Starting phenix.real_space_refine on Mon Mar 11 11:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/03_2024/8wca_37436_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/03_2024/8wca_37436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/03_2024/8wca_37436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/03_2024/8wca_37436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/03_2024/8wca_37436_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/03_2024/8wca_37436_neut_updated.pdb" } resolution = 3.48 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= -0.002 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5232 2.51 5 N 1374 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 215": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "R PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 42": "OE1" <-> "OE2" Residue "Y GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8160 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2336 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 5, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 11, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 127 Chain: "C" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1799 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2010 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'HIS:plan': 6, 'TYR:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "S" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1666 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "Y" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 340 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.60 Number of scatterers: 8160 At special positions: 0 Unit cell: (103.96, 117.76, 124.2, 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 55 16.00 O 1499 8.00 N 1374 7.00 C 5232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 3.22 Conformation dependent library (CDL) restraints added in 1.8 seconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 32.8% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'B' and resid 14 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.872A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.633A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 31 Processing helix chain 'C' and resid 46 through 53 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 275 through 278 No H-bonds generated for 'chain 'C' and resid 275 through 278' Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 299 through 318 removed outlier: 4.062A pdb=" N ILE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 357 removed outlier: 4.089A pdb=" N ALA C 339 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 46 Processing helix chain 'R' and resid 60 through 84 Proline residue: R 78 - end of helix Processing helix chain 'R' and resid 97 through 124 removed outlier: 4.267A pdb=" N SER R 107 " --> pdb=" O ASP R 103 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER R 108 " --> pdb=" O ILE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 130 No H-bonds generated for 'chain 'R' and resid 128 through 130' Processing helix chain 'R' and resid 137 through 160 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 178 Processing helix chain 'R' and resid 188 through 198 removed outlier: 3.784A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU R 193 " --> pdb=" O ILE R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 223 removed outlier: 4.090A pdb=" N CYS R 208 " --> pdb=" O SER R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 276 removed outlier: 3.757A pdb=" N LEU R 253 " --> pdb=" O ALA R 249 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 283 through 306 removed outlier: 3.867A pdb=" N VAL R 288 " --> pdb=" O THR R 284 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR R 298 " --> pdb=" O TYR R 294 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 318 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'Y' and resid 16 through 24 Processing helix chain 'Y' and resid 30 through 44 removed outlier: 3.626A pdb=" N ALA Y 34 " --> pdb=" O VAL Y 30 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.956A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.525A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.488A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.107A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 250 through 254 Processing sheet with id= F, first strand: chain 'B' and resid 284 through 288 Processing sheet with id= G, first strand: chain 'B' and resid 327 through 330 removed outlier: 3.728A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 253 through 259 removed outlier: 3.504A pdb=" N VAL C 225 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 220 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.684A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 93 through 99 removed outlier: 3.994A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.768A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 174 through 176 342 hydrogen bonds defined for protein. 