Starting phenix.real_space_refine on Fri Nov 15 07:49:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia7_35297/11_2024/8ia7_35297.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia7_35297/11_2024/8ia7_35297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia7_35297/11_2024/8ia7_35297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia7_35297/11_2024/8ia7_35297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia7_35297/11_2024/8ia7_35297.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia7_35297/11_2024/8ia7_35297.cif" } resolution = 3.1 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= 0.006 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 59 5.16 5 C 5489 2.51 5 N 1473 2.21 5 O 1565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8586 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2159 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 13, 'TRANS': 262} Chain breaks: 1 Chain: "B" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2471 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1723 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1802 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 2 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.31, per 1000 atoms: 0.62 Number of scatterers: 8586 At special positions: 0 Unit cell: (114.582, 114.582, 123.708, 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 59 16.00 O 1565 8.00 N 1473 7.00 C 5489 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.2 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 36.1% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'R' and resid 54 through 82 Processing helix chain 'R' and resid 87 through 108 removed outlier: 3.787A pdb=" N ALA R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 117 Proline residue: R 114 - end of helix Processing helix chain 'R' and resid 122 through 158 removed outlier: 4.370A pdb=" N ILE R 126 " --> pdb=" O PHE R 122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER R 139 " --> pdb=" O GLY R 135 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG R 158 " --> pdb=" O SER R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 164 removed outlier: 3.950A pdb=" N VAL R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 186 Processing helix chain 'R' and resid 187 through 192 Processing helix chain 'R' and resid 214 through 227 Processing helix chain 'R' and resid 227 through 248 removed outlier: 3.920A pdb=" N GLY R 248 " --> pdb=" O GLU R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 360 Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 360 through 367 Processing helix chain 'R' and resid 370 through 391 removed outlier: 3.523A pdb=" N PHE R 374 " --> pdb=" O ALA R 370 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER R 382 " --> pdb=" O LEU R 378 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA R 383 " --> pdb=" O SER R 379 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS R 384 " --> pdb=" O TYR R 380 " (cutoff:3.500A) Proline residue: R 387 - end of helix Processing helix chain 'R' and resid 396 through 403 removed outlier: 3.694A pdb=" N ALA R 400 " --> pdb=" O ARG R 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.665A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.622A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.554A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.522A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.901A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.528A pdb=" N ILE A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 269 through 277 removed outlier: 3.587A pdb=" N LEU A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 329 through 350 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.817A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.735A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.966A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.583A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.957A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.551A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.049A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.282A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.501A pdb=" N VAL E 135 " --> pdb=" O LYS E 232 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 143 through 148 Processing sheet with id=AB4, first strand: chain 