0.8485 (t0) cc_final: 0.8135 (t0) REVERT: B 228 ASP cc_start: 0.6822 (p0) cc_final: 0.6343 (p0) REVERT: B 249 THR cc_start: 0.7560 (m) cc_final: 0.7340 (p) REVERT: B 297 TRP cc_start: 0.8475 (m100) cc_final: 0.8142 (m100) REVERT: B 301 LYS cc_start: 0.7434 (mttp) cc_final: 0.7226 (mtpp) REVERT: B 339 TRP cc_start: 0.8150 (m100) cc_final: 0.7903 (m100) REVERT: S 110 PHE cc_start: 0.7844 (t80) cc_final: 0.7546 (t80) REVERT: S 128 MET cc_start: 0.7528 (mtp) cc_final: 0.6936 (mtp) REVERT: S 190 ARG cc_start: 0.7548 (mtm110) cc_final: 0.7303 (mtm110) REVERT: S 202 LEU cc_start: 0.8233 (tp) cc_final: 0.8009 (tt) REVERT: R 121 MET cc_start: 0.7006 (mmt) cc_final: 0.6803 (mmt) REVERT: R 152 MET cc_start: 0.5923 (tpt) cc_final: 0.5632 (tpt) REVERT: R 190 LEU cc_start: 0.6887 (mm) cc_final: 0.6646 (mp) REVERT: R 459 THR cc_start: 0.6469 (t) cc_final: 0.6212 (m) outliers start: 14 outliers final: 13 residues processed: 247 average time/residue: 0.2409 time to fit residues: 78.3754 Evaluate side-chains 253 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 110 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN R 417 ASN ** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8770 Z= 0.305 Angle : 0.643 11.044 11923 Z= 0.339 Chirality : 0.044 0.180 1387 Planarity : 0.004 0.058 1488 Dihedral : 6.355 58.421 1242 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.90 % Allowed : 16.70 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.76 (0.25), residues: 1104 helix: 0.58 (0.27), residues: 389 sheet: -2.29 (0.30), residues: 251 loop : -1.97 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 435 HIS 0.007 0.001 HIS S 35 PHE 0.014 0.002 PHE R 409 TYR 0.018 0.002 TYR S 102 ARG 0.006 0.001 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.845 Fit side-chains REVERT: A 8 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6939 (mt-10) REVERT: A 14 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6957 (tm-30) REVERT: A 53 MET cc_start: 0.5404 (mpp) cc_final: 0.4798 (mpp) REVERT: A 210 LYS cc_start: 0.7766 (tptt) cc_final: 0.7560 (tptt) REVERT: A 252 SER cc_start: 0.7503 (p) cc_final: 0.7136 (p) REVERT: A 255 ASN cc_start: 0.7252 (m-40) cc_final: 0.6858 (m110) REVERT: A 270 LYS cc_start: 0.7286 (mmmt) cc_final: 0.6951 (mmtp) REVERT: A 337 ASP cc_start: 0.7070 (t70) cc_final: 0.6835 (t70) REVERT: A 351 CYS cc_start: 0.7229 (m) cc_final: 0.6786 (m) REVERT: B 125 ASN cc_start: 0.8556 (t0) cc_final: 0.8167 (t0) REVERT: B 228 ASP cc_start: 0.7005 (p0) cc_final: 0.6294 (p0) REVERT: B 239 ASN cc_start: 0.8069 (m110) cc_final: 0.7830 (m-40) REVERT: B 249 THR cc_start: 0.7524 (m) cc_final: 0.7290 (p) REVERT: B 339 TRP cc_start: 0.8152 (m100) cc_final: 0.7722 (m100) REVERT: C 62 ARG cc_start: 0.5908 (mtm-85) cc_final: 0.5639 (mtt180) REVERT: S 128 MET cc_start: 0.7534 (mtp) cc_final: 0.7027 (mtp) REVERT: S 190 ARG cc_start: 0.7490 (mtm110) cc_final: 0.7278 (mtm110) REVERT: S 202 LEU cc_start: 0.8210 (tp) cc_final: 0.7995 (tt) REVERT: R 53 VAL cc_start: 0.7178 (m) cc_final: 0.6931 (p) REVERT: R 409 PHE cc_start: 0.6524 (t80) cc_final: 0.6313 (t80) REVERT: R 459 THR cc_start: 0.6596 (t) cc_final: 0.6126 (m) outliers start: 26 outliers final: 20 residues processed: 245 average time/residue: 0.2477 time to fit residues: 79.5262 Evaluate side-chains 246 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN ** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8770 Z= 0.241 Angle : 0.609 11.528 11923 Z= 0.317 