Starting phenix.real_space_refine on Mon May 12 15:33:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3q_41008/05_2025/8t3q_41008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3q_41008/05_2025/8t3q_41008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t3q_41008/05_2025/8t3q_41008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3q_41008/05_2025/8t3q_41008.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3q_41008/05_2025/8t3q_41008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3q_41008/05_2025/8t3q_41008.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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 5752 2.51 5 N 1562 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9035 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1800 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "N" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2372 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain breaks: 2 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'HXA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.41, per 1000 atoms: 0.60 Number of scatterers: 9035 At special positions: 0 Unit cell: (85.284, 124.2, 125.856, 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 1666 8.00 N 1562 7.00 C 5752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.03 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " 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: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 36.6% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.232A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.724A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.759A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.953A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.106A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.949A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.532A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.751A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 35 through 71 removed outlier: 3.568A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 89 Processing helix chain 'R' and resid 91 through 102 removed outlier: 3.653A pdb=" N THR R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 140 removed outlier: 3.539A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR R 119 " --> pdb=" O PHE R 115 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER R 123 " --> pdb=" O THR R 119 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 170 Processing helix chain 'R' and resid 171 through 176 Processing helix chain 'R' and resid 200 through 216 Processing helix chain 'R' and resid 216 through 245 removed outlier: 3.675A pdb=" N GLY R 220 " --> pdb=" O PHE R 216 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU R 245 " --> pdb=" O LEU R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 256 Processing helix chain 'R' and resid 258 through 291 Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 299 through 322 removed outlier: 3.824A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 316 " --> pdb=" O ALA R 312 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.773A pdb=" N VAL A 109 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.312A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.860A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.924A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.973A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.920A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.711A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.687A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'N' and resid 58 through 60 removed outlier: 4.952A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 141 through 142 Processing sheet with id=AB5, first strand: chain 'N' and resid 148 through 149 removed outlier: 3.788A pdb=" N VAL N 148 " --> pdb=" O LYS N 245 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N 247 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU N 175 " --> pdb=" O TYR N 191 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR N 191 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP N 177 " --> pdb=" O LEU N 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 180 through 181 445 hydrogen bonds defined for protein. 