'A' and resid 183 through 190 removed outlier: 4.231A pdb=" N VAL A 200 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY A 40 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LYS A 35 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N MET A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 37 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU A 223 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 39 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ALA A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 220 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE A 266 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 222 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN A 268 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 224 " --> pdb=" O ASN A 268 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1161 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: 2.38 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1742 1.33 - 1.45: 2110 1.45 - 1.57: 4826 1.57 - 1.69: 1 1.69 - 1.82: 87 Bond restraints: 8766 Sorted by residual: bond pdb=" O2 TYS L 2 " pdb=" S TYS L 2 " ideal model delta sigma weight residual 1.461 1.632 -0.171 2.00e-02 2.50e+03 7.35e+01 bond pdb=" OH TYS L 2 " pdb=" S TYS L 2 " ideal model delta sigma weight residual 1.679 1.534 0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" C ALA R 352 " pdb=" O ALA R 352 " ideal model delta sigma weight residual 1.237 1.207 0.030 1.17e-02 7.31e+03 6.49e+00 bond pdb=" CA ASN R 353 " pdb=" C ASN R 353 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.30e-02 5.92e+03 4.97e+00 bond pdb=" CA TRP R 355 " pdb=" C TRP R 355 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.30e-02 5.92e+03 3.76e+00 ... (remaining 8761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 11653 2.02 - 4.05: 211 4.05 - 6.07: 35 6.07 - 8.10: 8 8.10 - 10.12: 3 Bond angle restraints: 11910 Sorted by residual: angle pdb=" N THR R 193 " pdb=" CA THR R 193 " pdb=" C THR R 193 " ideal model delta sigma weight residual 108.56 118.68 -10.12 1.74e+00 3.30e-01 3.38e+01 angle pdb=" CA TYR R 189 " pdb=" C TYR R 189 " pdb=" N PRO R 190 " ideal model delta sigma weight residual 120.58 116.55 4.03 7.40e-01 1.83e+00 2.97e+01 angle pdb=" N TYR E 161 " pdb=" CA TYR E 161 " pdb=" C TYR E 161 " ideal model delta sigma weight residual 108.52 116.46 -7.94 1.74e+00 3.30e-01 2.08e+01 angle pdb=" C TYR R 189 " pdb=" N PRO R 190 " pdb=" CA PRO R 190 " ideal model delta sigma weight residual 119.05 123.92 -4.87 1.11e+00 8.12e-01 1.93e+01 angle pdb=" N ASP L 7 " pdb=" CA ASP L 7 " pdb=" C ASP L 7 " ideal model delta sigma weight residual 110.80 119.96 -9.16 2.13e+00 2.20e-01 1.85e+01 ... (remaining 11905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4728 17.74 - 35.49: 393 35.49 - 53.23: 48 53.23 - 70.97: 4 70.97 - 88.71: 1 Dihedral angle restraints: 5174 sinusoidal: 1924 harmonic: 3250 Sorted by residual: dihedral pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta harmonic sigma weight residual 180.00 137.63 42.37 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CA LEU R 203 " pdb=" C LEU R 203 " pdb=" N GLN R 204 " pdb=" CA GLN R 204 " ideal model delta harmonic sigma weight residual 180.00 153.25 26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ASP A 313 " pdb=" C ASP A 313 " pdb=" N SER A 314 " pdb=" CA SER A 314 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1227 0.070 - 0.139: 141 0.139 - 0.209: 5 0.209 - 0.278: 2 0.278 - 0.348: 1 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CA ASP L 7 " pdb=" N ASP L 7 " pdb=" C ASP L 7 " pdb=" CB ASP L 7 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA THR R 193 " pdb=" N THR R 193 " pdb=" C THR R 193 " pdb=" CB THR R 193 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PHE L 8 " pdb=" N PHE L 8 " pdb=" C PHE L 8 " pdb=" CB PHE L 8 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1373 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 223 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO E 224 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 224 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 224 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 188 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C PRO R 188 " 0.028 2.00e-02 2.50e+03 pdb=" O PRO R 188 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR R 189 