Chirality : 0.043 0.183 1387 Planarity : 0.004 0.058 1488 Dihedral : 6.214 56.918 1242 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.68 % Allowed : 16.26 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.65 (0.25), residues: 1104 helix: 0.62 (0.27), residues: 392 sheet: -2.30 (0.29), residues: 268 loop : -1.78 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 435 HIS 0.005 0.001 HIS S 35 PHE 0.013 0.002 PHE B 235 TYR 0.014 0.002 TYR B 105 ARG 0.004 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6877 (mt-10) REVERT: A 14 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6913 (tm-30) REVERT: A 210 LYS cc_start: 0.7740 (tptt) cc_final: 0.7536 (tptt) REVERT: A 252 SER cc_start: 0.7382 (p) cc_final: 0.7003 (p) REVERT: A 255 ASN cc_start: 0.7214 (m-40) cc_final: 0.6732 (m110) REVERT: A 270 LYS cc_start: 0.7265 (mmmt) cc_final: 0.6979 (mmtp) REVERT: A 337 ASP cc_start: 0.7017 (t70) cc_final: 0.6787 (t70) REVERT: A 351 CYS cc_start: 0.7224 (m) cc_final: 0.6786 (m) REVERT: B 13 GLN cc_start: 0.6124 (OUTLIER) cc_final: 0.5807 (tp40) REVERT: B 125 ASN cc_start: 0.8536 (t0) cc_final: 0.8161 (t0) REVERT: B 137 ARG cc_start: 0.7723 (tpp-160) cc_final: 0.7396 (tpp-160) REVERT: B 228 ASP cc_start: 0.6967 (p0) cc_final: 0.6320 (p0) REVERT: B 239 ASN cc_start: 0.8004 (m110) cc_final: 0.7747 (m-40) REVERT: B 249 THR cc_start: 0.7471 (m) cc_final: 0.7252 (p) REVERT: B 297 TRP cc_start: 0.8465 (m100) cc_final: 0.8236 (m100) REVERT: B 308 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6885 (mp) REVERT: B 339 TRP cc_start: 0.8137 (m100) cc_final: 0.7803 (m100) REVERT: S 128 MET cc_start: 0.7530 (mtp) cc_final: 0.7038 (mtp) REVERT: S 190 ARG cc_start: 0.7510 (mtm110) cc_final: 0.7232 (mtm110) REVERT: S 202 LEU cc_start: 0.8208 (tp) cc_final: 0.7998 (tt) REVERT: R 459 THR cc_start: 0.6295 (t) cc_final: 0.5800 (m) outliers start: 42 outliers final: 31 residues processed: 256 average time/residue: 0.2423 time to fit residues: 82.0297 Evaluate side-chains 268 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 68 ASN Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 0.0370 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN ** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8770 Z= 0.232 Angle : 0.621 12.170 11923 Z= 0.320 Chirality : 0.043 0.191 1387 Planarity : 0.004 0.056 1488 Dihedral : 6.143 55.422 1242 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.01 % Allowed : 17.93 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.43 (0.26), residues: 1104 helix: 0.63 (0.27), residues: 398 sheet: -2.08 (0.30), residues: 263 loop : -1.58 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 435 HIS 0.005 0.001 HIS S 35 PHE 0.013 0.002 PHE S 29 TYR 0.013 0.001 TYR R 113 ARG 0.005 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6775 (mt-10) REVERT: A 14 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6895 (tm-30) REVERT: A 249 LEU cc_start: 0.8310 (tt) cc_final: 0.8036 (tp) REVERT: A 252 SER cc_start: 0.6676 (p) cc_final: 0.6385 (p) REVERT: A 255 ASN cc_start: 0.7263 (m-40) cc_final: 0.6959 (m110) REVERT: A 270 LYS cc_start: 0.7267 (mmmt) cc_final: 0.7057 (mmtp) REVERT: A 337 ASP cc_start: 0.6996 (t70) cc_final: 0.6757 (t70) REVERT: B 13 GLN cc_start: 0.6093 (OUTLIER) cc_final: 0.5847 (tp40) REVERT: B 70 LEU cc_start: 0.8392 (mm) cc_final: 0.8170 (mp) REVERT: B 125 ASN cc_start: 0.8532 (t0) cc_final: 0.8163 (t0) REVERT: B 137 ARG cc_start: 0.7724 (tpp-160) cc_final: 