1254 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: 2.57 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1476 1.32 - 1.44: 2522 1.44 - 1.57: 5141 1.57 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 9218 Sorted by residual: bond pdb=" C HIS R 112 " pdb=" O HIS R 112 " ideal model delta sigma weight residual 1.236 1.313 -0.076 1.15e-02 7.56e+03 4.42e+01 bond pdb=" N VAL R 124 " pdb=" CA VAL R 124 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.08e-02 8.57e+03 1.35e+01 bond pdb=" N VAL R 117 " pdb=" CA VAL R 117 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.19e-02 7.06e+03 1.20e+01 bond pdb=" N VAL B 112 " pdb=" CA VAL B 112 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" C PRO R 108 " pdb=" O PRO R 108 " ideal model delta sigma weight residual 1.237 1.195 0.043 1.26e-02 6.30e+03 1.14e+01 ... (remaining 9213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 11667 2.34 - 4.68: 780 4.68 - 7.02: 44 7.02 - 9.35: 9 9.35 - 11.69: 2 Bond angle restraints: 12502 Sorted by residual: angle pdb=" N PRO N 237 " pdb=" CA PRO N 237 " pdb=" C PRO N 237 " ideal model delta sigma weight residual 110.95 99.26 11.69 1.62e+00 3.81e-01 5.21e+01 angle pdb=" N LEU R 120 " pdb=" CA LEU R 120 " pdb=" C LEU R 120 " ideal model delta sigma weight residual 113.12 105.33 7.79 1.25e+00 6.40e-01 3.88e+01 angle pdb=" N GLN R 290 " pdb=" CA GLN R 290 " pdb=" C GLN R 290 " ideal model delta sigma weight residual 112.23 104.42 7.81 1.26e+00 6.30e-01 3.84e+01 angle pdb=" N VAL R 124 " pdb=" CA VAL R 124 " pdb=" C VAL R 124 " ideal model delta sigma weight residual 113.42 106.79 6.63 1.17e+00 7.31e-01 3.21e+01 angle pdb=" C PHE B 151 " pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " ideal model delta sigma weight residual 109.80 100.71 9.09 1.64e+00 3.72e-01 3.07e+01 ... (remaining 12497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 4884 17.15 - 34.31: 438 34.31 - 51.46: 125 51.46 - 68.62: 23 68.62 - 85.77: 7 Dihedral angle restraints: 5477 sinusoidal: 2119 harmonic: 3358 Sorted by residual: dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual 93.00 157.25 -64.25 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" C TYR N 236 " pdb=" N TYR N 236 " pdb=" CA TYR N 236 " pdb=" CB TYR N 236 " ideal model delta harmonic sigma weight residual -122.60 -136.52 13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" N TYR N 236 " pdb=" C TYR N 236 " pdb=" CA TYR N 236 " pdb=" CB TYR N 236 " ideal model delta harmonic sigma weight residual 122.80 135.12 -12.32 0 2.50e+00 1.60e-01 2.43e+01 ... (remaining 5474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1197 0.100 - 0.200: 214 0.200 - 0.300: 25 0.300 - 0.401: 1 0.401 - 0.501: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA TYR N 236 " pdb=" N TYR N 236 " pdb=" C TYR N 236 " pdb=" CB TYR N 236 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA PHE B 151 " pdb=" N PHE B 151 " pdb=" C PHE B 151 " pdb=" CB PHE B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1435 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 HXA R 401 " 0.098 2.00e-02 2.50e+03 2.26e-01 5.11e+02 pdb=" C4 HXA R 401 " -0.301 2.00e-02 2.50e+03 pdb=" C5 HXA R 401 " 0.306 2.00e-02 2.50e+03 pdb=" C6 HXA R 401 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 HXA R 401 " -0.069 2.00e-02 2.50e+03 1.33e-01 1.77e+02 pdb=" C7 HXA R 401 " 0.175 2.00e-02 2.50e+03 pdb=" C8 HXA R 401 " -0.175 2.00e-02 2.50e+03 pdb=" C9 HXA R 401 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 HXA R 401 " 0.102 2.00e-02 2.50e+03 1.02e-01 1.04e+02 pdb=" C19 HXA R 401 " -0.101 2.00e-02 2.50e+03 pdb=" C20 HXA R 401 " -0.103 2.00e-02 2.50e+03 pdb=" C21 HXA R 401 " 0.102 2.00e-02 2.50e+03 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 323 2.69 - 3.25: 8908 3.25 - 3.80: 14332 3.80 - 4.35: 19120 4.35 - 4.90: 31430 Nonbonded interactions: 74113 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR N 176 " model vdw 2.144 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.144 3.040 nonbonded pdb=" OG SER N 157 " pdb=" OG1 THR N 214 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.292 3.040 nonbonded pdb=" NE2 HIS B 