945 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: 2.22 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1300 1.27 - 1.41: 2226 1.41 - 1.54: 4705 1.54 - 1.68: 35 1.68 - 1.81: 81 Bond restraints: 8347 Sorted by residual: bond pdb=" C ASN R 41 " pdb=" O ASN R 41 " ideal model delta sigma weight residual 1.236 1.138 0.099 1.26e-02 6.30e+03 6.13e+01 bond pdb=" C ARG C 356 " pdb=" O ARG C 356 " ideal model delta sigma weight residual 1.236 1.143 0.093 1.31e-02 5.83e+03 5.06e+01 bond pdb=" CA ARG C 356 " pdb=" C ARG C 356 " ideal model delta sigma weight residual 1.520 1.423 0.097 1.39e-02 5.18e+03 4.91e+01 bond pdb=" CA ASN R 41 " pdb=" C ASN R 41 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.35e-02 5.49e+03 3.92e+01 bond pdb=" C ARG B 49 " pdb=" O ARG B 49 " ideal model delta sigma weight residual 1.235 1.175 0.060 1.00e-02 1.00e+04 3.55e+01 ... (remaining 8342 not shown) Histogram of bond angle deviations from ideal: 98.39 - 106.01: 165 106.01 - 113.64: 4563 113.64 - 121.26: 4384 121.26 - 128.88: 2206 128.88 - 136.51: 68 Bond angle restraints: 11386 Sorted by residual: angle pdb=" N CYS R 96 " pdb=" CA CYS R 96 " pdb=" C CYS R 96 " ideal model delta sigma weight residual 113.43 101.23 12.20 1.26e+00 6.30e-01 9.37e+01 angle pdb=" N GLY R 92 " pdb=" CA GLY R 92 " pdb=" C GLY R 92 " ideal model delta sigma weight residual 111.93 122.92 -10.99 1.15e+00 7.56e-01 9.13e+01 angle pdb=" N LEU B 55 " pdb=" CA LEU B 55 " pdb=" C LEU B 55 " ideal model delta sigma weight residual 111.07 118.67 -7.60 1.07e+00 8.73e-01 5.04e+01 angle pdb=" N ARG C 356 " pdb=" CA ARG C 356 " pdb=" C ARG C 356 " ideal model delta sigma weight residual 114.31 105.32 8.99 1.29e+00 6.01e-01 4.85e+01 angle pdb=" N VAL R 192 " pdb=" CA VAL R 192 " pdb=" C VAL R 192 " ideal model delta sigma weight residual 110.42 103.94 6.48 9.60e-01 1.09e+00 4.56e+01 ... (remaining 11381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4452 17.98 - 35.97: 305 35.97 - 53.95: 64 53.95 - 71.93: 6 71.93 - 89.92: 6 Dihedral angle restraints: 4833 sinusoidal: 1604 harmonic: 3229 Sorted by residual: dihedral pdb=" N LEU R 193 " pdb=" C LEU R 193 " pdb=" CA LEU R 193 " pdb=" CB LEU R 193 " ideal model delta harmonic sigma weight residual 122.80 134.87 -12.07 0 2.50e+00 1.60e-01 2.33e+01 dihedral pdb=" C ARG B 49 " pdb=" N ARG B 49 " pdb=" CA ARG B 49 " pdb=" CB ARG B 49 " ideal model delta harmonic sigma weight residual -122.60 -110.73 -11.87 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" C TYR R 90 " pdb=" N TYR R 90 " pdb=" CA TYR R 90 " pdb=" CB TYR R 90 " ideal model delta harmonic sigma weight residual -122.60 -111.10 -11.50 0 2.50e+00 1.60e-01 2.12e+01 ... (remaining 4830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1272 0.120 - 0.240: 40 0.240 - 0.361: 6 0.361 - 0.481: 2 0.481 - 0.601: 3 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA LEU R 193 " pdb=" N LEU R 193 " pdb=" C LEU R 193 " pdb=" CB LEU R 193 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.03e+00 chirality pdb=" CA ASN R 41 " pdb=" N ASN R 41 " pdb=" C ASN R 41 " pdb=" CB ASN R 41 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CA SER R 198 " pdb=" N SER R 198 " pdb=" C SER R 198 " pdb=" CB SER R 198 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.46e+00 ... (remaining 1320 not shown) Planarity restraints: 1443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 35 " -0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C LEU R 35 " 0.083 2.00e-02 2.50e+03 pdb=" O LEU R 35 " -0.032 2.00e-02 2.50e+03 pdb=" N THR R 36 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 355 " -0.024 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C LEU C 355 " 0.083 2.00e-02 2.50e+03 pdb=" O LEU C 355 " -0.029 2.00e-02 2.50e+03 pdb=" N ARG C 356 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 96 " 0.022 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C CYS R 96 " -0.074 2.00e-02 2.50e+03 pdb=" O CYS R 96 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS R 97 " 0.025 2.00e-02 2.50e+03 ... (remaining 1440 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 160 2.66 - 3.22: 7553 3.22 - 3.78: 11832 3.78 - 4.34: 15585 4.34 - 4.90: 26743 Nonbonded interactions: 61873 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.105 2.440 nonbonded pdb=" OD1 ASN R 296 " pdb=" ND2 ASN R 300 " model vdw 2.188 2.520 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.218 2.440 nonbonded pdb=" OE2 GLU C 14 " pdb=" OG SER S 52 " model vdw 2.225 2.440 nonbonded pdb=" O SER R 198 " pdb=" OG SER R 198 " model vdw 2.243 2.440 ... (remaining 61868 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.920 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.780 Find NCS groups from input model: 0.220 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.006 0.099 8347 Z= 0.411 Angle : 0.875 12.199 11386 Z= 0.542 Chirality : 0.063 0.601 1323 Planarity : 0.006 0.090 1443 Dihedral : 13.523 89.915 2741 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.89 % Allowed : 0.89 % Favored : 98.22 % Cbeta Deviations : 0.48 % 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: -0.41 (0.26), residues: 1088 helix: 0.83 (0.29), residues: 372 sheet: 0.07 (0.34), residues: 267 loop : -1.39 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 291 HIS 0.006 0.001 HIS B 225 PHE 0.044 0.002 PHE R 154 TYR 0.017 0.001 TYR R 90 ARG 0.010 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 0.856 Fit side-chains REVERT: B 251 ARG cc_start: 0.7651 (mmt90) cc_final: 0.7358 (mmt-90) REVERT: C 22 GLN cc_start: 0.8398 (tp40) cc_final: 0.7978 (tp40) REVERT: C 345 ASP cc_start: 0.7465 (m-30) cc_final: 0.7260 (m-30) REVERT: S 5 VAL cc_start: 0.7306 (t) cc_final: 0.7046 (p) outliers start: 7 outliers final: 5 residues processed: 160 average time/residue: 0.1860 time to fit residues: 41.0955 Evaluate side-chains 121 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 89 TRP Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 154 PHE Chi-restraints excluded: chain R residue 185 PHE Chi-restraints excluded: chain R residue 194 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 0.0670 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN S 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8347 Z= 0.182 Angle : 0.568 9.722 11386 Z= 0.292 Chirality : 0.044 0.144 1323 Planarity : 0.004 0.058 1443 Dihedral : 5.353 65.633 1194 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.03 % Allowed : 9.53 % Favored : 88.44 % 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: -0.09 (0.26), residues: 1088 helix: 1.20 (0.28), residues: 371 sheet: 0.20 (0.34), residues: 267 loop : -1.28 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 291 HIS 0.004 0.001 HIS R 99 PHE 0.013 0.001 PHE C 223 TYR 0.013 0.001 TYR R 304 ARG 0.004 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 0.845 Fit side-chains REVERT: B 251 ARG cc_start: 0.7696 (mmt90) cc_final: 0.7425 (mmt-90) REVERT: C 22 GLN cc_start: 0.8576 (tp40) cc_final: 0.8286 (tp40) outliers start: 16 outliers final: 15 residues processed: 139 average time/residue: 0.1775 time to fit residues: 34.6861 Evaluate side-chains 138 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain R residue 89 TRP Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 30.0000 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8347 Z= 0.223 Angle : 0.561 8.566 11386 Z= 0.293 Chirality : 0.044 0.150 1323 Planarity : 0.004 0.046 1443 Dihedral : 4.823 52.435 1189 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.54 % Allowed : 12.45 % Favored : 85.01 % 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: 0.05 (0.26), residues: 1088 helix: 1.48 (0.28), residues: 367 sheet: 0.14 (0.34), residues: 266 loop : -1.24 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.005 0.001 HIS S 35 PHE 0.013 0.001 PHE R 268 TYR 0.014 0.001 TYR C 30 ARG 0.004 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 0.934 Fit side-chains REVERT: C 22 GLN cc_start: 0.8645 (tp40) cc_final: 0.8312 (tp40) outliers start: 20 outliers final: 16 residues processed: 139 average time/residue: 0.1969 time to fit residues: 37.7884 Evaluate side-chains 140 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8347 Z= 0.282 Angle : 0.591 12.503 11386 Z= 0.309 Chirality : 0.045 0.159 1323 Planarity : 0.004 0.042 1443 Dihedral : 4.454 42.902 1186 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.92 % Allowed : 14.74 % Favored : 82.34 % 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: -0.04 (0.26), residues: 1088 helix: 1.49 (0.28), residues: 367 sheet: 0.05 (0.34), residues: 266 loop : -1.35 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 291 HIS 0.005 0.001 HIS S 35 PHE 0.017 0.002 PHE R 268 TYR 0.015 0.002 TYR C 30 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.869 Fit side-chains REVERT: C 22 GLN cc_start: 0.8701 (tp40) cc_final: 0.8388 (tp40) REVERT: S 83 MET cc_start: 0.7197 (ptp) cc_final: 0.6966 (ptp) outliers start: 23 outliers final: 19 residues processed: 131 average time/residue: 0.1910 time to fit residues: 34.7610 Evaluate side-chains 136 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain R residue 89 TRP Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 0 optimal weight: 30.0000 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8347 Z= 0.181 Angle : 0.534 7.999 11386 Z= 0.280 Chirality : 0.043 0.157 1323 Planarity : 0.004 0.035 1443 Dihedral : 4.204 35.982 1186 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.54 % Allowed : 16.52 % Favored : 80.94 % 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: 0.10 (0.26), residues: 1088 helix: 1.65 (0.28), residues: 366 sheet: 0.06 (0.34), residues: 277 loop : -1.27 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 291 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.001 PHE R 185 TYR 0.011 0.001 TYR C 30 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.822 Fit side-chains REVERT: C 22 GLN cc_start: 0.8552 (tp40) cc_final: 0.8295 (tp40) REVERT: S 83 MET cc_start: 0.7242 (ptp) cc_final: 0.7028 (ptp) outliers start: 20 outliers final: 15 residues processed: 137 average time/residue: 0.1768 time to fit residues: 34.2823 Evaluate side-chains 134 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.0470 chunk 26 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 30.0000 chunk 101 optimal weight: 0.0050 overall best weight: 0.4492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN C 238 ASN C 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 8347 Z= 0.149 Angle : 0.509 7.163 11386 Z= 0.265 Chirality : 0.042 0.159 1323 Planarity : 0.004 0.035 1443 Dihedral : 3.930 25.955 1186 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.03 % Allowed : 17.53 % Favored : 80.43 % 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: 0.28 (0.27), residues: 1088 helix: 1.75 (0.28), residues: 369 sheet: 0.14 (0.34), residues: 278 loop : -1.13 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 291 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE R 185 TYR 0.015 0.001 TYR R 172 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.921 Fit side-chains REVERT: S 83 MET cc_start: 0.7250 (ptp) cc_final: 0.7021 (ptp) outliers start: 16 outliers final: 12 residues processed: 132 average time/residue: 0.1773 time to fit residues: 33.0185 Evaluate side-chains 131 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8347 Z= 0.189 Angle : 0.530 7.355 11386 Z= 0.279 Chirality : 0.043 0.160 1323 Planarity : 0.004 0.034 1443 Dihedral : 3.930 20.824 1186 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.67 % Allowed : 17.92 % Favored : 79.42 % 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 (0.27), residues: 1088 helix: 1.77 (0.28), residues: 365 sheet: 0.10 (0.34), residues: 269 loop : -1.17 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 291 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE R 185 TYR 0.012 0.001 TYR C 30 ARG 0.003 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 0.935 Fit side-chains REVERT: S 83 MET cc_start: 0.7245 (ptp) cc_final: 0.7011 (ptp) outliers start: 21 outliers final: 17 residues processed: 134 average time/residue: 0.1786 time to fit residues: 33.8741 Evaluate side-chains 142 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain R residue 89 TRP Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain S residue 184 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 0.0030 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8347 Z= 0.172 Angle : 0.529 7.295 11386 Z= 0.276 Chirality : 0.043 0.174 1323 Planarity : 0.004 0.034 1443 Dihedral : 3.893 17.158 1186 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.29 % Allowed : 19.31 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.27), residues: 1088 helix: 1.80 (0.28), residues: 365 sheet: 0.13 (0.34), residues: 278 loop : -1.17 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 291 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE R 185 TYR 0.010 0.001 TYR C 30 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 0.904 Fit side-chains REVERT: S 83 MET cc_start: 0.7189 (ptp) cc_final: 0.6962 (ptp) outliers start: 18 outliers final: 17 residues processed: 133 average time/residue: 0.1846 time to fit residues: 35.0513 Evaluate side-chains 136 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8347 Z= 0.186 Angle : 0.544 7.638 11386 Z= 0.283 Chirality : 0.043 0.202 1323 Planarity : 0.003 0.032 1443 Dihedral : 3.904 16.928 1186 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.54 % Allowed : 18.93 % Favored : 78.53 % 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: 0.28 (0.27), residues: 1088 helix: 1.76 (0.28), residues: 368 sheet: 0.08 (0.33), residues: 280 loop : -1.09 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 291 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE R 185 TYR 0.012 0.001 TYR C 30 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.902 Fit side-chains REVERT: R 105 MET cc_start: 0.7622 (ttp) cc_final: 0.7372 (ttp) REVERT: S 83 MET cc_start: 0.7231 (ptp) cc_final: 0.7008 (ptp) outliers start: 20 outliers final: 19 residues processed: 135 average time/residue: 0.1762 time to fit residues: 33.7381 Evaluate side-chains 141 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 312 ARG Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8347 Z= 0.209 Angle : 0.564 8.170 11386 Z= 0.293 Chirality : 0.044 0.200 1323 Planarity : 0.004 0.032 1443 Dihedral : 3.960 17.240 1186 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.16 % Allowed : 19.44 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.27), residues: 1088 helix: 1.75 (0.28), residues: 369 sheet: 0.09 (0.33), residues: 278 loop : -1.20 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 291 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.001 PHE R 185 TYR 0.013 0.001 TYR C 30 ARG 0.003 0.000 ARG C 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.927 Fit side-chains REVERT: R 105 MET cc_start: 0.7632 (ttp) cc_final: 0.7384 (ttp) REVERT: S 83 MET cc_start: 0.7241 (ptp) cc_final: 0.7019 (ptp) outliers start: 17 outliers final: 16 residues processed: 128 average time/residue: 0.1779 time to fit residues: 32.4826 Evaluate side-chains 133 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.199344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.162109 restraints weight = 9239.355| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.15 r_work: 0.3638 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8347 Z= 0.231 Angle : 0.579 8.546 11386 Z= 0.302 Chirality : 0.044 0.206 1323 Planarity : 0.004 0.048 1443 Dihedral : 4.046 17.659 1186 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.54 % Allowed : 19.31 % Favored : 78.14 % 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 (0.27), residues: 1088 helix: 1.79 (0.28), residues: 366 sheet: -0.01 (0.34), residues: 271 loop : -1.21 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.001 PHE R 185 TYR 0.014 0.001 TYR C 30 ARG 0.003 0.000 ARG C 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.01 seconds wall clock time: 35 minutes 11.76 seconds (2111.76 seconds total)