0.7413 (tpp-160) REVERT: B 228 ASP cc_start: 0.6940 (p0) cc_final: 0.6487 (p0) REVERT: B 239 ASN cc_start: 0.7972 (m110) cc_final: 0.7732 (m-40) REVERT: B 249 THR cc_start: 0.7336 (m) cc_final: 0.7129 (p) REVERT: B 297 TRP cc_start: 0.8526 (m100) cc_final: 0.8262 (m100) REVERT: B 308 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6858 (mp) REVERT: B 339 TRP cc_start: 0.8145 (m100) cc_final: 0.7842 (m100) REVERT: S 18 ARG cc_start: 0.5622 (OUTLIER) cc_final: 0.5339 (mmm160) REVERT: S 128 MET cc_start: 0.7509 (mtp) cc_final: 0.7069 (mtp) REVERT: S 162 LEU cc_start: 0.8027 (tt) cc_final: 0.7695 (tt) REVERT: S 166 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7366 (tt) REVERT: S 190 ARG cc_start: 0.7539 (mtm110) cc_final: 0.7230 (mtm110) REVERT: S 202 LEU cc_start: 0.8198 (tp) cc_final: 0.7974 (tt) outliers start: 45 outliers final: 36 residues processed: 257 average time/residue: 0.2344 time to fit residues: 79.8589 Evaluate side-chains 277 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 68 ASN Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 0.0170 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8770 Z= 0.201 Angle : 0.614 11.358 11923 Z= 0.314 Chirality : 0.042 0.195 1387 Planarity : 0.004 0.056 1488 Dihedral : 6.064 55.936 1242 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.24 % Allowed : 18.04 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.24 (0.26), residues: 1104 helix: 0.75 (0.27), residues: 399 sheet: -1.87 (0.31), residues: 264 loop : -1.51 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 169 HIS 0.006 0.001 HIS S 35 PHE 0.018 0.001 PHE S 29 TYR 0.012 0.001 TYR S 178 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 0.926 Fit side-chains REVERT: A 8 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6714 (mt-10) REVERT: A 14 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6890 (tm-30) REVERT: A 249 LEU cc_start: 0.8289 (tt) cc_final: 0.8024 (tp) REVERT: A 252 SER cc_start: 0.6663 (p) cc_final: 0.6446 (p) REVERT: A 337 ASP cc_start: 0.6992 (t70) cc_final: 0.6761 (t70) REVERT: B 13 GLN cc_start: 0.6107 (OUTLIER) cc_final: 0.5893 (tp40) REVERT: B 70 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 125 ASN cc_start: 0.8523 (t0) cc_final: 0.8155 (t0) REVERT: B 137 ARG cc_start: 0.7722 (tpp-160) cc_final: 0.7451 (tpp-160) REVERT: B 169 TRP cc_start: 0.8226 (m100) cc_final: 0.7755 (m100) REVERT: B 228 ASP cc_start: 0.6939 (p0) cc_final: 0.6490 (p0) REVERT: B 249 THR cc_start: 0.7322 (m) cc_final: 0.7122 (p) REVERT: B 297 TRP cc_start: 0.8526 (m100) cc_final: 0.8249 (m100) REVERT: B 308 LEU cc_start: 0.7341 (tp) cc_final: 0.6771 (mp) REVERT: B 339 TRP cc_start: 0.8094 (m100) cc_final: 0.7824 (m100) REVERT: S 18 ARG cc_start: 0.5548 (OUTLIER) cc_final: 0.5256 (mmm160) REVERT: S 29 PHE cc_start: 0.7885 (t80) cc_final: 0.7401 (t80) REVERT: S 108 PHE cc_start: 0.8120 (m-80) cc_final: 0.7859 (m-80) REVERT: S 128 MET cc_start: 0.7516 (mtp) cc_final: 0.7114 (mtp) REVERT: S 162 LEU cc_start: 0.8051 (tt) cc_final: 0.7758 (tt) REVERT: S 190 ARG cc_start: 0.7576 (mtm110) cc_final: 0.7362 (mtm110) REVERT: S 202 LEU cc_start: 0.8194 (tp) cc_final: 0.7987 (tt) REVERT: R 86 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.6006 (mpt) REVERT: R 419 MET cc_start: 0.5082 (ppp) cc_final: 0.4881 (ppp) outliers start: 56 outliers final: 42 residues processed: 263 average time/residue: 0.2344 time to fit residues: 82.0627 Evaluate side-chains 285 