311 " pdb=" OG1 THR B 329 " model vdw 2.297 3.120 ... (remaining 74108 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 22.490 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 9221 Z= 0.573 Angle : 1.152 11.693 12508 Z= 0.813 Chirality : 0.074 0.501 1438 Planarity : 0.009 0.226 1589 Dihedral : 14.658 85.772 3294 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % Rotamer: Outliers : 1.75 % Allowed : 16.63 % Favored : 81.62 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.25), residues: 1141 helix: -0.17 (0.27), residues: 375 sheet: -0.39 (0.32), residues: 270 loop : -1.33 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.009 0.002 HIS A 209 PHE 0.021 0.002 PHE B 151 TYR 0.032 0.002 TYR N 236 ARG 0.013 0.001 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.20773 ( 445) hydrogen bonds : angle 7.48234 ( 1254) SS BOND : bond 0.00327 ( 3) SS BOND : angle 1.93044 ( 6) covalent geometry : bond 0.00793 ( 9218) covalent geometry : angle 1.15104 (12502) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.6652 (m-40) cc_final: 0.6419 (m-40) REVERT: B 197 ARG cc_start: 0.6821 (mmt180) cc_final: 0.6391 (mmt180) REVERT: B 214 ARG cc_start: 0.7733 (mpt180) cc_final: 0.7266 (ttp80) REVERT: B 217 MET cc_start: 0.6285 (mtt) cc_final: 0.5734 (ptp) REVERT: B 219 ARG cc_start: 0.6923 (mtt-85) cc_final: 0.6638 (mtp85) REVERT: N 235 GLU cc_start: 0.6954 (pt0) cc_final: 0.6604 (mt-10) REVERT: R 22 ARG cc_start: 0.4006 (mmp-170) cc_final: 0.2996 (mpp-170) REVERT: R 24 ARG cc_start: 0.6991 (mtp85) cc_final: 0.6574 (mtp180) REVERT: R 106 LEU cc_start: 0.8623 (mt) cc_final: 0.8415 (mt) REVERT: R 118 MET cc_start: 0.6056 (ttp) cc_final: 0.5672 (mtp) REVERT: R 215 ASN cc_start: 0.8202 (m-40) cc_final: 0.7360 (m-40) outliers start: 17 outliers final: 5 residues processed: 159 average time/residue: 0.2473 time to fit residues: 52.0967 Evaluate side-chains 133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 118 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS A 244 ASN B 9 GLN B 36 ASN B 44 GLN B 88 ASN R 112 HIS R 142 HIS R 182 GLN R 258 GLN R 290 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.183401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125942 restraints weight = 9974.456| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.84 r_work: 0.3287 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9221 Z= 0.138 Angle : 0.603 9.755 12508 Z= 0.318 Chirality : 0.043 0.167 1438 Planarity : 0.005 0.076 1589 Dihedral : 6.181 59.380 1280 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.77 % Allowed : 16.22 % Favored : 81.01 % 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: -0.57 (0.25), residues: 1141 helix: 0.57 (0.26), residues: 380 sheet: -0.19 (0.33), residues: 252 loop : -1.16 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.019 0.001 PHE R 27 TYR 0.014 0.001 TYR N 191 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 445) hydrogen bonds : angle 5.02109 ( 1254) SS BOND : bond 0.00327 ( 3) SS BOND : angle 1.55037 ( 6) covalent geometry : bond 0.00298 ( 9218) covalent geometry : angle 0.60200 (12502) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7215 (tttm) cc_final: 0.6902 (tttm) REVERT: A 199 ASP cc_start: 0.6887 (m-30) cc_final: 0.6648 (m-30) REVERT: A 238 MET cc_start: 0.7079 (ttm) cc_final: 0.6866 (ttm) REVERT: A 244 ASN cc_start: 0.8076 (m-40) cc_final: 0.7769 (m-40) REVERT: B 59 TYR cc_start: 0.7903 (m-80) cc_final: 0.6923 (m-80) REVERT: B 191 SER cc_start: 0.8727 (t) cc_final: 0.8379 (t) REVERT: B 197 ARG cc_start: 0.7571 (mmt180) cc_final: 0.7148 (mmt180) REVERT: B 214 ARG cc_start: 0.7982 (mpt180) cc_final: 0.7184 (ttp80) REVERT: B 217 MET cc_start: 0.7122 (mtt) cc_final: 0.6749 (ptp) REVERT: R 22 ARG cc_start: 0.4194 (mmp-170) cc_final: 0.2926 (mtm-85) REVERT: R 25 PHE cc_start: 0.7278 (t80) cc_final: 0.6473 (t80) REVERT: R 101 THR cc_start: 0.6914 (m) cc_final: 0.6700 (p) REVERT: R 118 MET cc_start: 0.6390 (ttp) cc_final: 0.5980 (mtp) REVERT: R 137 MET cc_start: 0.7335 (tmm) cc_final: 0.7110 (tmm) REVERT: R 196 LEU cc_start: 0.6813 (mt) cc_final: 0.6053 (mt) REVERT: R 290 GLN cc_start: 0.6347 (tp40) cc_final: 0.5904 (tp-100) outliers start: 27 outliers final: 19 residues