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 179 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.00e+00 pdb=" C ARG E 179 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG E 179 " 0.009 2.00e-02 2.50e+03 pdb=" N MET E 180 " 0.008 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 797 2.74 - 3.28: 8289 3.28 - 3.82: 13600 3.82 - 4.36: 16186 4.36 - 4.90: 28937 Nonbonded interactions: 67809 Sorted by model distance: nonbonded pdb=" O SER E 194 " pdb=" OG1 THR E 201 " model vdw 2.202 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.224 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.262 3.040 nonbonded pdb=" O SER E 106 " pdb=" OG SER E 106 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR R 189 " pdb=" OD2 ASP L 7 " model vdw 2.286 3.040 ... (remaining 67804 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: 0.290 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.420 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 8766 Z= 0.265 Angle : 0.727 10.122 11910 Z= 0.434 Chirality : 0.045 0.348 1376 Planarity : 0.004 0.062 1500 Dihedral : 12.552 88.713 3072 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.00 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.23), residues: 1101 helix: 0.12 (0.26), residues: 357 sheet: -1.07 (0.31), residues: 251 loop : -2.99 (0.24), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 346 HIS 0.005 0.001 HIS B 183 PHE 0.012 0.001 PHE A 49 TYR 0.015 0.001 TYR E 94 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.028 Fit side-chains REVERT: R 189 TYR cc_start: 0.7404 (m-80) cc_final: 0.7051 (m-80) REVERT: R 244 GLU cc_start: 0.6481 (mp0) cc_final: 0.5780 (mp0) REVERT: B 215 GLU cc_start: 0.7815 (tt0) cc_final: 0.7457 (tt0) REVERT: B 304 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7867 (ttp-170) REVERT: C 29 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8459 (mmtt) REVERT: C 48 ASP cc_start: 0.8917 (t0) cc_final: 0.8705 (t0) REVERT: E 103 TYR cc_start: 0.8681 (t80) cc_final: 0.8357 (t80) REVERT: A 230 ASP cc_start: 0.8047 (m-30) cc_final: 0.7838 (m-30) REVERT: L 6 MET cc_start: 0.7200 (ttt) cc_final: 0.6797 (ttp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2224 time to fit residues: 54.7636 Evaluate side-chains 143 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 0.2980 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 33 optimal weight: 0.0770 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 72 ASN R 204 GLN R 353 ASN B 32 GLN E 167 GLN E 174 GLN A 293 GLN A 311 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8766 Z= 0.218 Angle : 0.583 7.774 11910 Z= 0.298 Chirality : 0.043 0.229 1376 Planarity : 0.004 0.053 1500 Dihedral : 4.704 42.784 1220 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 1.78 % Allowed : 12.49 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.09 (0.25), residues: 1101 helix: 1.39 (0.27), residues: 363 sheet: -0.72 (0.31), residues: 270 loop : -2.52 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS B 183 PHE 0.013 0.001 PHE B 253 TYR 0.015 0.002 TYR R 192 ARG 0.003 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.848 Fit side-chains REVERT: R 189 TYR cc_start: 0.7616 (m-80) cc_final: 0.7204 (m-80) REVERT: R 333 ARG cc_start: 0.6914 (ttm170) cc_final: 0.6037 (ttp80) REVERT: R 367 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6300 (pp) REVERT: B 259 GLN cc_start: 0.8785 (pt0) cc_final: 0.8537 (pt0) REVERT: C 29 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8443 (mmtt) REVERT: E 103 TYR cc_start: 0.8698 (t80) cc_final: 0.8348 (t80) REVERT: L 6 MET cc_start: 0.7032 (ttt) cc_final: 0.6728 (ttp) outliers start: 16 outliers final: 10 residues processed: 144 average time/residue: 0.1926 time to fit residues: 38.8688 Evaluate side-chains 140 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8766 Z= 0.253 Angle : 0.583 7.710 11910 Z= 0.297 Chirality : 0.043 0.177 1376 Planarity : 0.004 0.054 1500 Dihedral : 4.674 43.362 1220 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 2.68 % Allowed : 14.83 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.63 (0.26), residues: 1101 helix: 1.83 (0.28), residues: 364 sheet: -0.52 (0.31), residues: 268 loop : -2.26 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.005 0.001 HIS B 183 PHE 0.013 0.001 PHE B 253 TYR 0.034 0.002 TYR R 192 ARG 0.003 