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 68 ASN Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 105 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8770 Z= 0.225 Angle : 0.635 12.903 11923 Z= 0.321 Chirality : 0.043 0.194 1387 Planarity : 0.004 0.055 1488 Dihedral : 6.081 53.849 1242 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.90 % Allowed : 20.04 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.21 (0.26), residues: 1104 helix: 0.72 (0.27), residues: 399 sheet: -1.72 (0.31), residues: 261 loop : -1.55 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 435 HIS 0.005 0.001 HIS S 35 PHE 0.011 0.001 PHE B 234 TYR 0.013 0.001 TYR R 113 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6748 (mt-10) REVERT: A 14 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6899 (tm-30) REVERT: A 249 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8036 (tp) REVERT: A 252 SER cc_start: 0.6642 (p) cc_final: 0.6421 (p) REVERT: A 337 ASP cc_start: 0.7028 (t70) cc_final: 0.6792 (t70) REVERT: B 13 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.5899 (tp40) REVERT: B 70 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8162 (mp) REVERT: B 125 ASN cc_start: 0.8526 (t0) cc_final: 0.8133 (t0) REVERT: B 137 ARG cc_start: 0.7704 (tpp-160) cc_final: 0.7452 (tpp-160) REVERT: B 228 ASP cc_start: 0.6936 (p0) cc_final: 0.6471 (p0) REVERT: B 249 THR cc_start: 0.7321 (m) cc_final: 0.7089 (p) REVERT: B 308 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6755 (mp) REVERT: B 339 TRP cc_start: 0.8130 (m100) cc_final: 0.7866 (m100) REVERT: S 18 ARG cc_start: 0.5540 (OUTLIER) cc_final: 0.5272 (mmm160) REVERT: S 108 PHE cc_start: 0.8066 (m-80) cc_final: 0.7813 (m-80) REVERT: S 162 LEU cc_start: 0.8085 (tt) cc_final: 0.7766 (tt) REVERT: S 174 GLN cc_start: 0.7601 (pm20) cc_final: 0.7334 (pm20) REVERT: S 190 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7336 (mtm110) REVERT: S 202 LEU cc_start: 0.8217 (tp) cc_final: 0.7989 (tt) REVERT: R 86 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.6026 (mpt) outliers start: 53 outliers final: 44 residues processed: 261 average time/residue: 0.2612 time to fit residues: 89.7083 Evaluate side-chains 288 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 68 ASN Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 0.0770 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 0.0010 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 0.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8770 Z= 0.171 Angle : 0.621 12.695 11923 Z= 0.311 Chirality : 0.042 0.184 1387 Planarity : 0.003 0.055 1488 Dihedral : 5.939 54.318 1242 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.12 % Allowed : 21.27 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.06 (0.26), residues: 1104 helix: 0.81 (0.27), residues: 403 sheet: -1.69 (0.30), residues: 269 loop : -1.39 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 435 HIS 0.006 0.001 HIS S 35 PHE 0.020 0.001 PHE S 29 TYR 0.012 0.001 TYR R 113 ARG 0.005 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 247 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6660 (mt-10) REVERT: A 14 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6871 (tm-30) REVERT: A 249 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7939 (tp) REVERT: A 252 SER cc_start: 0.6632 (p) cc_final: 0.6404 (p) REVERT: A 337 ASP cc_start: 0.7005 (t70) cc_final: 0.6792 (t70) REVERT: A 351 CYS cc_start: 0.7218 (m) cc_final: 0.6768 (m) REVERT: B 70 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8136 (mp) REVERT: B 125 ASN cc_start: 0.8455 (t0) cc_final: 0.8071 (t0) REVERT: B 145 TYR cc_start: 0.7671 (p90) cc_final: 0.7371 (p90) REVERT: B 228 ASP cc_start: 0.6934 (p0) cc_final: 0.6479 (p0) REVERT: B 249 THR cc_start: 0.7304 (m) cc_final: 0.7095 (p) REVERT: B 297 TRP cc_start: 0.8476 (m100) cc_final: 0.8129 (m100) REVERT: B 308 LEU cc_start: 0.7336 (tp) cc_final: 0.6796 (mp) REVERT: B 339 TRP cc_start: 0.8048 (m100) cc_final: 0.7810 (m100) REVERT: S 18 ARG cc_start: 0.5411 (OUTLIER) cc_final: 0.5153 (mmm160) REVERT: S 38 ARG cc_start: 0.8223 (ptt180) cc_final: 0.7884 (ptp90) REVERT: S 108 PHE cc_start: 0.7989 (m-80) cc_final: 0.7699 (m-80) REVERT: S 174 GLN cc_start: 0.7567 (pm20) cc_final: 0.7274 (pm20) REVERT: S 190 ARG cc_start: 0.7554 (mtm110) cc_final: 0.7299 (mtm110) REVERT: R 86 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5978 (mpt) REVERT: R 215 TYR cc_start: 0.7636 (m-10) cc_final: 0.7300 (m-80) outliers start: 46 outliers final: 39 residues processed: 264 average time/residue: 0.2391 time to fit residues: 82.8548 Evaluate side-chains 285 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 68 ASN Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.0570 chunk 100 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 88 optimal weight: 0.4980 chunk 92 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8770 Z= 0.193 Angle : 0.640 12.832 11923 Z= 0.319 Chirality : 0.042 0.235 1387 Planarity : 0.003 0.054 1488 Dihedral : 5.947 53.008 1242 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.35 % Allowed : 22.72 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.00 (0.26), residues: 1104 helix: 0.86 (0.27), residues: 402 sheet: -1.67 (0.30), residues: 272 loop : -1.32 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 169 HIS 0.006 0.001 HIS S 35 PHE 0.023 0.001 PHE S 29 TYR 0.013 0.001 TYR R 113 ARG 0.004 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6766 (mt-10) REVERT: A 14 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6868 (tm-30) REVERT: A 249 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7956 (tp) REVERT: A 252 SER cc_start: 0.6645 (p) cc_final: 0.6420 (p) REVERT: B 70 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8138 (mp) REVERT: B 125 ASN cc_start: 0.8453 (t0) cc_final: 0.8092 (t0) REVERT: B 137 ARG cc_start: 0.7633 (tpp-160) cc_final: 0.7308 (tpp-160) REVERT: B 145 TYR cc_start: 0.7671 (p90) cc_final: 0.7368 (p90) REVERT: B 169 TRP cc_start: 0.8006 (m100) cc_final: 0.7201 (m100) REVERT: B 228 ASP cc_start: 0.6956 (p0) cc_final: 0.6543 (p0) REVERT: B 249 THR cc_start: 0.7294 (m) cc_final: 0.7076 (p) REVERT: B 297 TRP cc_start: 0.8443 (m100) cc_final: 0.8195 (m100) REVERT: B 308 LEU cc_start: 0.7381 (tp) cc_final: 0.6758 (mp) REVERT: S 18 ARG cc_start: 0.5431 (OUTLIER) cc_final: 0.5190 (mmm160) REVERT: S 38 ARG cc_start: 0.8233 (ptt180) cc_final: 0.7886 (ptp90) REVERT: S 67 ARG cc_start: 0.5098 (mtp180) cc_final: 0.4838 (mtp180) REVERT: S 87 ARG cc_start: 0.7453 (mpt-90) cc_final: 0.7180 (mpt-90) REVERT: S 174 GLN cc_start: 0.7611 (pm20) cc_final: 0.7293 (pm20) REVERT: S 190 ARG cc_start: 0.7541 (mtm110) cc_final: 0.7338 (mtm110) REVERT: R 86 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5979 (mpt) REVERT: R 138 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6613 (mp) REVERT: R 215 TYR cc_start: 0.7664 (m-10) cc_final: 0.7340 (m-80) outliers start: 48 outliers final: 39 residues processed: 263 average time/residue: 0.2378 time to fit residues: 83.2442 Evaluate side-chains 280 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 68 ASN Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8770 Z= 0.250 Angle : 0.686 12.610 11923 Z= 0.344 Chirality : 0.044 0.251 1387 Planarity : 0.004 0.053 1488 Dihedral : 6.070 51.500 1242 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.79 % Allowed : 23.83 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.06 (0.26), residues: 1104 helix: 0.85 (0.27), residues: 400 sheet: -1.75 (0.30), residues: 272 loop : -1.36 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.022 0.001 PHE S 29 TYR 0.013 0.001 TYR R 113 ARG 0.005 0.000 ARG S 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6829 (mt-10) REVERT: A 14 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6881 (tm-30) REVERT: A 249 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8153 (tp) REVERT: A 252 SER cc_start: 0.6625 (p) cc_final: 0.6327 (p) REVERT: A 255 ASN cc_start: 0.7180 (m-40) cc_final: 0.6925 (m110) REVERT: A 351 CYS cc_start: 0.7314 (m) cc_final: 0.6886 (m) REVERT: B 70 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8221 (mp) REVERT: B 125 ASN cc_start: 0.8488 (t0) cc_final: 0.8110 (t0) REVERT: B 137 ARG cc_start: 0.7613 (tpp-160) cc_final: 0.7255 (tpp80) REVERT: B 186 ASP cc_start: 0.7586 (p0) cc_final: 0.7115 (p0) REVERT: B 228 ASP cc_start: 0.6979 (p0) cc_final: 0.6557 (p0) REVERT: B 249 THR cc_start: 0.7287 (m) cc_final: 0.7065 (p) REVERT: B 297 TRP cc_start: 0.8487 (m100) cc_final: 0.8193 (m100) REVERT: B 308 LEU cc_start: 0.7436 (tp) cc_final: 0.6993 (mp) REVERT: B 327 VAL cc_start: 0.8444 (t) cc_final: 0.7972 (m) REVERT: S 18 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.5262 (mmm160) REVERT: S 174 GLN cc_start: 0.7589 (pm20) cc_final: 0.7253 (pm20) REVERT: S 176 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7602 (mt) REVERT: S 190 ARG cc_start: 0.7523 (mtm110) cc_final: 0.7302 (mtm110) REVERT: R 86 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.6026 (mpt) outliers start: 43 outliers final: 37 residues processed: 258 average time/residue: 0.2375 time to fit residues: 81.3039 Evaluate side-chains 279 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 68 ASN Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.3980 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 88 optimal weight: 0.3980 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.151636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133934 restraints weight = 13693.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.137462 restraints weight = 6418.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139715 restraints weight = 3649.984| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8770 Z= 0.189 Angle : 0.658 12.403 11923 Z= 0.328 Chirality : 0.043 0.202 1387 Planarity : 0.004 0.064 1488 Dihedral : 5.981 52.425 1242 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.90 % Allowed : 24.16 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.06 (0.26), residues: 1104 helix: 0.91 (0.27), residues: 396 sheet: -1.74 (0.30), residues: 272 loop : -1.41 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.023 0.001 PHE S 29 TYR 0.012 0.001 TYR R 113 ARG 0.008 0.000 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2284.23 seconds wall clock time: 42 minutes 24.46 seconds (2544.46 seconds total)