processed: 173 average time/residue: 0.2108 time to fit residues: 50.0541 Evaluate side-chains 150 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 9 optimal weight: 0.0030 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN R 257 GLN R 291 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.181637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.124975 restraints weight = 10094.809| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.81 r_work: 0.3280 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9221 Z= 0.121 Angle : 0.573 14.220 12508 Z= 0.294 Chirality : 0.042 0.176 1438 Planarity : 0.004 0.063 1589 Dihedral : 5.504 49.210 1279 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.98 % Allowed : 18.07 % Favored : 78.95 % 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 (0.25), residues: 1141 helix: 1.05 (0.26), residues: 383 sheet: -0.26 (0.33), residues: 258 loop : -1.05 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS R 112 PHE 0.013 0.001 PHE R 27 TYR 0.012 0.001 TYR N 236 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 445) hydrogen bonds : angle 4.64337 ( 1254) SS BOND : bond 0.00279 ( 3) SS BOND : angle 1.27410 ( 6) covalent geometry : bond 0.00266 ( 9218) covalent geometry : angle 0.57243 (12502) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.7226 (tttp) cc_final: 0.6664 (ttmm) REVERT: A 195 LYS cc_start: 0.6993 (tttm) cc_final: 0.6738 (tttm) REVERT: A 199 ASP cc_start: 0.6901 (m-30) cc_final: 0.6555 (m-30) REVERT: A 244 ASN cc_start: 0.8021 (m-40) cc_final: 0.7687 (m110) REVERT: B 191 SER cc_start: 0.8801 (t) cc_final: 0.8458 (t) REVERT: B 197 ARG cc_start: 0.7459 (mmt180) cc_final: 0.7228 (mmt180) REVERT: B 214 ARG cc_start: 0.7813 (mpt180) cc_final: 0.7166 (ttp80) REVERT: B 217 MET cc_start: 0.7428 (mtt) cc_final: 0.7020 (ptp) REVERT: B 277 SER cc_start: 0.8704 (p) cc_final: 0.8333 (m) REVERT: N 74 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: N 236 TYR cc_start: 0.5845 (OUTLIER) cc_final: 0.5085 (t80) REVERT: G 38 MET cc_start: 0.6914 (mmm) cc_final: 0.6613 (mmm) REVERT: R 22 ARG cc_start: 0.4541 (mmp-170) cc_final: 0.3013 (mtm-85) REVERT: R 25 PHE cc_start: 0.7328 (t80) cc_final: 0.6453 (t80) REVERT: R 118 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5848 (mtp) REVERT: R 137 MET cc_start: 0.7089 (tmm) cc_final: 0.6882 (tmm) REVERT: R 215 ASN cc_start: 0.7931 (m-40) cc_final: 0.7341 (m-40) REVERT: R 294 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6093 (pp30) outliers start: 29 outliers final: 17 residues processed: 158 average time/residue: 0.2034 time to fit residues: 44.2968 Evaluate side-chains 147 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 294 GLN Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 0.0570 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 5 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN R 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.179897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123484 restraints weight = 10102.835| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.78 r_work: 0.3271 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9221 Z= 0.126 Angle : 0.558 11.079 12508 Z= 0.288 Chirality : 0.041 0.176 1438 Planarity : 0.004 0.057 1589 Dihedral : 5.066 49.777 1279 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.70 % Allowed : 18.17 % Favored : 78.13 % 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: -0.14 (0.25), residues: 1141 helix: 1.24 (0.27), residues: 385 sheet: -0.41 (0.33), residues: 266 loop : -0.93 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS R 112 PHE 0.026 0.001 PHE R 303 TYR 0.012 0.001 TYR N 191 ARG 0.006 0.000 ARG N 161 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 445) hydrogen bonds : angle 4.53571 ( 1254) SS BOND : bond 0.00301 ( 3) SS BOND : angle 1.09937 ( 6) covalent geometry : bond 0.00281 ( 9218) covalent geometry : angle 0.55739 (12502) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7556 (pp30) cc_final: 0.7328 (pp30) REVERT: A 199 ASP cc_start: 0.6901 (m-30) cc_final: 0.6536 (m-30) REVERT: A 244 ASN cc_start: 0.7986 (m-40) cc_final: 0.7640 (m110) REVERT: B 59 TYR cc_start: 0.8037 (m-80) cc_final: 0.7158 (m-80) REVERT: B 