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.157 Fit side-chains REVERT: R 244 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5756 (mp0) REVERT: R 333 ARG cc_start: 0.6908 (ttm170) cc_final: 0.6000 (ttp80) REVERT: R 367 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6367 (pp) REVERT: B 259 GLN cc_start: 0.8636 (pt0) cc_final: 0.8324 (pt0) REVERT: B 291 ASP cc_start: 0.7912 (m-30) cc_final: 0.7444 (m-30) REVERT: C 29 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8463 (mmtt) REVERT: E 103 TYR cc_start: 0.8713 (t80) cc_final: 0.8373 (t80) REVERT: L 6 MET cc_start: 0.7014 (ttt) cc_final: 0.6721 (ttp) outliers start: 24 outliers final: 18 residues processed: 143 average time/residue: 0.2010 time to fit residues: 40.9164 Evaluate side-chains 148 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8766 Z= 0.266 Angle : 0.585 7.779 11910 Z= 0.298 Chirality : 0.043 0.165 1376 Planarity : 0.004 0.053 1500 Dihedral : 4.700 43.357 1220 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 3.12 % Allowed : 16.05 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.39 (0.26), residues: 1101 helix: 1.97 (0.28), residues: 365 sheet: -0.35 (0.32), residues: 272 loop : -2.11 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.004 0.001 HIS B 183 PHE 0.014 0.001 PHE B 253 TYR 0.017 0.002 TYR R 192 ARG 0.002 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.016 Fit side-chains REVERT: R 244 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5718 (mp0) REVERT: R 333 ARG cc_start: 0.6900 (ttm170) cc_final: 0.5994 (ttp80) REVERT: R 367 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6395 (pp) REVERT: B 101 MET cc_start: 0.8727 (mtp) cc_final: 0.8268 (mmm) REVERT: B 226 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7740 (pt0) REVERT: B 291 ASP cc_start: 0.7915 (m-30) cc_final: 0.7404 (m-30) REVERT: E 103 TYR cc_start: 0.8719 (t80) cc_final: 0.8375 (t80) REVERT: A 52 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7764 (tp-100) REVERT: L 6 MET cc_start: 0.7071 (ttt) cc_final: 0.6758 (ttp) outliers start: 28 outliers final: 22 residues processed: 145 average time/residue: 0.1885 time to fit residues: 39.3081 Evaluate side-chains 150 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 226 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: 0.9980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8766 Z= 0.212 Angle : 0.563 7.550 11910 Z= 0.287 Chirality : 0.042 0.159 1376 Planarity : 0.003 0.050 1500 Dihedral : 4.548 41.382 1220 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 3.34 % Allowed : 16.39 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1101 helix: 2.15 (0.28), residues: 365 sheet: -0.28 (0.32), residues: 271 loop : -1.99 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.003 0.001 HIS A 212 PHE 0.012 0.001 PHE B 253 TYR 0.010 0.001 TYR R 61 ARG 0.002 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.876 Fit side-chains REVERT: R 244 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5733 (mp0) REVERT: R 333 ARG cc_start: 0.6851 (ttm170) cc_final: 0.5967 (ttp80) REVERT: R 367 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6334 (pp) REVERT: B 70 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8312 (pt) REVERT: B 101 MET cc_start: 0.8714 (mtp) cc_final: 0.8283 (mmm) REVERT: B 118 ASP cc_start: 0.8027 (p0) cc_final: 0.7812 (p0) REVERT: B 226 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7739 (pt0) REVERT: B 291 ASP cc_start: 0.7916 (m-30) cc_final: 0.7437 (m-30) REVERT: C 47 GLU cc_start: 0.7225 (pm20) cc_final: 0.6777 (pt0) REVERT: E 103 TYR cc_start: 0.8696 (t80) cc_final: 0.8381 (t80) REVERT: A 52 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7736 (tp-100) REVERT: L 6 MET cc_start: 0.7066 (ttt) cc_final: 0.6771 (ttp) outliers start: 30 outliers final: 24 residues processed: 147 average time/residue: 0.2109 time to fit residues: 43.1137 Evaluate side-chains 154 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 368 SER Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 183 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.0060 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 26 optimal weight: 0.1980 chunk 105 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 ASN R 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8766 Z= 0.142 Angle : 0.534 7.144 11910 Z= 0.269 Chirality : 0.041 0.151 1376 Planarity : 