191 SER cc_start: 0.8800 (t) cc_final: 0.8450 (t) REVERT: B 197 ARG cc_start: 0.7510 (mmt180) cc_final: 0.7248 (mmt180) REVERT: B 214 ARG cc_start: 0.7782 (mpt180) cc_final: 0.7121 (ttp80) REVERT: B 217 MET cc_start: 0.7313 (mtt) cc_final: 0.7051 (ptp) REVERT: B 277 SER cc_start: 0.8705 (p) cc_final: 0.8325 (m) REVERT: N 74 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: N 161 ARG cc_start: 0.7731 (ttp-110) cc_final: 0.7360 (mtm110) REVERT: N 236 TYR cc_start: 0.5901 (OUTLIER) cc_final: 0.4985 (t80) REVERT: G 37 LEU cc_start: 0.5540 (OUTLIER) cc_final: 0.5045 (tt) REVERT: G 38 MET cc_start: 0.6884 (mmm) cc_final: 0.6628 (mmm) REVERT: G 58 GLU cc_start: 0.7816 (tp30) cc_final: 0.7603 (tp30) REVERT: R 22 ARG cc_start: 0.4522 (mmp-170) cc_final: 0.3111 (mtm-85) REVERT: R 25 PHE cc_start: 0.7361 (t80) cc_final: 0.6527 (t80) REVERT: R 118 MET cc_start: 0.6227 (ttp) cc_final: 0.5825 (mtp) REVERT: R 137 MET cc_start: 0.6885 (tmm) cc_final: 0.6662 (tmm) REVERT: R 215 ASN cc_start: 0.8042 (m-40) cc_final: 0.7434 (m-40) REVERT: R 294 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6034 (pp30) outliers start: 36 outliers final: 19 residues processed: 168 average time/residue: 0.2073 time to fit residues: 48.3696 Evaluate side-chains 152 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 194 SER Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 294 GLN Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 7 optimal weight: 0.0370 chunk 31 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 80 ASN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.177340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120414 restraints weight = 10040.161| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.88 r_work: 0.3238 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9221 Z= 0.131 Angle : 0.569 11.381 12508 Z= 0.289 Chirality : 0.042 0.176 1438 Planarity : 0.004 0.052 1589 Dihedral : 4.711 51.472 1276 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.49 % Allowed : 18.48 % Favored : 78.03 % 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: -0.06 (0.25), residues: 1141 helix: 1.41 (0.26), residues: 385 sheet: -0.41 (0.32), residues: 270 loop : -0.95 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 112 PHE 0.017 0.001 PHE R 303 TYR 0.012 0.001 TYR N 236 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 445) hydrogen bonds : angle 4.48270 ( 1254) SS BOND : bond 0.00283 ( 3) SS BOND : angle 0.93332 ( 6) covalent geometry : bond 0.00297 ( 9218) covalent geometry : angle 0.56883 (12502) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7790 (m-30) cc_final: 0.7525 (m-30) REVERT: A 75 GLN cc_start: 0.7600 (pp30) cc_final: 0.7354 (pp30) REVERT: A 93 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6923 (ptp90) REVERT: A 199 ASP cc_start: 0.6984 (m-30) cc_final: 0.6629 (m-30) REVERT: B 59 TYR cc_start: 0.8026 (m-80) cc_final: 0.7246 (m-80) REVERT: B 191 SER cc_start: 0.8858 (t) cc_final: 0.8524 (t) REVERT: B 197 ARG cc_start: 0.7540 (mmt180) cc_final: 0.7290 (mmt180) REVERT: B 214 ARG cc_start: 0.7795 (mpt180) cc_final: 0.7166 (ttp80) REVERT: B 228 ASP cc_start: 0.8325 (p0) cc_final: 0.8096 (p0) REVERT: B 277 SER cc_start: 0.8755 (p) cc_final: 0.8398 (m) REVERT: N 74 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: N 161 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7422 (mtm110) REVERT: N 236 TYR cc_start: 0.5862 (OUTLIER) cc_final: 0.5113 (t80) REVERT: G 37 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5309 (tt) REVERT: G 58 GLU cc_start: 0.7974 (tp30) cc_final: 0.7652 (tp30) REVERT: R 22 ARG cc_start: 0.4797 (mmp-170) cc_final: 0.3268 (mtm-85) REVERT: R 25 PHE cc_start: 0.7473 (t80) cc_final: 0.6545 (t80) REVERT: R 118 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.5974 (mtp) REVERT: R 137 MET cc_start: 0.6859 (tmm) cc_final: 0.6586 (tmm) REVERT: R 171 LEU cc_start: 0.6701 (tt) cc_final: 0.6482 (tt) REVERT: R 215 ASN cc_start: 0.8087 (m-40) cc_final: 0.7372 (m-40) outliers start: 34 outliers final: 22 residues processed: 161 average time/residue: 0.2257 time to fit residues: 49.3375 Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 194 SER Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 67 optimal weight: 0.1980 chunk 23 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.178303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119903 restraints weight = 9971.090| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.94 r_work: 0.3233 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9221 Z= 0.121 Angle : 0.551 11.195 12508 Z= 0.281 Chirality : 0.041 0.163 1438 Planarity : 0.004 0.052 1589 Dihedral : 4.635 55.395 1276 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.18 % Allowed : 18.89 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1141 helix: 1.58 (0.27), residues: 386 sheet: -0.41 (0.32), residues: 276 loop : -0.88 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS R 112 PHE 0.015 0.001 PHE R 303 TYR 0.011 0.001 TYR N 191 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 445) hydrogen bonds : angle 4.40990 ( 1254) SS BOND : bond 0.00271 ( 3) SS BOND : angle 0.80885 ( 6) covalent geometry : bond 0.00274 ( 9218) covalent geometry : angle 0.55098 (12502) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7873 (m-30) cc_final: 0.7666 (m-30) REVERT: A 75 GLN cc_start: 0.7598 (pp30) cc_final: 0.7361 (pp30) REVERT: A 93 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6683 (ptp90) REVERT: A 199 ASP cc_start: 0.7059 (m-30) cc_final: 0.6695 (m-30) REVERT: B 59 TYR cc_start: 0.8047 (m-80) cc_final: 0.7605 (m-80) REVERT: B 191 SER cc_start: 0.8818 (t) cc_final: 0.8488 (t) REVERT: B 197 ARG cc_start: 0.7433 (mmt180) cc_final: 0.7204 (mmt180) REVERT: B 214 ARG cc_start: 0.7861 (mpt180) cc_final: 0.7232 (ttp80) REVERT: B 228 ASP cc_start: 0.8368 (p0) cc_final: 0.8136 (p0) REVERT: B 277 SER cc_start: 0.8761 (p) cc_final: 0.8416 (m) REVERT: N 161 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7416 (mtm110) REVERT: N 236 TYR cc_start: 0.5740 (OUTLIER) cc_final: 0.4995 (t80) REVERT: G 58 GLU cc_start: 0.8095 (tp30) cc_final: 0.7456 (tm-30) REVERT: R 25 PHE cc_start: 0.7521 (t80) cc_final: 0.6589 (t80) REVERT: R 118 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.5975 (mtp) REVERT: R 137 MET cc_start: 0.6752 (tmm) cc_final: 0.6507 (tmm) REVERT: R 196 LEU cc_start: 0.6747 (mt) cc_final: 0.6320 (pt) REVERT: R 215 ASN cc_start: 0.8097 (m-40) cc_final: 0.7404 (m-40) outliers start: 31 outliers final: 22 residues processed: 163 average time/residue: 0.2148 time to fit residues: 48.1229 Evaluate side-chains 159 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 194 SER Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.175084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116356 restraints weight = 10137.317| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.95 r_work: 0.3185 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9221 Z= 0.160 Angle : 0.588 11.672 12508 Z= 0.300 Chirality : 0.042 0.199 1438 Planarity : 0.004 0.054 1589 Dihedral : 4.761 59.743 1274 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.70 % Allowed : 18.28 % Favored : 78.03 % 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: -0.03 (0.25), residues: 1141 helix: 1.47 (0.26), residues: 388 sheet: -0.48 (0.31), residues: 275 loop : -0.93 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.002 PHE R 27 TYR 0.013 0.001 TYR N 236 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 445) hydrogen bonds : angle 4.51140 ( 1254) SS BOND : bond 0.00318 ( 3) SS BOND : angle 0.85570 ( 6) covalent geometry : bond 0.00376 ( 9218) covalent geometry : angle 0.58811 (12502) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7567 (pp30) cc_final: 0.7345 (pp30) REVERT: A 93 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6716 (ptp90) REVERT: A 199 ASP cc_start: 0.7047 (m-30) cc_final: 0.6687 (m-30) REVERT: B 59 TYR cc_start: 0.8207 (m-80) cc_final: 0.7728 (m-80) REVERT: B 197 ARG cc_start: 0.7467 (mmt180) cc_final: 0.7170 (mmt180) REVERT: B 214 ARG cc_start: 0.7876 (mpt180) cc_final: 0.7237 (ttp80) REVERT: N 161 ARG cc_start: 0.7818 (ttp-110) cc_final: 0.7441 (mtm110) REVERT: N 236 TYR cc_start: 0.6082 (OUTLIER) cc_final: 0.5529 (t80) REVERT: R 25 PHE cc_start: 0.7470 (t80) cc_final: 0.6803 (t80) REVERT: R 118 MET cc_start: 0.6403 (OUTLIER) cc_final: 0.5976 (mtp) REVERT: R 215 ASN cc_start: 0.8116 (m-40) cc_final: 0.7379 (m-40) outliers start: 36 outliers final: 29 residues processed: 161 average time/residue: 0.2429 time to fit residues: 53.0109 Evaluate side-chains 159 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 194 SER Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.176269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118785 restraints weight = 10187.819| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.95 r_work: 0.3206 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9221 Z= 0.122 Angle : 0.558 11.979 12508 Z= 0.285 Chirality : 0.041 0.163 1438 Planarity : 0.004 0.052 1589 Dihedral : 4.647 57.455 1274 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.39 % Allowed : 19.10 % Favored : 77.52 % 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: 0.06 (0.25), residues: 1141 helix: 1.54 (0.27), residues: 389 sheet: -0.46 (0.32), residues: 273 loop : -0.85 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS N 35 PHE 0.012 0.001 PHE R 303 TYR 0.011 0.001 TYR N 191 ARG 0.009 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 445) hydrogen bonds : angle 4.46385 ( 1254) SS BOND : bond 0.00278 ( 3) SS BOND : angle 0.68638 ( 6) covalent geometry : bond 0.00277 ( 9218) covalent geometry : angle 0.55814 (12502) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7587 (pp30) cc_final: 0.7347 (pp30) REVERT: A 93 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6716 (ptp90) REVERT: A 199 ASP cc_start: 0.7038 (m-30) cc_final: 0.6664 (m-30) REVERT: B 59 TYR cc_start: 0.8155 (m-80) cc_final: 0.7662 (m-80) REVERT: B 191 SER cc_start: 0.8789 (t) cc_final: 0.8462 (t) REVERT: B 197 ARG cc_start: 0.7435 (mmt180) cc_final: 0.7139 (mmt180) REVERT: B 214 ARG cc_start: 0.7894 (mpt180) cc_final: 0.7245 (ttp80) REVERT: B 228 ASP cc_start: 0.8353 (p0) cc_final: 0.8101 (p0) REVERT: N 18 ARG cc_start: 0.8136 (tpt-90) cc_final: 0.7801 (tpt-90) REVERT: N 82 GLN cc_start: 0.7637 (tp40) cc_final: 0.7420 (tp40) REVERT: N 90 ASP cc_start: 0.8682 (m-30) cc_final: 0.8384 (m-30) REVERT: N 161 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7421 (mtm110) REVERT: N 236 TYR cc_start: 0.5670 (OUTLIER) cc_final: 0.5002 (t80) REVERT: G 62 ARG cc_start: 0.6501 (ptp90) cc_final: 0.6180 (ptp90) REVERT: R 25 PHE cc_start: 0.7494 (t80) cc_final: 0.6805 (t80) REVERT: R 118 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.5984 (mtp) REVERT: R 215 ASN cc_start: 0.7971 (m-40) cc_final: 0.7267 (m-40) outliers start: 33 outliers final: 27 residues processed: 163 average time/residue: 0.2210 time to fit residues: 49.2794 Evaluate side-chains 161 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 194 SER Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 0.0170 chunk 49 optimal weight: 0.0040 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 4 optimal weight: 0.0070 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.3848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.179854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122383 restraints weight = 10023.838| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.91 r_work: 0.3270 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9221 Z= 0.100 Angle : 0.537 12.270 12508 Z= 0.273 Chirality : 0.041 0.166 1438 Planarity : 0.004 0.055 1589 Dihedral : 4.446 57.092 1274 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.87 % Allowed : 20.02 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1141 helix: 1.69 (0.27), residues: 390 sheet: -0.39 (0.32), residues: 274 loop : -0.76 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS N 35 PHE 0.012 0.001 PHE R 303 TYR 0.010 0.001 TYR N 191 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 445) hydrogen bonds : angle 4.33510 ( 1254) SS BOND : bond 0.00260 ( 3) SS BOND : angle 0.62315 ( 6) covalent geometry : bond 0.00213 ( 9218) covalent geometry : angle 0.53682 (12502) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6714 (ptp90) REVERT: A 199 ASP cc_start: 0.7074 (m-30) cc_final: 0.6675 (m-30) REVERT: B 59 TYR cc_start: 0.8119 (m-80) cc_final: 0.7534 (m-80) REVERT: B 191 SER cc_start: 0.8794 (t) cc_final: 0.8443 (t) REVERT: B 197 ARG cc_start: 0.7413 (mmt180) cc_final: 0.7171 (mmt180) REVERT: B 214 ARG cc_start: 