0.003 0.045 1500 Dihedral : 4.269 37.798 1220 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.90 % Allowed : 17.06 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.07 (0.26), residues: 1101 helix: 2.43 (0.28), residues: 366 sheet: -0.14 (0.32), residues: 263 loop : -1.86 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 346 HIS 0.003 0.001 HIS R 207 PHE 0.014 0.001 PHE A 49 TYR 0.010 0.001 TYR A 289 ARG 0.002 0.000 ARG R 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.996 Fit side-chains REVERT: R 108 MET cc_start: 0.7269 (tpp) cc_final: 0.7006 (tpp) REVERT: R 244 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.5618 (mp0) REVERT: R 333 ARG cc_start: 0.6807 (ttm170) cc_final: 0.5950 (ttp80) REVERT: R 367 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6260 (pp) REVERT: B 70 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8355 (pt) REVERT: B 98 SER cc_start: 0.8671 (p) cc_final: 0.8464 (p) REVERT: B 101 MET cc_start: 0.8650 (mtp) cc_final: 0.8161 (mmm) REVERT: C 47 GLU cc_start: 0.7102 (pm20) cc_final: 0.6741 (pt0) REVERT: E 103 TYR cc_start: 0.8619 (t80) cc_final: 0.8229 (t80) outliers start: 26 outliers final: 20 residues processed: 150 average time/residue: 0.2202 time to fit residues: 45.3526 Evaluate side-chains 146 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 368 SER Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 59 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 161 GLN A 311 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8766 Z= 0.254 Angle : 0.576 7.579 11910 Z= 0.293 Chirality : 0.042 0.139 1376 Planarity : 0.003 0.046 1500 Dihedral : 4.487 40.630 1220 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.34 % Allowed : 17.61 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1101 helix: 2.31 (0.28), residues: 366 sheet: -0.16 (0.32), residues: 269 loop : -1.92 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS A 212 PHE 0.012 0.001 PHE A 49 TYR 0.016 0.001 TYR A 229 ARG 0.002 0.000 ARG R 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.031 Fit side-chains REVERT: R 244 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.5711 (mp0) REVERT: R 333 ARG cc_start: 0.6839 (ttm170) cc_final: 0.6011 (ttp80) REVERT: R 367 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6564 (pp) REVERT: B 70 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8329 (pt) REVERT: B 291 ASP cc_start: 0.7895 (m-30) cc_final: 0.7482 (m-30) REVERT: C 47 GLU cc_start: 0.7250 (pm20) cc_final: 0.6723 (pt0) REVERT: E 103 TYR cc_start: 0.8708 (t80) cc_final: 0.8391 (t80) REVERT: L 7 ASP cc_start: 0.7502 (t0) cc_final: 0.6905 (t0) outliers start: 30 outliers final: 25 residues processed: 145 average time/residue: 0.2076 time to fit residues: 41.8268 Evaluate side-chains 151 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 368 SER Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 272 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 ASN R 161 GLN R 353 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8766 Z= 0.183 Angle : 0.554 7.377 11910 Z= 0.280 Chirality : 0.041 0.139 1376 Planarity : 0.003 0.045 1500 Dihedral : 4.360 39.100 1220 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.12 % Allowed : 19.06 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1101 helix: 2.42 (0.27), residues: 366 sheet: -0.18 (0.32), residues: 266 loop : -1.88 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 346 HIS 0.003 0.001 HIS A 212 PHE 0.014 0.001 PHE L 8 TYR 0.010 0.001 TYR A 289 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.980 Fit side-chains REVERT: R 108 MET cc_start: 0.7320 (tpp) cc_final: 0.7081 (tpp) REVERT: R 244 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5609 (mp0) REVERT: R 333 ARG cc_start: 0.6795 (ttm170) cc_final: 0.5969 (ttp80) REVERT: R 367 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6475 (pp) REVERT: B 70 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8320 (pt) REVERT: B 98 SER cc_start: 0.8669 (p) cc_final: 0.8448 (p) REVERT: B 101 MET cc_start: 0.8713 (mtp) cc_final: 0.8306 (mmm) REVERT: C 47 GLU cc_start: 0.7195 (pm20) cc_final: 0.6699 (pt0) REVERT: E 103 TYR cc_start: 0.8652 (t80) cc_final: 0.8276 (t80) REVERT: L 7 ASP cc_start: 0.7554 (t0) cc_final: 0.7214 (t0) outliers start: 28 outliers final: 22 residues processed: 140 average time/residue: 0.1877 time to fit residues: 37.2697 Evaluate side-chains 149 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 368 SER Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 272 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 58 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 ASN R 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8766 Z= 0.151 Angle : 0.538 7.189 11910 Z= 0.272 Chirality : 0.041 0.181 1376 Planarity : 0.003 0.042 1500 Dihedral : 4.173 36.944 1220 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.12 % Allowed : 18.95 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.24 (0.26), residues: 1101 helix: 2.54 (0.27), residues: 368 sheet: -0.17 (0.31), residues: 276 loop : -1.70 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 346 HIS 0.002 0.001 HIS A 212 PHE 0.014 0.001 PHE A 49 TYR 0.009 0.001 TYR A 289 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.886 Fit side-chains REVERT: R 108 MET cc_start: 0.7456 (tpp) cc_final: 0.7241 (tpp) REVERT: R 244 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5475 (mp0) REVERT: R 333 ARG cc_start: 0.6771 (ttm170) cc_final: 0.5957 (ttp80) REVERT: B 70 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8359 (pt) REVERT: B 98 SER cc_start: 0.8621 (p) cc_final: 0.8418 (p) REVERT: B 127 LYS cc_start: 0.8765 (mttm) cc_final: 0.8035 (mptt) REVERT: C 47 GLU cc_start: 0.7193 (pm20) cc_final: 0.6699 (pt0) REVERT: E 103 TYR cc_start: 0.8611 (t80) cc_final: 0.8190 (t80) outliers start: 28 outliers final: 21 residues processed: 151 average time/residue: 0.1937 time to fit residues: 41.4431 Evaluate side-chains 151 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain R residue 368 SER Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8766 Z= 0.210 Angle : 0.567 8.788 11910 Z= 0.288 Chirality : 0.042 0.181 1376 Planarity : 0.003 0.043 1500 Dihedral : 4.275 38.509 1220 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.90 % Allowed : 18.84 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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 (0.26), residues: 1101 helix: 2.45 (0.27), residues: 368 sheet: -0.16 (0.31), residues: 276 loop : -1.79 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.002 0.001 HIS A 212 PHE 0.023 0.001 PHE L 8 TYR 0.015 0.001 TYR A 229 ARG 0.003 0.000 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.982 Fit side-chains REVERT: R 108 MET cc_start: 0.7456 (tpp) cc_final: 0.7231 (tpp) REVERT: R 244 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.5548 (mp0) REVERT: R 333 ARG cc_start: 0.6783 (ttm170) cc_final: 0.5962 (ttp80) REVERT: R 367 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6552 (pp) REVERT: B 70 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8312 (pt) REVERT: B 98 SER cc_start: 0.8652 (p) cc_final: 0.8425 (p) REVERT: B 101 MET cc_start: 0.8732 (mtp) cc_final: 0.8331 (mmm) REVERT: B 127 LYS cc_start: 0.8796 (mttm) cc_final: 0.8341 (mmtm) REVERT: B 219 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.7947 (mmt-90) REVERT: C 47 GLU cc_start: 0.7222 (pm20) cc_final: 0.6712 (pt0) REVERT: E 103 TYR cc_start: 0.8655 (t80) cc_final: 0.8253 (t80) REVERT: L 7 ASP cc_start: 0.7598 (t0) cc_final: 0.7288 (t0) outliers start: 26 outliers final: 21 residues processed: 145 average time/residue: 0.1983 time to fit residues: 40.5641 Evaluate side-chains 152 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 368 SER Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 161 GLN 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 = 0.168139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131983 restraints weight = 9856.835| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.38 r_work: 0.3374 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8766 Z= 0.165 Angle : 0.546 7.275 11910 Z= 0.278 Chirality : 0.042 0.177 1376 Planarity : 0.003 0.042 1500 Dihedral : 4.182 37.248 1220 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.68 % Allowed : 19.18 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.24 (0.26), residues: 1101 helix: 2.56 (0.27), residues: 368 sheet: -0.17 (0.31), residues: 271 loop : -1.71 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 5 HIS 0.002 0.001 HIS B 311 PHE 0.018 0.001 PHE L 8 TYR 0.009 0.001 TYR A 289 ARG 0.003 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.26 seconds wall clock time: 39 minutes 56.48 seconds (2396.48 seconds total)