0.7881 (mpt180) cc_final: 0.7300 (ttp80) REVERT: B 228 ASP cc_start: 0.8357 (p0) cc_final: 0.7877 (p0) REVERT: B 277 SER cc_start: 0.8786 (p) cc_final: 0.8418 (m) REVERT: N 82 GLN cc_start: 0.7629 (tp40) cc_final: 0.7427 (tp40) REVERT: N 90 ASP cc_start: 0.8646 (m-30) cc_final: 0.8331 (m-30) REVERT: N 161 ARG cc_start: 0.7846 (ttp-110) cc_final: 0.7313 (mtm110) REVERT: N 236 TYR cc_start: 0.5332 (OUTLIER) cc_final: 0.4709 (t80) REVERT: G 62 ARG cc_start: 0.6621 (ptp90) cc_final: 0.6318 (ptp90) REVERT: R 25 PHE cc_start: 0.7561 (t80) cc_final: 0.6905 (t80) REVERT: R 118 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6129 (mtp) REVERT: R 215 ASN cc_start: 0.7887 (m-40) cc_final: 0.7173 (m-40) outliers start: 28 outliers final: 21 residues processed: 164 average time/residue: 0.2233 time to fit residues: 50.1988 Evaluate side-chains 157 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 194 SER Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 4 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN G 44 HIS ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.172616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113929 restraints weight = 10192.910| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.96 r_work: 0.3167 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9221 Z= 0.192 Angle : 0.613 12.007 12508 Z= 0.316 Chirality : 0.045 0.306 1438 Planarity : 0.004 0.051 1589 Dihedral : 4.805 56.135 1274 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.87 % Allowed : 20.64 % Favored : 76.49 % 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: 0.06 (0.25), residues: 1141 helix: 1.49 (0.26), residues: 390 sheet: -0.53 (0.32), residues: 273 loop : -0.76 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.003 0.001 HIS N 35 PHE 0.013 0.002 PHE B 234 TYR 0.013 0.002 TYR N 236 ARG 0.009 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 445) hydrogen bonds : angle 4.56794 ( 1254) SS BOND : bond 0.00375 ( 3) SS BOND : angle 0.68199 ( 6) covalent geometry : bond 0.00455 ( 9218) covalent geometry : angle 0.61314 (12502) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6743 (ptp90) REVERT: A 199 ASP cc_start: 0.7115 (m-30) cc_final: 0.6748 (m-30) REVERT: B 214 ARG cc_start: 0.7945 (mpt180) cc_final: 0.7376 (ttp80) REVERT: B 304 ARG cc_start: 0.8755 (ttm170) cc_final: 0.8092 (ttm110) REVERT: N 82 GLN cc_start: 0.7730 (tp40) cc_final: 0.7527 (tp40) REVERT: N 90 ASP cc_start: 0.8691 (m-30) cc_final: 0.8416 (m-30) REVERT: N 161 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7340 (mtm110) REVERT: N 236 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.5637 (t80) REVERT: R 25 PHE cc_start: 0.7517 (t80) cc_final: 0.6867 (t80) REVERT: R 118 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.6097 (mtp) REVERT: R 215 ASN cc_start: 0.8123 (m-40) cc_final: 0.7425 (m-40) outliers start: 28 outliers final: 24 residues processed: 163 average time/residue: 0.2383 time to fit residues: 52.0009 Evaluate side-chains 162 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 194 SER Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.174849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.116571 restraints weight = 10043.125| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.92 r_work: 0.3185 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9221 Z= 0.144 Angle : 0.575 12.023 12508 Z= 0.296 Chirality : 0.043 0.313 1438 Planarity : 0.004 0.063 1589 Dihedral : 4.670 53.119 1274 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.29 % Allowed : 20.74 % Favored : 75.98 % 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: 0.13 (0.26), residues: 1141 helix: 1.57 (0.26), residues: 391 sheet: -0.55 (0.32), residues: 273 loop : -0.70 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS N 35 PHE 0.013 0.001 PHE R 177 TYR 0.012 0.001 TYR N 236 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 445) hydrogen bonds : angle 4.48944 ( 1254) SS BOND : bond 0.00326 ( 3) SS BOND : angle 0.62459 ( 6) covalent geometry : bond 0.00337 ( 9218) covalent geometry : angle 0.57541 (12502) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4775.31 seconds wall clock time: 83 minutes 39.36 seconds (5019.36 seconds total)